Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Genetic Variation: Genotypic differences observed among individuals in a population.Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Chromosomes, Human: Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.DNA, Satellite: Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Tandem Repeat Sequences: Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Genome, Insect: The genetic complement of an insect (INSECTS) as represented in its DNA.Genomic Structural Variation: Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Centromere: The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.Genome Size: The amount of DNA (or RNA) in one copy of a genome.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Isochores: Large regions of the GENOME that contain local similarities in BASE COMPOSITION.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Pan troglodytes: The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Gene Order: The sequential location of genes on a chromosome.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Cosmids: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.PrimatesMutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Dendrobium: A plant genus of the family ORCHIDACEAE that contains dihydroayapin (COUMARINS) and phenanthraquinones.Primed In Situ Labeling: A technique that labels specific sequences in whole chromosomes by in situ DNA chain elongation or PCR (polymerase chain reaction).3' Flanking Region: The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Endogenous Retroviruses: Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Gene Dosage: The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Segmental Duplications, Genomic: Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Genome, Protozoan: The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.GC Rich Sequence: A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Genetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Synteny: The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.Chromosome Walking: A technique with which an unknown region of a chromosome can be explored. It is generally used to isolate a locus of interest for which no probe is available but that is known to be linked to a gene which has been identified and cloned. A fragment containing a known gene is selected and used as a probe to identify other overlapping fragments which contain the same gene. The nucleotide sequences of these fragments can then be characterized. This process continues for the length of the chromosome.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Sequence Tagged Sites: Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Deoxyribonuclease BamHI: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence G/GATCC at the slash. BamHI is from Bacillus amyloliquefaciens N. Numerous isoschizomers have been identified. EC 3.1.21.-.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Dinucleotide Repeats: The most common of the microsatellite tandem repeats (MICROSATELLITE REPEATS) dispersed in the euchromatic arms of chromosomes. They consist of two nucleotides repeated in tandem; guanine and thymine, (GT)n, is the most frequently seen.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.Genes, Plant: The functional hereditary units of PLANTS.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Chromosomes, Artificial, Yeast: Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Genetic Diseases, Inborn: Diseases that are caused by genetic mutations present during embryo or fetal development, although they may be observed later in life. The mutations may be inherited from a parent's genome or they may be acquired in utero.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Prototheca: A genus of achlorophyllic algae in the family Chlorellaceae, and closely related to CHLORELLA. It is found in decayed matter; WATER; SEWAGE; and SOIL; and produces cutaneous and disseminated infections in various VERTEBRATES including humans.Telomere: A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Inverted Repeat Sequences: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.National Human Genome Research Institute (U.S.): Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports research into the mapping of the human genome and other organism genomes. The National Center for Human Genome Research was established in 1989 and re-named the National Human Genome Research Institute in 1997.Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Hybrid Cells: Any cell, other than a ZYGOTE, that contains elements (such as NUCLEI and CYTOPLASM) from two or more different cells, usually produced by artificial CELL FUSION.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Chromosome Inversion: An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Chromosome Breakage: A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Genetics, Medical: A subdiscipline of human genetics which entails the reliable prediction of certain human disorders as a function of the lineage and/or genetic makeup of an individual or of any two parents or potential parents.Chromosome Banding: Staining of bands, or chromosome segments, allowing the precise identification of individual chromosomes or parts of chromosomes. Applications include the determination of chromosome rearrangements in malformation syndromes and cancer, the chemistry of chromosome segments, chromosome changes during evolution, and, in conjunction with cell hybridization studies, chromosome mapping.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.DNA Replication: The process by which a DNA molecule is duplicated.Genes, Viral: The functional hereditary units of VIRUSES.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Nucleic Acid Denaturation: Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Genetics, Population: The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.Chromosomes, Fungal: Structures within the nucleus of fungal cells consisting of or containing DNA, which carry genetic information essential to the cell.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Genome, Plastid: The genetic complement of PLASTIDS as represented in their DNA.Radiation Hybrid Mapping: A method for ordering genetic loci along CHROMOSOMES. The method involves fusing irradiated donor cells with host cells from another species. Following cell fusion, fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells. Molecular probing of DNA obtained from the fused cells is used to determine if two or more genetic loci are located within the same fragment of donor cell DNA.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Polyploidy: The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.Terminal Repeat Sequences: Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.Deoxyribonuclease EcoRI: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequence G/AATTC at the slash. EcoRI is from E coliRY13. Several isoschizomers have been identified. EC 3.1.21.-.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Trinucleotide Repeats: Microsatellite repeats consisting of three nucleotides dispersed in the euchromatic arms of chromosomes.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.DNA Copy Number Variations: Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.Y Chromosome: The male sex chromosome, being the differential sex chromosome carried by half the male gametes and none of the female gametes in humans and in some other male-heterogametic species in which the homologue of the X chromosome has been retained.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.DNA, Protozoan: Deoxyribonucleic acid that makes up the genetic material of protozoa.Physarum: A genus of protozoa, formerly also considered a fungus. Characteristics include the presence of violet to brown spores.Virus Integration: Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.Chromosomes, Human, Pair 22: A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.X Chromosome: The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.Linkage Disequilibrium: Nonrandom association of linked genes. This is the tendency of the alleles of two separate but already linked loci to be found together more frequently than would be expected by chance alone.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Genes, Bacterial: The functional hereditary units of BACTERIA.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Frameshift Mutation: A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.DNA, Circular: Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)5' Flanking Region: The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.Takifugu: A genus of pufferfish commonly used for research.Triticum: A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.2-Acetylaminofluorene: A hepatic carcinogen whose mechanism of activation involves N-hydroxylation to the aryl hydroxamic acid followed by enzymatic sulfonation to sulfoxyfluorenylacetamide. It is used to study the carcinogenicity and mutagenicity of aromatic amines.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Karyotyping: Mapping of the KARYOTYPE of a cell.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.

*Genome survey sequence

... in mammalian genome. There are about 300 to 500 thousand copies of Alu repetitive element in human genome, which means one Alu ... Alu repetitive element is member of Short Interspersed Elements (SINE) ... Genome survey sequencing is a new way to map the genome sequences since it is not dependent on mRNA. Current genome sequencing ... "ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)." Bmc Bioinformatics 9.1 (2008): 366. ...

*Long non-coding RNA

February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. doi:10.1038/35057062. PMID ... The short interspersed nuclear (SINE) Alu elements in humans and analogous B1 and B2 elements in mice have succeeded in ... The ability to quickly mediate global changes is also apparent in the rapid expression of non-coding repetitive sequences. ... Large-scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate ...

*Long interspersed nuclear element

February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. doi:10.1038/35057062. PMID ... Kapitonov, Vladimir V.; Pavlicek, Adam; Jurka, Jerzy (2006-01-01). Anthology of Human Repetitive DNA. Wiley-VCH Verlag GmbH & ... In the first human genome draft the fraction of LINE elements of the human genome was given as 21% and their copy number as ... of the human genome and have a copy number of around 1.5 million. Recent estimates show the typical human genome contains on ...

*Alu element

Chimpanzee Sequencing Analysis Consortium (2005). "Initial sequence of the chimpanzee genome and comparison with the human ... and interspersed repetitive DNA (mutated copies of active elements). The functional retinoic acid response element hexamer ... including the evolution of humans.[citation needed] The Alu family is a family of repetitive elements in the human genome. ... There are over one million Alu elements interspersed throughout the human genome, and it is estimated that about 10.7% of the ...

*Gene family

Short Interspersed Elements) families are highly repetitive DNA sequences spread all throughout the genome. The LINEs contain a ... For example, a single gene in the ancestor of humans and chimpanzees now occurs in both species and can be thought of as having ... Whole genome duplication doubles the number of copies of every gene and gene family. Whole genome duplication or ... The positions of exons within the coding sequence can be used to infer common ancestry. Knowing the sequence of the protein ...

*Short interspersed nuclear elements (SINEs)

Singer M. (March 1982). SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell 28(3 ... Jurka J. (December 2004). Evolutionary impact of human Alu repetitive elements. Current Opinion in Genetics & Development 14(6 ... a short-interspersed nuclear element of about 300 nucleotides is located at over a million copies throughout the human genome, ... SINEs or Short Interspersed Nuclear Elements are sequences of non-coding DNA present at high frequencies in various eukaryotic ...

*Mammalian-wide interspersed repeat

2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. doi:10.1038/35057062. PMID 11237011 ... Jurka, Jerzy; Walichiewicz, Jolanta; Milosavljevic, Aleksandar (October 1992). "Prototypic sequences for human repetitive DNA ... It is estimated that there are around 368,000 MIRs in the human genome. The MIR consensus sequence is 260 basepairs long and ... Mammalian-wide interspersed repeats (MIRs) are transposable elements in the genomes of some organisms and belong to the group ...

*Retrotransposon

... of the human genome and approximately 10% of the mouse genome. In plant genomes, LTR retrotransposons are the major repetitive ... Singer MF (March 1982). "SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes". Cell. 28 ... they enlarge the genome. The human genome, for example, contains about 500,000 LINEs, which is roughly 17% of the genome. Of ... February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. doi:10.1038/35057062. PMID ...

*Variable number tandem repeat

Repetitive DNA, representing over 40% of the human genome, is arranged in a bewildering array of patterns. Repeats were first ... The use of restriction enzymes showed that some repeat blocks were interspersed throughout the genome. DNA sequencing later ... A variable number tandem repeat (or VNTR) is a location in a genome where a short nucleotide sequence is organized as a tandem ... Now that many genomes have been sequenced, VNTRs have become essential to forensic crime investigations, via DNA fingerprinting ...

*Repeated sequence (DNA)

... with over two-thirds of the sequence consisting of repetitive elements in humans. Repetitive elements found in genomes fall ... Short Interspersed Nuclear Elements) LINEs (Long Interspersed Nuclear Elements) SVAs In primates, the majority of LINEs are ... "Repetitive elements may comprise over two-thirds of the human genome." PLoS Genet 7.12 (2011): e1002384. Ohno, Susumu. "So much ... Repeated sequences (also known as repetitive elements, or repeats) are patterns of nucleic acids (DNA or RNA) that occur in ...

*Exon shuffling

Singer, Maxine F (1982). "SINEs and LINEs: Highly repeated short and long interspersed sequences in mammalian genomes". Cell. ... Helitron transposons were first discovered during studies of repetitive DNA segments of rice, worm and the thale crest genomes ... The human ATM gene is responsible for the human autosomal-recessive disorder ataxia-telangiectasia and is located on chromosome ... Long interspersed element (LINE)-1[edit]. A potential mechanism for exon shuffling is the long interspersed element (LINE) -1 ...

*Jürgen Brosius

... in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 2013;5(3):578-90. doi: 10.1093/gbe/ ... repetitive elements, classified as SINEs, short interspersed repeats, located in the introns of brain-specific genes by making ... Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov ... There, he sequenced the first large ribosomal RNAs via their genes utilizing the Maxam-Gilbert sequencing method. It took ~2.5 ...

*Exon shuffling

Singer, M. F. (1982). "SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes". Cell. 28 ( ... Helitron transposons were first discovered during studies of repetitive DNA segments of rice, worm and the thale crest genomes ... The human ATM gene is responsible for the human autosomal-recessive disorder ataxia-telangiectasia and is located on chromosome ... Long interspersed element (LINE)-1Edit. A model of how L1 retrotransposition can mobilize sequences. At the top is the model ...

*BC200 lncRNA

As a long non-coding cytoplasmic RNA, BC200 RNA is a part of the largest group of non-coding transcripts in the human genome, ... The 5' region of monomeric Alu short interspersed repetitive elements (SINEs) allows for BC200 RNA transposition and has been ... In addition to upstream elements, there is an upstream TATGAAA sequence (similar to TATA box sequence) at positions -28 to -22 ... a TATA-like sequence, TATA-box binding protein (TBP), and RNA polymerase III. There is a deletion of sequences between -100 to ...

*Noncoding DNA

Alu sequences, classified as a short interspersed nuclear element, are the most abundant mobile elements in the human genome. ... Telomeres are regions of repetitive DNA at the end of a chromosome, which provide protection from chromosomal deterioration ... International Human Genome Sequencing Consortium (February 2001). "Initial sequencing and analysis of the human genome". Nature ... Mutation within these retro-transcribed sequences can inactivate the viral genome. Over 8% of the human genome is made up of ( ...

*Mycobacterium tuberculosis

The M. tuberculosis genome was sequenced in 1998. M. tuberculosis is part of a complex that has at least 9 species: M. ... Hawkey PM, Smith EG, Evans JT, Monk P, Bryan G, Mohamed HH, Bardhan M, Pugh RN (2003). "Mycobacterial interspersed repetitive ... tuberculosis phylogeny to human mitochondrial genomes and found impressive similarities in the patterns and geographical ... This method makes use of the presence of repeated DNA sequences within the M. tuberculosis genome. Three generations of VNTR ...

*CFDP1

"An Alu-linked repetitive sequence corresponding to 280 amino acids is expressed in a novel bovine protein, but not in its human ... Human CFDP1 genome location and CFDP1 gene details page in the UCSC Genome Browser. Iwashita S (2002). "[A novel type protein, ... Bcnt, that includes the region derived from a long interspersed nucleotide element]". Seikagaku. 73 (12): 1435-8. PMID 11831036 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...

*FAM185A

The FAM185A (Gene Family with sequence similarity 185, member A) is a protein that in humans is encoded by the FAM185A gene. ... It is described as a Long Interspersed Nuclear Element (LINE), a subclass of penaeid repetitive elements (PREs). Homologs have ... "Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon". BMC Genomics. 12: 242 ... Only one paralog, a pseudogene, for FAM185A exists in humans. The pseudogene, known as FAM185BP (Family of sequence similarity ...

*Conserved non-coding sequence

2007). "Fast-evolving noncoding sequences in the human genome". Genome Biology. 8 (6): R118. doi:10.1186/gb-2007-8-6-r118. PMC ... Repetitive elements can accumulate in an organism's genome as the result of a few different transposition processes. The extent ... These are further divided into long terminal repeat (LTR) retrotransposons, long interspersed nuclear elements (LINEs), and ... A conserved non-coding sequence (CNS) is a DNA sequence of noncoding DNA that is evolutionarily conserved. These sequences are ...

*Pseudogene

For example, somewhere between 30-44% of the human genome consists of repetitive elements such as SINEs and LINEs (see ... A high sequence identity means that it is highly likely that these two sequences diverged from a common ancestral sequence (are ... Pavlícek A, Paces J, Zíka R, Hejnar J (October 2002). "Length distribution of long interspersed nucleotide elements (LINEs) and ... Torrents D, Suyama M, Zdobnov E, Bork P (December 2003). "A genome-wide survey of human pseudogenes". Genome Research. 13 (12 ...

*Interspersed repeat

Interspersed repetitive DNA is found in all eukaryotic genomes. They differ from tandem repeat DNA in that rather than the ... Some types of interspersed repetitive DNA elements allow new genes to evolve by uncoupling similar DNA sequences from gene ... Hess JF, Fox M, Schmid C, Shen CK (October 1983). "Molecular evolution of the human adult alpha-globin-like gene region: ... Interspersed Repetitive Sequences at the US National Library of Medicine Medical Subject Headings (MeSH). ...

*Human evolutionary genetics

The human genome has been sequenced, as well as the chimpanzee genome. Humans have 23 pairs of chromosomes, while chimpanzees, ... For example, the sequence divergence varies between 0% to 2.66% between non-coding, non-repetitive genomic regions of humans ... This is further supported by Alu-like short interspersed nuclear elements (SINEs) which have been found only in members of the ... Human evolutionary genetics studies how one human genome differs from another human genome, the evolutionary past that gave ...

*Satellite DNA

Several RU sequences were cloned and sequenced to reveal conserved regions of conventional DNA sequences interspersed with five ... of the entire genome. Polymerase chain reaction Gene expression Knight, Julian C. (2009). Human Genetic Diversity: Functional ... G mononucleotide repeat within one of the repetitive pyrimidine:purine divergent domains. Conserved sequences showed virtually ... This was demonstrated in the land crab Gecarcinus lateralis, whose genome contains 3% of a GC-rich sequence consisting of ...

*Microsatellite

... interspersed repetitive element Microsatellite instability Mobile element Short interspersed repetitive element Simple sequence ... The human genome contains many (>16,000) short sequence repeats in regulatory regions, which provide 'tuning knobs' on the ... Because microsatellites consist of such repetitive sequences, DNA polymerase may make errors at a higher rate in these sequence ... Microsatellites are distributed throughout the genome. The human genome for example contains 50,000-100,000 dinucleotide ...

*Microsatellite

The human genome contains many (,16,000) short sequence repeats in regulatory regions, which provide 'tuning knobs' on the ... Long interspersed repetitive element. *Microsatellite instability. *Mobile element. *Short interspersed repetitive element ... Microsatellites are distributed throughout the genome.[6][1][7] The human genome for example contains 50,000-100,000 ... Because microsatellites consist of such repetitive sequences, DNA polymerase may make errors at a higher rate in these sequence ...
Stern, M.J., Ames, G.F.L., Smith, N.H., Robinson, E.C. and Higgins, C.F. (1984) Repetitive Extragenic Palindromic Sequences A Major Component of the Bacterial Genome. Cell, 37, 1015-1026.
Since the human genome draft sequence was in public for the first time in 2000, genomic analyses have been intensively extended to the population level. The following three international projects are good examples for large-scale studies of human genome variations: 1) HapMap Data (1,417 individuals) (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2010-08_phaseII+III/forward/), 2) HGDP (Human Genome Diversity Project) Data (940 individuals) (http://www.hagsc.org/hgdp/files.html), 3) 1000 genomes Data (2,504 individuals) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ If we can integrate all three data into a single volume of data, we should be able to conduct a more detailed analysis of human genome variations for a total number of 4,861 individuals (= 1,417+940+2,504 individuals). In fact, we successfully integrated these ...
The first edition of Human Genome Epidemiology, published in 2004, discussed how the epidemiologic approach provides an important scientific foundation for studying the continuum from gene discovery to the development, applications and evaluation of human genome information in improving health and preventing disease. Since that time, advances in human genomics have continued to occur at a breathtaking pace.
The first edition of Human Genome Epidemiology, published in 2004, discussed how the epidemiologic approach provides an important scientific foundation for studying the continuum from gene discovery to the development, applications and evaluation of human genome information in improving health and preventing disease. Since that time, advances in human genomics have continued to occur at a breathtaking pace.
The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the ...
The Society runs two themed meetings each year as satellites to either the American or European Societies of Human Genetics annual meeting as a forum for scientists to exchange ideas and form collaborations. Prominent speakers in the field are invited. The meetings are designed to update and increase knowledge of human genome variation and generally attract a stimulating and interesting collection of abstracts in all fields of human genome variation making it an ideal forum to share information and results. We invite members and non-members alike to attend these meetings.. FORTHCOMING HGVS MEETINGS ...
In a group paper published in the June 14 issue of Nature and in 28 companion papers published in the June issue of Genome Research, the ENCyclopedia Of DNA Elements (ENCODE) consortium, which is organized by the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), reported results of its exhaustive, four-year effort to build a parts list of all biologically functional elements in 1 percent of the human genome. Carried out by 35 groups from 80 organizations around the world, the research served as a pilot to test the feasibility of a full-scale initiative to produce a comprehensive catalog of all components of the human genome crucial for biological function.. "This impressive effort has uncovered many exciting surprises and blazed the way for future efforts to explore the functional landscape of the entire human ...
The question of the hypothetical function of the 98% non-coding DNA of the human genome remains one of the major open problems of Genetics. In 2010, we prooved that the entire human genome codon population is fine-tuned around the "Golden ratio" ("Codon Populations in single-stranded DNA Whole Human Genome Are fractal and fine-tuned by the Golden Ratio 1618" , 2010, Interdisciplinary Science). We show how, across the entire human genome, there appears to be an overall balance in the whole single-stranded DNA. This digital balance fits neatly around 2 attractors whose predominant values are 1 and (3-Phi)/2, where Phi is the Golden Ratio. Yet, the same analysis applied to each of our 24 chromosomes and to each of the 25 chromosomes of the chimpanzee (book "Codex Biogenesis", 2009), will reveal a strange phenomenon: while this study shows that populations of the respective ...
The question of the hypothetical function of the 98% non-coding DNA of the human genome remains one of the major open problems of Genetics. In 2010, we prooved that the entire human genome codon population is fine-tuned around the "Golden ratio" ("Codon Populations in single-stranded DNA Whole Human Genome Are fractal and fine-tuned by the Golden Ratio 1618" , 2010, Interdisciplinary Science). We show how, across the entire human genome, there appears to be an overall balance in the whole single-stranded DNA. This digital balance fits neatly around 2 attractors whose predominant values are 1 and (3-Phi)/2, where Phi is the Golden Ratio. Yet, the same analysis applied to each of our 24 chromosomes and to each of the 25 chromosomes of the chimpanzee (book "Codex Biogenesis", 2009), will reveal a strange phenomenon: while this study shows that populations of the respective ...
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother-father-child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of ...
CALL FOR PAPERS Human Genomic Variation: Disease, drug response and clinical phenotypes January 3-7, 2002 Island of Kauai, Hawaii, USA A session of the Pacific Symposium on Biocomputing 2002 The recent completion of the first assembly of the human genome has provided an invaluable tool for investigating the biology of our species. Several academic and industrial laboratories are working to add value to this raw genome sequence by generating DNA variation and gene expression data. However, researchers are encountering substantial challenges regarding the management, annotation and analysis of this information. Many of the critical issues involved in linking genetic variation to clinical phenotypes are complicated by a need to synthesize biological and computational expertise. For example, there is a need to apply and extend population genetic analyses to high- throughput data to elucidate underlying patterns of variation in the ...
More than 15 years have passed since work began sequencing the 2.85 billion nucleotides of the human genome. While the draft sequence was published in Nature in 2001, researchers at the Human Genome Project continued to fill the gaps and subject individual chromosomes to ever more detailed analyses.. Now Nature presents the complete and comprehensive DNA sequence of the human genome as a freely available resource, plus new commentary by NHGRI Director Francis S. Collins, past Department of Energy Director Aristides Patrinos and former director of the Sanger Centre John Sulston, among others.. Among the four sponsors for the Collection, NHGRI joined the U.S. Department of Energy, the Wellcome Trust and corporate sponsor Applied Biosystems in funding the creation of this issue. Nature carries sole responsibility for all editorial content.. Go to: Human Genome Collection. ...
The 72 kDa IE1 protein of human cytomegalovirus (HCMV) is one of a few viral regulatory proteins expressed immediately after infection of a host cell. Although it is now well-established that IE1 is a potent transcriptional activator of the human immunodeficiency virus (HIV) long terminal repeat (LTR), the identity of the nucleotide sequence responsive to IE1 remains elusive and the molecular mechanism of this interaction is not well-understood. We have constructed various LTR mutants and tested them for their ability to be activated by IE1 using transient transfection assays. Mutations in the NF-κB sites, of either a few changes in the nucleotide sequence or a deletion of the entire region, abrogated IE1-driven transactivation. Deletion of the Tat-responsive element (TAR) had no significant effect on reporter expression. Mutations in the Sp1 sites or the TATA box significantly lowered LTR activity, but this is probably due to an effect on the general transcription system, ...
Bethesda, Md., Wed., August 20, 2008 - The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), today awarded more than $20 million in grants to develop innovative sequencing technologies inexpensive and efficient enough to sequence a persons DNA as a routine part of biomedical research and health care. "The ability to sequence any individuals genome inexpensively and accurately is the quantum leap needed to usher in an age of personalized medicine, in which healthcare providers will routinely use an individuals genetic code to prevent, diagnose, and treat diseases," said Alan E. Guttmacher, M.D., acting director of the National Human Genome Research Institute. DNA sequencing costs have fallen dramatically over the past decade, fueled in large part by tools, technologies and process improvements developed as part of the Human Genome project, ...
TY - JOUR. T1 - Meta-analysis of five genome-wide linkage studies for body mass index reveals significant evidence for linkage to chromosome 8p. AU - Johnson, L.. AU - Luke, A.. AU - Deng, H. W.. AU - Mitchell, B. D.. AU - Comuzzie, A. G.. AU - Cole, S. A.. AU - Blangero, J.. AU - Perola, M.. AU - Teare, M. Dawn. PY - 2005/4. Y1 - 2005/4. N2 - OBJECTIVE: To perform a meta-analysis of genome-wide linkage scans using body mass index (BMI) to identify genetic loci predisposing to obesity. DATA: A total of 13 published genome scans on obesity have used BMI as their primary end point. Five of these 13 groups agreed to provide detailed results from their scans that were required for a meta-analysis. Collectively, these five studies included a total of 2814 individuals from 505 families. METHODS: The results of the five studies were analysed using the GSMA (genome scans meta-analysis) method. RESULTS: The analysis revealed significant evidence for ...
article{221460, abstract = {The distribution of the ribosomal RNA (rRNA) genes and three classes of highly repetitive DNA in the chromatin of interphase nuclei of Arabidopsis thaliana was studied for the first time through non-isotopic in situ hybridization and luminescence digital imaging microscopy. Each of the three classes of highly repetitive DNA exhibited a characteristic hybridization pattern, and one class was seen to be primarily localized on two chromocentres, which would allow it to distinguish a particular chromosome. The rDNA was consistently localized on the two largest chromocentres and on one or two smaller chromocentres. A limited number of nuclei exhibited more than four labelled chromocentres, indicative of either polypoidy or differential amplification of the rDNA. In nuclei where the nucleolus could be clearly observed, the nucleolar associated chromocentres (NACs) were seen to be labelled by the ribosomal DNA (rDNA) probe.}, author = {Bauwens, Serge and ...
There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to ...
The stored 5.3 billion base pairs represent 2.58 billion base pairs of unique sequence which have been calculated to cover about 81 percent of an estimated genome size of 3.18 billion base pairs. These data, combined with all of the "finished" and "draft" human genome sequence data from the public databases, give Celera coverage of 90 percent of the human genome. The companys sequencing was performed on 300 PE Biosystems ABI Prism 3700 DNA Analysers.. The whole genome shotgun technique concentrates on sequencing the entire genome at once, allowing for real time discovery of human genes across the entire genome, according to J. Craig Venter, Ph.D., who is Celeras president and chief scientific officer. "The early phase of sequencing the human genome using the whole genome shotgun process is especially ...
Human Genome Project Results - Human Genome Project results have told us that we have far fewer genes than expected. What other Human Genome Project results have surprised us?
In a DER SPIEGEL interview, genetic scientist Craig Venter discusses the 10 years he spent sequencing the human genome, why we have learned so little from it a decade on and the potential for mass production of artificial life forms that could be used to produce fuels and other resources.. SPIEGEL: Mr. Venter, when the elite among gene researchers undertook the decoding of the human genome, you were their greatest enemy. They called you "Frankenstein," "blood sucker," "Darth Venter" and even "asshole." Why do you attract so much hostility?. Venter: Well, nobody likes to be beaten -- by superior intelligence, planning and technology. That gets people upset.. SPIEGEL: Every area of science is competitive. But it doesnt lead to that kind of hostility in all areas.. Venter: The human genome project was completely different, it was supposed to be the biggest thing in the history of biological sciences. Billions ...
Release of the first human genome assembly was a landmark achievement, and after nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and compl
SAN FRANCISCO (WebMD) -- Ninety percent of "the blueprint of human beings," the Human Genome Project, will be finished by the spring of 2000, much earlier than the original goal of 2005, according to Dr. Francis Collins, director of the National Human Genome Research Institute at the National Institutes of Health (NIH). Collins spoke on Thursday at an American Medical Association media briefing in San Francisco. Implications for research The Human Genome Project (HGP), started in 1990 as a 15-year program, is coordinated by the Department of Energy and the NIH. Its goal is to identify all of the 80,000 genes in human DNA, as well as to develop tools to analyze the 3 billion pairs of chemical bases of which DNA is made. A genome is a map of all the DNA in an organism. Genetic analysis will enable doctors to screen people for serious diseases including cancer ...
Human Genome Project The worldwide effort, originally named the Human Genome Initiative but later known as the Human Genome Project or HGP, began in 1987 and was celebrated as complete in 2001. When begun, HGP was dubbed big science comparable to placing human beings on the moon.
Sequencing the human genome depended on many technological improvements in the production and analysis of sequence data. Key innovations were developed both within and outside the Human Genome Project. Laboratory innovations included four-colour fluorescence-based sequence detection, improved fluorescent dyes, dye-labelled terminators, polymerases specifically designed for sequencing, cycle sequencing and capillary gel electrophoresis. These studies contributed to substantial improvements in the automation, quality and throughput of collecting raw DNA sequence. Human Genome Project, Nature ...
Milestone crossed on the 15th anniversary of the completion of the Human Genome Project, as the worldwide estimate for whole human genomes sequenced approaches one million
The Human Genome Project (HGP), according to the National Human Genome Research Institute, was the international, collaborative research program formed to complete the mapping and understanding of all the genes of human beings. All our genes together are known as our "genome.". Our hereditary material is the double helix of deoxyribonucleic acid (DNA), which contains all human genes. DNA, in turn, is made up of four chemical bases, pairs of which form the "rungs" of the twisted, ladder-shaped DNA molecules. All genes are made up of stretches of these four bases, arranged in different ways and in different lengths.. During the HGP, researchers deciphered the human genome in three major ways: determining the order, or "sequence," of all the bases in our genomes DNA; making maps that show the locations of genes for major sections of all our ...
Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform. The hypothesis was tested using a case study of a set of dizygotic X-chromosome monosomy 53,X sheep twins. Genome-wide SNP data were available from the Illumina platform (11 082 autosomal and 191 X-chromosome SNPs) on 1848 male and 8954 female sheep and available from the AxiomTM platform (11 128 ...
Jiahao Wu, a graduate student in the Department of Mechanical Engineering at Louisiana State University, is working on one groundbreaking innovation to reading the human genome, a process known as nanoscale DNA sequencing, under the guidance of award-winning Professor Dr. Steven Soper. Wu believes that cheap microchips equipped with tiny channels, channels small enough to allow single DNA molecules to be manipulated and analyzed individually, could revolutionize point-of-care genetic testing.. Nano-scale DNA sequencing could potentially be much cheaper and faster than conventional methods, allowing researchers to read parts of the human genome in seconds instead of hours. Faster and cheaper approaches to DNA sequencing are of vast importance in genetic studies and personalized medicine, especially in developing countries.. DNA sequencing involves determining the order of DNA bases - A, G, C, or T - like four different colored pearls, along a ...
... Thomas R. Gingeras, Affymetrix Inc., Santa Clara, CA. The first drafts of complete human genome sequence have brought with them the opportunities to map the RNA transcription patterns that are characteristic of each differentiated and undifferentiated cell type and characterize the sequence variations that underlie the phenotypic differences observed in the human population. By using the very high information content inherent in high-density oligonucleotide arrays it will be possible to map the locations of RNA transcription along the length of the entire human genome. Such a transcriptome map will provide information concerning: 1) the identification of novel transcription domains of the genome, 2) the predominant utilization of exon sequences during differentially spliced gene expression and 3) a empirically derived set of results which can be compared to the sequence annotation now ...
How is Human Genome Research Centre (French) abbreviated? GENETHON stands for Human Genome Research Centre (French). GENETHON is defined as Human Genome Research Centre (French) somewhat frequently.
Received January 23, 2003 The recent sequencing of the human genome, resulting from two independent global efforts, is poised to revolutionize all aspects of human health. This landmark achievement has also vindicated two different methodologies that can now be used to target other important large genomes. The human genome sequence has revealed several novel/surprising features notably the probable presence of a mere 30-35,000 genes. In depth comparisons have led to classification of protein families and identification of several orthologues and paralogues. Information regarding non-protein coding genes as well as regulatory regions has thrown up several new areas of research. Although still incomplete, the sequence is poised to become a boon to pharmaceutical companies with the promise of delivering several new drug targets. Several ethical concerns have also been raised and need to be addressed in earnest. ...
Repetitive sequences are DNA sequences that occur many times in the genome. It has been experimentally shown that repetitive sequences can increase or decrease the expression levels of nearby genes by a variety of mechanisms and that the ability of repetitive sequences to alter gene expression depends on their epigenetic states. The epigenetic states of repetitive sequences depend on random epigenetic drift, stress, the genomic environment of the repetitive sequence, epigenetic inheritance, mutations in the genome, and other factors. Since repetitive sequences constitute approximately one half of the human and mouse genomes, the influence of repetitive sequences on gene expression in the mammalian ...
The etiologic paradigm of complex human disorders such as autism is that genetic and environmental risk factors are independent and additive, but the interactive effects at the epigenetic interface are largely ignored. Genomic technologies have radically changed perspective on the human genome and how the epigenetic interface may impact complex human disorders.. Here, I review recent genomic, environmental and epigenetic findings that suggest a new paradigm of "integrative genomics" in which genetic variation in genomic size may be impacted by dietary and environmental factors that influence the genomic saturation of DNA methylation.. Human genomes are highly repetitive, but the interface of large-scale genomic differences with environmental factors that alter the DNA methylome such as dietary folate is under-explored. In addition to obvious direct effects of some environmental toxins on the ...
The Chimpanzee Genome Project is an effort to determine the DNA sequence of the Chimpanzee genome. It is expected that by comparing the genomes of humans and other apes, it will be possible to better understand what makes humans distinct from other species from a genetic perspective. It will also aid in the study of diseases that affect (or, conversely, do not affect) various primate species. Human and chimpanzee chromosomes are very similar. The primary difference is that humans have one fewer pair of chromosomes than do other great apes. Humans have 23 pairs of chromosomes and other great apes have 24 pairs of chromosomes. In the human evolutionary lineage, two ancestral ape chromosomes fused at their telomeres, producing human chromosome 2. There are nine other major chromosomal differences between chimpanzees and humans: ...
TY - JOUR. T1 - 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. AU - Greshock, Joel. AU - Naylor, Tara L.. AU - Margolin, Adam. AU - Diskin, Sharon. AU - Cleaver, Stephen H.. AU - Futreal, P. Andrew. AU - deJong, Pieter J.. AU - Zhao, Shaying. AU - Liebman, Michael. AU - Weber, Barbara L.. PY - 2004/1/1. Y1 - 2004/1/1. N2 - Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilization of aCGH has been limited by the lack of well characterized, high-resolution clone sets optimized for consistent performance in aCGH assays and specifically designed analytic software. We have assembled a set of ∼4100 publicly available human bacterial artificial ...
View Notes - chapter_1 from WE BIBI000000 at Ghent University. Mutations and variation in the human genome. the human genome 2003 marked the 50th anniversary of the double helix model by Watson and
Asthma and allergy are complex multifactorial disorders, with both genetic and environmental components determining disease expression. The use of molecular genetics holds great promise for the identification of novel drug targets for the treatment of asthma and allergy. Genome-wide linkage studies have identified a number of potential disease susceptibility loci but replication remains inconsistent. The aim of the current study was to complete a meta-analysis of data from genome-wide linkage studies of asthma and related phenotypes and provide inferences about the consistency of results and to identify novel regions for future gene discovery. The rank based genome-scan meta-analysis (GSMA) method was used to combine linkage data for asthma and related traits; bronchial hyper-responsiveness (BHR), allergen positive skin prick test (SPT) and total serum Immunoglobulin E (IgE) from nine Caucasian asthma populations. Significant evidence for susceptibility loci ...
The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference. The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection. We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples.
Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large. Since the first sequenced genomes became available in the late 1970s, scientists have been using comparative genomics to study the differences and similarities between various genomes. Genome sequencing has progressed over time to include more and more complex genomes including the eventual sequencing of the ...
TY - JOUR. T1 - Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. AU - Pei, Lirong. AU - Choi, Jeong-Hyeon. AU - Liu, Jimei. AU - Lee, Eun Joon. AU - McCarthy, Brian. AU - Wilson, James M.. AU - Speir, Ethan. AU - Awan, Farrukh. AU - Tae, Hongseok. AU - Arthur, Gerald. AU - Schnabel, Jennifer L.. AU - Taylor, Kristen H.. AU - Wang, Xinguo. AU - Xu, Dong. AU - Ding, Hanfei. AU - Munn, David H. AU - Caldwell, Charles W.. AU - Shi, Huidong. PY - 2012/6. Y1 - 2012/6. N2 - We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from chronic lymphocytic leukemia (CLL) patients and normal control samples using reduced representation bisulfite sequencing (RRBS). The methylation status of 1.8-2.3 million CpGs in the CLL genome was determined; about 45% of these CpGs were located in more than 23,000 CpG islands (CGIs). While global CpG methylation was similar between CLL and normal B-cells, 1,764 gene ...
... contain 89 genes selected for targeted studies of the human hematopoietic stem cells and hematopoiesis pathway. Arrayit Pathways™ Microarrays gene content is derived from our H25K Whole Human Genome Microarray constructed using highly optimized and unique long-mer oligonucleotides designed to maximize detection of the greatest number of cellular transcripts in the human transcriptome with greater
Multiple displacement amplification (MDA) is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples) before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA) technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ...
NHGRI is devoted to advancing health through genome research. The Institute led NIHs contribution to the Human Genome Project, which was successfully completed in 2003 ahead of schedule and under budget. Building on the foundation laid by the sequencing of the human genome, NHGRIs work now encompasses a broad range of research aimed at expanding understanding of human
Do intellectual property (IP) rights on existing technologies hinder subsequent innovation? Using newly-collected data on the sequencing of the human genome by the public Human Genome Project and the private firm Celera, this paper estimates the impact of Celeras gene-level IP on subsequent scientific research and product development. Genes initially sequenced by Celera were held with IP for up to two years, but moved into the public domain once re-sequenced by the public effort. Across a range of empirical specifications, I find evidence that Celeras IP led to reductions in subsequent scientific research and product development on the order of 20 to 30 percent. Taken together, these results suggest that Celeras short-term IP had persistent negative effects on subsequent innovation relative to a counterfactual of Celera genes having always been in the public domain. ...
About a decade ago the first large catalogs of copy number variants (CNVs) in the human genome were presented [1, 2]. Numerous studies later, CNVs are known to contribute to the genomic variation to a larger extent than single nucleotide polymorphisms (SNPs) in terms of number of nucleotide differences [3, 4]. CNVs are defined as DNA segments of variable length, up to several megabases (Mb), that varies in copy numbers in comparison to a reference genome [5]. The different types of CNVs include deletions and duplications, while consequences of CNVs include e.g. altered gene dosage and regulation, changed gene structure and unmasking of recessive alleles [5]. The effect of CNVs varies from being benign or neutral, to having subtle effects on disease predisposition or directly causing disease. The contribution and importance of CNVs for phenotypic diversity and disease susceptibility has been repeatedly shown in human and ...
Using computer programmes, he produced a "comparative map" that revealed duplications unique to each of these four genomes, along with those that are shared between them. The map showed that about a third of the duplications in the human genome are unique to us, and most of the remaining duplications are ones we share with chimps. The rate at which these duplications cropped up had greatly accelerated in the part of the primate family tree that includes humans and the African great apes. These rates doubled and hit their peak in the last common ancestor of ourselves and chimpanzees. As a result, both chimps and humans have far more of these doubles than either orang-utans or macaques. This burst of activity coincided with a time when other types of mutation, such as changes to single nucleotides, were slowing down. Marques-Bonet thinks that these accelerated rates of gene duplication played a pivotal role in the success and ...
Using computer programmes, he produced a "comparative map" that revealed duplications unique to each of these four genomes, along with those that are shared between them. The map showed that about a third of the duplications in the human genome are unique to us, and most of the remaining duplications are ones we share with chimps. The rate at which these duplications cropped up had greatly accelerated in the part of the primate family tree that includes humans and the African great apes. These rates doubled and hit their peak in the last common ancestor of ourselves and chimpanzees. As a result, both chimps and humans have far more of these doubles than either orang-utans or macaques. This burst of activity coincided with a time when other types of mutation, such as changes to single nucleotides, were slowing down. Marques-Bonet thinks that these accelerated rates of gene duplication played a pivotal role in the success and ...
Laureates Work Has Great Impact on Human Genome Project Research. Phillip Sharp (Massachusetts Institute of Technology) and Richard Roberts (formerly Cold Spring Harbor Laboratory, now New England Biolabs) were jointly awarded the 1993 Nobel Prize in Medicine and Physiology for their 1977 work on gene splicing. Sharp served on the Program Advisory Committee of the NIH National Center for Human Genome Research from 1988 to 1991.. Working independently, Sharp and Roberts discovered that genes in eukaryotic cells are distributed among widely spaced segments separated by introns (DNA segments that have no apparent protein message); about 99% of human genes are believed to share this structure. In a dramatic change from commonly accepted theories, human genes were thus shown to differ markedly from often-studied bacterial genes, which run continuously along the DNA strand. Research indicates that some introns ...
Genome-wide association studies are important tools to reconstruct the genotype phenotype map to understand the underlying genetic architecture of complex traits. This enables us to better understand the genetic architecture of these phenotypes. With the advances in genotyping and high throughput sequencing technologies, millions of markers can be identified for individual populations in very short durations of time. Due to the multiple loci control nature of complex phenotypes, there is great interest to test markers simultaneously instead of one by one. In chapter 2, we compare three model selection methods for genome wide association studies using simulations: the Stochastic Search Variable Selection (SSVS), the Least Absolute Shrinkage and Selection Operator (LASSO) and the Elastic Net. We apply the three methods to identify genetic variants that are associated with daunorubicin-induced cytotoxicity. We also compare the LASSO and the SSVS to a dataset of two quantitative ...
BACKGROUND: Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples. RESULTS: We demonstrate an asymmetry in the detection of the two alleles for each SNP, which deleteriously influences both allelic proportions and copy number estimates. The asymmetry is caused by a remaining bias between the two dyes used in the Infinium II assay after using the normalization method in Illuminas proprietary software (BeadStudio). We propose a quantile normalization strategy for correction of this dye bias. We tested ...
Health,The National Human Genome Research Institute (NHGRI) a part of Nationa...Comparing the genomes of other species to humans is an exceptional...NHGRIs Large-Scale Sequencing Research Network and their internat... The gibbon genome sequence will provide researchers with crucial ...The gibbon genome is unique because it carries an extraordinary hi...,NHGRI,Aims,To,Sequence,Primate,Genomes,medicine,medical news today,latest medical news,medical newsletters,current medical news,latest medicine news
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes ,99% of SNP variants with a frequency of ,1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies ...
OBJECTIVE: Recent genome-wide association studies have resulted in a dramatic increase in our knowledge of the genetic loci involved in type 2 diabetes. In a complementary approach to these single-marker studies, we attempted to identify biological pathways associated with type 2 diabetes. This approach could allow us to identify additional risk loci. RESEARCH DESIGN AND METHODS: We used individual level genotype data generated from the Wellcome Trust Case Control Consortium (WTCCC) type 2 diabetes study, consisting of 393,143 autosomal SNPs, genotyped across 1,924 case subjects and 2,938 control subjects. We sought additional evidence from summary level data available from the Diabetes Genetics Initiative (DGI) and the Finland-United States Investigation of NIDDM Genetics (FUSION) studies. Statistical analysis of pathways was performed using a modification of the Gene Set Enrichment Algorithm (GSEA). A total of 439 pathways were analyzed from the Kyoto Encyclopedia of Genes and ...
CREST. The accurate identification of structural variations using whole-genome DNA sequencing data generated by next-generation sequencing technology is extremely difficult. To address this challenge, we have developed CREST, an algorithm that uses sequencing reads with partial alignments to the reference human genome (so-called soft-clipped reads) to directly map the breakpoints of somatic structural variations. We applied CREST to paired tumor/normal whole genome sequencing data from five cases of T-lineage acute lymphoblastic leukemia (T-ALL). A total of 110 somatic structural variants were identified, ,80% of which were validated by genomic PCR and Sanger sequencing. The validated structural variants included 31 inter-chromosomal translocations, 19 intra-chromosomal translocations, one inversion, 22 deletions and 16 insertions. A comparison of the results generated with CREST to those obtained using the traditional paired-end discordant ...
Microorganisms widely exist in nature and are closely related to human life and production. They are generally divided into fungi, actinomycetes, bacteria, spirulina, rickettsia, chlamydia, mycoplasma and viruses. Microbial whole genome sequencing is an important tool for mapping genomes of novel organisms, finishing genomes of known organisms, or comparing genomes across multiple samples. Sequencing the entire microbial genome is important for construction of accurate reference genomes, microbial identification, and other comparative genomic studies. Comparative genomic analysis based on whole genome sequencing plays an irreplaceable role in studying pathogenic mechanisms of pathogenic microorganism, evolution of pathogenic genes and screening of novel, efficient drug targets. Microbial whole genome sequencing can be widely used in various fields.. Diseases ...
Assembly/Alignment/Annotation of 12 related Drosophila species: »Assembly/Alignment/Annotation, LBNL, USA BDGP Single Nucleotide Polymorphism (SNP) Project: »Berkeley Drosophila Genome Project, University of California, Berkeley, USA Berkeley Drosophila Genome Project (BDGP): »BDGP, University of California, Berkeley, USA BDTNP, ChIP/chip in vivo DNA binding data: »Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA CluSTr protein sequence similarity analysis of Drosophila: »CluSTr proteome analysis, EBI, UK D. pseudoobscura genome project: »Human Genome Sequencing Center, Baylor College of Medicine, USA D. simulans genome project: »Genome Sequencing Center, Washington University, USA D. yakuba genome project: »Genome Sequencing Center, Washington University, USA D.melanogaster UCSC Genome Browser ...
Comprehensive genome-wide DNA methylation profiling is critical to gain insights into epigenetic reprogramming during development and disease processes. Among the different genome-wide DNA methylation technologies, whole genome bisulphite sequencing (WGBS) is considered the gold standard for assaying genome-wide DNA methylation at single base resolution. However, the high sequencing cost to achieve the optimal depth of coverage limits its application in both basic and clinical research. To achieve 15× coverage of the human methylome, using WGBS, requires approximately three lanes of 100-bp-paired-end Illumina HiSeq 2500 sequencing. It is important, therefore, for advances in sequencing technologies to be developed to enable cost-effective high-coverage sequencing. In this study, we provide an optimised WGBS methodology, from library preparation to sequencing and data processing, to enable 16-20× genome-wide ...
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating ...
Array-based comparative genomic hybridization (CGH) allows high-throughput genome-wide survey for DNA copy number aberrations, providing a powerful tool for investigating genetic disorders and for developing diagnostic and therapeutic targets. Arrays used in this study consist of approximately 43,000 60-mer oligonucleotide probes that span coding and noncoding regions of the whole human genome with an average spatial resolution of around 35 kb. Furthermore, the sensitivity of these arrays is capable of detecting and mapping regions of single-copy losses, homozygous deletions, and amplicons of various sizes even when using full-complexity genomic samples. In this study, the investigators will conduct an array-based comparative genomic hybridization (CGH) with genomic DNA of many affected members from schizophrenia families (the investigators classified families according to the presence or absence of two or more affected members) to identify a set of ...
Elia, J., Glessner, J.T., Wang, K., Takahashi, N., Shtir, C.J., Hadley, D., Sleiman, P.M.A., Zhang, H., Kim, C.E., Robison, R., Lyon, G.J., Flory, J.H., Bradfield, J.P., Imielinski, M., Hou, C., Frackelton, E.C., Chiavacci, R.M., Sakurai, T., Rabin, C., Middleton, F.A., Thomas, K.A., Garris, M., Mentch, F., Freitag, C.M., Steinhausen, H.-C., Todorov, A.A., Reif, A., Rothenberger, A., Franke, B., Mick, E.O., Roeyers, H., Buitelaar, J., Lesch, K.-P., Banaschewski, T., Ebstein, R.P., Mulas, F., Oades, R.D., Sergeant, J., Sonuga-Barke, E., Renner, T.J., Romanos, M., Romanos, J., Warnke, A., Walitza, S., Meyer, J., Pálmason, H., Seitz, C., Loo, S.K., Smalley, S.L., Biederman, J., Kent, L., Asherson, P., Anney, R.J.L., Gaynor, J.W., Shaw, P., Devoto, M., White, P.S., Grant, S.F.A., Buxbaum, J.D., Rapoport, J.L., Williams, N.M., Nelson, S.F., Faraone, S.V., Hakonarson, H. (2012-01). Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention ...
Copy number variation (CNV) comprises a recently discovered kind of variation involving deletion and duplication of DNA segments of variable size, ranging from a few hundred basepairs to several million. By altering gene dosage levels or disrupting proximal or distant regulatory elements CNVs create human diversity. They represent also an important factor in human evolution and play a role in many disorders including cancer. Array-based comparative genomic hybridization as well as expression arrays are powerful and suitable methods for determination of copy number variations or gene expression changes in the human genome. In paper I we established a 32K clone-based genomic array, covering 99% of the current assembly of the human genome with high resolution and applied it in the profiling of 71 healthy individuals from three ethnic groups. Novel and previously reported CNVs, involving ~3.5% of the ...
Davison, A.J., Marsden, H.S. and Wilkie, N.M. (1981) One functional copy of the long terminal repeat gene specifying the immediate-early polypeptide IE 110 suffices for a productive infection of human foetal lung cells by herpes simplex virus. Journal of General Virology, 55(1), pp. 179-191. (doi:10.1099/0022-1317-55-1-179) ...
Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining similar to 14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P , 5 x 10(-8). Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be ...
In regions where malaria is endemic, individuals are often infected with multiple distinct parasite genotypes, a situation that may impact on evolution of parasite virulence and drug resistance. Most approaches to studying genotypic diversity have involved analysis of a modest number of polymorphic loci, although whole genome sequencing enables a broader characterisation of samples. PCR-based microsatellite typing of a panel of ten loci was performed on Plasmodium falciparum in 95 clinical isolates from a highly endemic area in the Republic of Guinea, to characterize within-isolate genetic diversity. Separately, single nucleotide polymorphism (SNP) data from genome-wide short-read sequences of the same samples were used to derive within-isolate fixation indices (F ws), an inverse measure of diversity within each isolate compared to overall local genetic diversity. The latter indices were compared with the microsatellite results, and also with indices derived ...
The entire functional NANOG gene (according to our sequencing data) and NANOGP1 are present in both the human and chimpanzee genome assemblies at orthologous chromosomal positions. In the 3 UTR of the NANOG gene, there is an Alu element, which is missing from NANOGP1 in both genomes. Therefore, the NANOGP1 unprocessed pseudogene arose through duplication of the chromosomal region containing NANOG before the human-chimpanzee (H/C) divergence and before insertion of the Alu element into the NANOG gene. Because the same Alu element is present in both the human and chimpanzee NANOG genes, its insertion must also have preceded the H/C divergence. The processed pseudogenes NANOGP2, NANOGP3, NANOGP4, NANOGP5, NANOGP6, NANOGP7, NANOGP9, and NANOGP10 lack this Alu element. They thus likely arose before its insertion and, therefore, also predate the H/C divergence. The presence of the NANOGP11 pseudogene fragment in both the ...
TY - JOUR. T1 - RefCNV. T2 - Identification of gene-based copy number variants using whole exome sequencing. AU - Chang, Lun Ching. AU - Das, Biswajit. AU - Lih, Chih Jian. AU - Si, Han. AU - Camalier, Corinne E.. AU - McGregor, Paul M.. AU - Polley, Eric. PY - 2016/4/27. Y1 - 2016/4/27. N2 - With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The construction of the reference set includes an evaluation of the sources of variability in the coverage distribution. We observed that the processing steps had an impact on the coverage distribution. For each exon, we ...
AbstractMultilocus haplotype analysis of candidate variants with genome wide association studies (GWAS) data may provide evidence of association with disease, even when the individual loci themselves do not. Unfortunately, when a large number of candidate variants are investigated, identifying risk haplotypes can be very difficult. To meet the challenge, a number of approaches have been put forward in recent years. However, most of them are not directly linked to the disease-penetrances of haplotypes and thus may not be efficient. To fill this gap, we propose a mixture model-based approach for detecting risk haplotypes. Under the mixture model, haplotypes are clustered directly according to their estimated disease penetrances. A theoretical justification of the above model is provided. Furthermore, we introduce a hypothesis test for haplotype inheritance patterns which underpin this model. The performance of the proposed approach is evaluated by simulations and real data analysis. The ...
TY - JOUR. T1 - Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. AU - Rioux, John D.. AU - Xavier, Ramnik J.. AU - Taylor, Kent D.. AU - Silverberg, Mark S.. AU - Goyette, Philippe. AU - Huett, Alan. AU - Green, Todd. AU - Kuballa, Petric. AU - Barmada, M. Michael. AU - Datta, Lisa. AU - Shugart, Yin Yao. AU - Griffiths, Anne M.. AU - Targan, Stephan R.. AU - Ippoliti, Andrew F.. AU - Bernard, Edmond Jean. AU - Mei, Ling. AU - Nicolae, Dan L.. AU - Regueiro, Miguel. AU - Schumm, L. Philip. AU - Steinhart, A. Hillary. AU - Rotter, Jerome I.. AU - Duerr, Richard H.. AU - Cho, Judy H.. AU - Daly, Mark J.. AU - Brant, Steven R.. PY - 2007/5. Y1 - 2007/5. N2 - We present a genome-wide association study of ileal Crohn disease and two independent replication studies that identify several new regions of association to Crohn disease. Specifically, in addition to the previously established CARD15 and ...
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Biosis http://www.biosis.org Biological/biochemical information CABI Publishing http://www.cabi-publishing.org/ Abstracts/databases CAS http://www.cas.org Chemistry, toxicology, chemical engineering information Centers for Disease Control and Prevention http://www.cdc.gov CINAHL http://www.cinahl.com Nursing and allied health information Cochrane Library http://www.update-software.com/cochrane EMBASE.com http://www.embase.com Biomedical and pharmacological information Gale Directory of Online, Portable, and Internet Databases http://library.dialog.com/bluesheets/html/bl0230.html GDB Human Genome Database http://www.gdb.org Human Genome Organization (HUGO) http://www.genenames.org Human Genome Variation Society http://www.hgvs.org Institute of Medicine http://www.nas.edu/iom MEDNDX http://www.medicalndx.com/ Medical search engine Medstract.org http://www.medstract.org Acronyms and initialisms specific to ...
Human genetic variation is distributed nonrandomly across the genome, though the principles governing its distribution are only partially known. DNA replication creates opportunities for mutation, and the timing of DNA replication correlates with the density of SNPs across the human genome. To enable deeper investigation of how DNA replication timing relates to human mutation and variation, we generated a high-resolution map of the human genomes replication timing program and analyzed its relationship to point mutations, copy number variations, and the meiotic recombination hotspots utilized by males and females. DNA replication timing associated with point mutations far more strongly than predicted from earlier analyses and showed a stronger relationship to transversion than transition mutations. Structural mutations arising from recombination-based mechanisms and recombination hotspots ...
TY - JOUR. T1 - Two-stage Genome-wide Methylation Profiling in Childhood-onset Crohns Disease Implicates Epigenetic Alterations at the VMP1/MIR21 and HLA Loci. AU - Adams, Alex T. AU - Kennedy, Nicholas A. AU - Hansen, Richard. AU - Ventham, Nicholas T. AU - OʼLeary, Kate R. AU - Drummond, Hazel E. AU - Noble, Colin L. AU - El-Omar, Emad. AU - Russell, Richard K. AU - Wilson, David C. AU - Nimmo, Elaine R. AU - Hold, Georgina L. AU - Satsangi, Jack. PY - 2014/10. Y1 - 2014/10. N2 - BACKGROUND: As a result of technological and analytical advances, genome-wide characterization of key epigenetic alterations is now feasible in complex diseases. We hypothesized that this may provide important insights into gene-environmental interactions in Crohns disease (CD) and is especially pertinent to early onset disease.METHODS: The Illumina 450K platform was applied to assess epigenome-wide methylation profiles in circulating leukocyte DNA in discovery and replication ...
In 1976, the genome of the RNA virus Bacteriophage MS2 was the first complete genome to be determined, by Walter Fiers and his team at the University of Ghent (Ghent, Belgium).[13] The idea for the shotgun technique came from the use of an algorithm that combined sequence information from many small fragments of DNA to reconstruct a genome. This technique was pioneered by Frederick Sanger to sequence the genome of the Phage Φ-X174, a virus (bacteriophage) that primarily infects bacteria that was the first fully sequenced genome (DNA-sequence) in 1977.[14] The technique was called shotgun sequencing because the genome was broken into millions of pieces as if it had been blasted with a shotgun. In order to scale up the method, both the sequencing and genome assembly had to be automated, as they were in the 1980s.. Those techniques were shown applicable to sequencing of the first free-living ...
TY - JOUR. T1 - Genomic Evidence of Local Adaptation to Climate and Diet in Indigenous Siberians. AU - Hallmark, Brian. AU - Karafet, Tatiana. AU - Hsieh, Ping Hsun. AU - Osipova, Ludmila P.. AU - Watkins, Joseph C. AU - Hammer, Michael F. PY - 2019/2/1. Y1 - 2019/2/1. N2 - The indigenous inhabitants of Siberia live in some of the harshest environments on earth, experiencing extended periods of severe cold temperatures, dramatic variation in photoperiod, and limited and highly variable food resources. While the successful long-term settlement of this area by humans required multiple behavioral and cultural innovations, the nature of the underlying genetic changes has generally remained elusive. In this study, we used a three-part approach to identify putative targets of positive natural selection in Siberians. We first performed selection scans on whole exome and genome-wide single nucleotide polymorphism array data from multiple Siberian populations. We then annotated ...
Scientists now know why it has been so difficult to sequence a region of the Y-chromosome linked to infertility. The AZFc region contains six massive and virtually identical stretches of repetitive DNA, according to a new study. The repeat elements were too large and too similar to be distinguished by conventional sequencing techniques. David C. Page, of the Whitehead Institute in Boston, and colleagues uncovered the regions details using a modified sequencing-mapping strategy. They identified 27 potential genes in the region, all of which are expressed predominantly or exclusively in the testis. Men with low or no sperm production frequently have deletions in the AZFc region, but the deletions do not seem to cause other health problems. The researchers propose that the repetitive structures in this region cause fertility problems by improperly binding to each other as the Y-chromosome reorganizes over time. DNA is either lost or misplaced. The repetitive ...
BACKGROUND AND PURPOSE: Although a genetic contribution to ischemic stroke is well recognized, only a handful of stroke loci have been identified by large-scale genetic association studies to date. Hypothesizing that genetic effects might be stronger for early- versus late-onset stroke, we conducted a 2-stage meta-analysis of genome-wide association studies, focusing on stroke cases with an age of onset |60 years. METHODS: The discovery stage of our genome-wide association studies included 4505 cases and 21 968 controls of European, South-Asian, and African ancestry, drawn from 6 studies. In Stage 2, we selected the lead genetic variants at loci with association P|5×10(-6) and performed in silico association analyses in an independent sample of ≤1003 cases and 7745 controls. RESULTS: One stroke susceptibility locus at 10q25 reached genome-wide significance in the combined analysis of all samples from the discovery and follow-up stages (rs11196288; odds ratio ...
Long non-coding RNAs (lncRNAs), representing a large proportion of non-coding transcripts across the human genome, are evolutionally conserved and biologically functional. At least one-third of the phenotype-related loci identified by genome-wide association studies (GWAS) are mapped to non-coding intervals. However, the relationships between phenotype-related loci and lncRNAs are largely unknown. Utilizing the 1000 Genomes data, we compared single-nucleotide polymorphisms (SNPs) within the sequences of lncRNA and protein-coding genes as defined in the Ensembl database. We further annotated the phenotype-related SNPs reported by GWAS at lncRNA intervals. Because prostate cancer (PCa) risk-related loci were enriched in lncRNAs, we then performed meta-analysis of two existing GWAS for discovery and an additional sample set for replication, revealing PCa risk-related loci at lncRNA regions. The SNP density in regions of lncRNA ...
Epigenetic alternation is a common contributing factor to neoplastic transformation. Although previous studies have reported a cluster of aberrant promoter methylation changes associated with silencing of tumor suppressor genes, little is known concerning their sequential DNA methylation changes during the carcinogenetic process. The aim of the present study was to address a genome-wide search for identifying potentially important methylated changes and investigate the onset and pattern of methylation changes during the progression of colorectal neoplasia. A three-phase design was employed in this study. In the screening phase, DNA methylation profile of 12 pairs of colorectal cancer (CRC) and adjacent normal tissues was analyzed by using the Illumina MethylationEPIC BeadChip. Significant CpG sites were selected based on a cross-validation analysis from The Cancer Genome Atlas (TCGA) database. Methylation levels of candidate CpGs were assessed using pyrosequencing in the ...
BACKGROUND. The genetic contribution to sporadic amyotrophic lateral sclerosis (ALS) has not been fully elucidated. There are increasing efforts to characterise the role of copy number variants (CNVs) in human diseases; two previous studies concluded that CNVs may influence risk of sporadic ALS, with multiple rare CNVs more important than common CNVs. A little-explored issue surrounding genome-wide CNV association studies is that of post-calling filtering and merging of raw CNV calls. We undertook simulations to define filter thresholds and considered optimal ways of merging overlapping CNV calls for association testing, taking into consideration possibly overlapping or nested, but distinct, CNVs and boundary estimation uncertainty.. METHODOLOGY AND PRINCIPAL FINDINGS. In this study we screened Illumina 300K SNP genotyping data from 730 ALS cases and 789 controls for copy number variation. Following quality control filters using thresholds defined by simulation, a total of ...
Matthew Brown, John Reveille and colleagues report a genome-wide association study for ankylosing spondylitis. They identify four genetic loci outside of the MHC newly associated to AS susceptibility. To identify susceptibility loci for ankylosing spondylitis, we undertook a genome-wide association study in 2,053 unrelated ankylosing spondylitis cases among people of European descent and 5,140 ethnically matched controls, with replication in an independent cohort of 898 ankylosing spondylitis cases and 1,518 controls. Cases were genotyped with Illumina HumHap370 genotyping chips. In addition to strong association with the major histocompatibility complex (MHC; P | 10−800), we found association with SNPs in two gene deserts at 2p15 (rs10865331; combined P = 1.9 × 10−19) and 21q22 (rs2242944; P = 8.3 × 10−20), as well as in the genes ANTXR2 (rs4333130; P = 9.3 × 10−8) and IL1R2 (rs2310173; P = 4.8 × 10−7). We also replicated previously reported associations at IL23R ...
We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels. We present three methods to fit the model-Markov chain Monte Carlo sampling, the Expectation Maximization algorithm, and a Classification Expectation Maximization algorithm. The performance of our method on individuals simulated to be admixed with European and West African ancestry shows it to be comparable to HAPMIX, the ancestry calls of the two methods agreeing at 99.26% of loci ...
The two methods of repair for DSBs are homologous recombination (HR) and non-homologous end-joining (NHEJ). In HR the nucleotide sequences of two sets of DNA are exchanged to repair the broken strands. For this to occur one of the sets of DNA must be undamaged. The 3 strand of the DSB invades the undamaged double stranded DNA and partially unwinds it for homologous pairing. The strands form branch migrations and Holiday junctions to restore the DNA with the DSB without any crossing over of the two sets 2. In NHEJ of a DSB, the broken pieces are ligated together (via the KU heterodimer) without the need of an undamaged, homologous set of DNA. However, there can be degradation at the ends of the break that can result in errors and the loss of DNA sequences2. DSBs caused from IR are usually repaired by this method4. DSBs can also be repaired by single-strand annealing (SSA) if the break occurs between two repeated sequences. The repeated ...
TY - JOUR. T1 - A versatile statistical analysis algorithm to detect genome copy number variation. AU - Daruwala, Raoul Sam. AU - Rudra, Archisman. AU - Ostrer, Harry. AU - Lucito, Robert. AU - Wigler, Michael. AU - Mishra, Bud. PY - 2004/11/16. Y1 - 2004/11/16. N2 - We have developed a versatile statistical analysis algorithm for the detection of genomic aberrations in human cancer cell lines. The algorithm analyzes genomic data obtained from a variety of array technologies, such as oligonucleotide array, bacterial artificial chromosome array, or array-based comparative genomic hybridization, that operate by hybridizing with genomic material obtained from cancer and normal cells and allow detection of regions of the genome with altered copy number. The number of probes (i.e., resolution), the amount of uncharacterized noise per probe, and the severity of chromosomal aberrations per chromosomal region may vary with the underlying technology, biological ...
A small proportion of human immunodeficiency virus-1 (HIV-1) infected individuals, termed HIV-1 controllers, suppress viral replication to very low levels in the absence of therapy. Genetic investigations of this phenotype have strongly implicated variation in the class I major histocompatibility complex (MHC) region as key to HIV-1 control. We collected sequence-based classical class I HLA genotypes at 4-digit resolution in HIV-1-infected African American controllers and progressors (n = 1107), and tested them for association with host control using genome-wide single nucleotide polymorphism data to account for population structure. Several classical alleles at HLA-B were associated with host control, including B*57:03 [odds ratio (OR) = 5.1; P= 3.4 × 10(-18)] and B*81:01 (OR = 4.8; P= 1.3 × 10(-9)). Analysis of variable amino acid positions demonstrates that HLA-B position 97 is the most significant association with host control in African Americans (omnibus P = 1.2 × ...
Genome-wide association studies (GWAS) are widely used to identify loci associated with phenotypic traits in the domestic dog that has emerged as a model for Mendelian and complex traits. However, a disadvantage of GWAS is that it always requires subsequent fine-mapping or sequencing to pinpoint causal mutations. Here, we performed whole exome sequencing (WES) and canine high-density (cHD) SNP genotyping of 28 dogs from 3 breeds to compare the SNP and linkage disequilibrium characteristics together with the power and mapping precision of exome-guided GWAS (EG-GWAS) versus cHD-based GWAS. Using simulated phenotypes, we showed that EG-GWAS has a higher power than cHD to detect associations within target regions and less power outside target regions, with power being influenced further by sample size and SNP density. We analyzed two real phenotypes (hair length and furnishing), that are fixed in certain breeds to characterize mapping precision of the known causal mutations. EG-GWAS identified ...
We present the first detailed genome-wide analysis of recent segmental duplication content of the bovine genome. Global studies of segmental duplication content have become an effective measure to assess one aspect of the quality of whole-genome sequence assemblies [1, 51]. Regions of recent segmental duplication remain one of the greatest challenges to finishing a genome assembly. The underlying problem is the same--the correct placement and resolution of large sequence that can be assigned to multiple positions within the genome. An initial assessment of bovine segmental duplication content therefore provides an important level of annotation for the user of genome sequence information in the design and interpretation of future experiments. Moreover, these initial analyses precisely delineate potential regions where whole-genome shotgun or a BAC-enrichment strategy will provide insufficient ...
Idiopathic generalized epilepsies account for 30% of all epilepsies. Despite a predominant genetic aetiology, the genetic factors predisposing to idiopathic generalized epilepsies remain elusive. Studies of structural genomic variations have revealed a significant excess of recurrent microdeletions at 1q21.1, 15q11.2, 15q13.3, 16p11.2, 16p13.11 and 22q11.2 in various neuropsychiatric disorders including autism, intellectual disability and schizophrenia. Microdeletions at 15q13.3 have recently been shown to constitute a strong genetic risk factor for common idiopathic generalized epilepsy syndromes, implicating that other recurrent microdeletions may also be involved in epileptogenesis. This study aimed to investigate the impact of five microdeletions at the genomic hotspot regions 1q21.1, 15q11.2, 16p11.2, 16p13.11 and 22q11.2 on the genetic risk to common idiopathic generalized epilepsy syndromes. The candidate microdeletions were assessed by high-density single nucleotide polymorphism arrays ...
Rapid development of sequencing technologies and bioinformatic tools makes the complete genome sequencing of many species possible, which provides a starting point to unravel the tremendous genetic variation and diversity at the genome scale. Amongst several model organisms examined to date, such as human, mouse, Arabidopsis, rice, and maize, genome-wide patterns of genetic variation are able to be captured by sampling a relatively small number of genomes [14, 20, 50-52]. By resequencing two sweet and one grain sorghum inbred lines, we uncovered nearly two million SNPs and indels, along with large numbers of PAVs and CNVs. This is a first report on the genome-wide patterns of genetic variation in sorghum, which will be valuable for further genotype-phenotype studies and for molecular breeding of this important C4 model crop.. Our study shows that the proportions of genic SNPs identified as in coding regions, ...
nearly causes my machine to run out of memory (16G), takes a couple of days to run, and results in a blast output of 5.1G and 84 million rows--thats 84 million blast hits with an e-value below 0.001! By definition, that output is dominated by the repetitive elements. Repetitive elements are interesting, but in the case were we want to look at synteny, we have to wade through that 5.1G of stuff to find the very small chunk of data we need. This adds time to run the sequence comparison, time to parse, time to plot, time to analyze, and data to store, etc ...
PRIMARY OBJECTIVES:. I. To compare progression-free survival (PFS) in patients with newly diagnosed myeloma treated with lenalidomide plus low dose dexamethasone versus bortezomib plus lenalidomide and low dose dexamethasone.. SECONDARY OBJECTIVES:. I. Assess response using the new international response criteria. II. To bank specimens for future translational medicine research. III. Follow patients to assess overall survival and other long-term outcomes stratified by intent to transplant at progression.. TERTIARY OBJECTIVES:. I. To evaluate custom and genome-wide single nucleotide polymorphisms in correlation with biology, prognosis and outcome for both treatment regimens combined; to verify the findings recently obtained with the custom Bank on a Cure program (BOAC) single nucleotide polymorphism (SNP) chip on Total Therapy 2 (TT2) data with respect to bone disease in the cooperative group setting.. II. To use baseline gene expression profiling as a tool to evaluate the biology, prognostic ...
AUSTRALIAS capacity to detect, respond to and control infectious threats, and to improve regional health security is hampered by the lack of a national approach to whole genome sequencing resources, and data sharing, according to the authors of a Perspective published in the Medical Journal of Australia.. Whole genome sequencing involves parsing out the entire genome of a pathogen, the data from which can be used to determine the pathogens identity, predict its resistance to antimicrobials and its virulence traits and understand the relationships between pathogens.. University of Melbourne Associate Professor Deborah Williamson, Deputy Director of the Microbiological Diagnostic Unit Public Health Laboratory at the Doherty Institute, and colleagues wrote that the use of whole genome sequencing "has the potential to transform the investigation and surveillance of communicable diseases by providing the highest possible characterisation of ...
Summary All levels of life entail cooperation and conflict. Genes cooperate to build up a functional genome, which can yet be undermined by selfish genetic elements. Humans and animals cooperate to build up societies, which can yet be subverted by cheats. There is a long-standing interest among biologists to comprehend the tug-of-war between cooperation and conflict. Recently, research on bacteria was successful in identifying key factors that can tip the balance in favour or against cooperation. Bacteria cooperate through the formation of protective biofilms, cell-to-cell communication, and the secretion of shareable public goods. However, the advantage of bacteria being fast replicating units, easily cultivatable in high numbers, is also their disadvantage: they are small and imperceptible, such that measures of cooperation typically rely on averaged responses across millions of cells. Thus, we still know very little about bacterial cooperation at the biological relevant ...
Purpose: Unless clones derived from genomic human DNA are known to be single copy, they can be assumed to contain highly repetitive sequences such as Alu. Hybridizing a probe withrepeats to a human DNA Southern blot will result in a signal in each human lane that looks very much like the ethidium bromide stained pattern: a continuous smear with little or no additional signal from the unique sequences on the probe. To reduce or eliminate the lane background due to the repetitive sequences, we add a large amount of unlabeled human DNA (sonicated to an average size of 400-700 bp for highest efficiency) to the labeled probes immediately before the denaturing and hybridizing steps. The excess number of repeat sequences in the human genomic DNA competes with the probe sequences for those on the blot, effectively ...
in Molecular psychiatry (2014), 19(10), 1085-94. Anorexia nervosa (AN) is a complex and heritable eating disorder characterized by dangerously low body weight. Neither candidate gene studies nor an initial genome-wide association study (GWAS) have ... [more ▼]. Anorexia nervosa (AN) is a complex and heritable eating disorder characterized by dangerously low body weight. Neither candidate gene studies nor an initial genome-wide association study (GWAS) have yielded significant and replicated results. We performed a GWAS in 2907 cases with AN from 14 countries (15 sites) and 14 860 ancestrally matched controls as part of the Genetic Consortium for AN (GCAN) and the Wellcome Trust Case Control Consortium 3 (WTCCC3). Individual association analyses were conducted in each stratum and meta-analyzed across all 15 discovery data sets. Seventy-six (72 independent) single nucleotide polymorphisms were taken forward for in silico (two data sets) or de novo (13 data sets) replication ...
TY - JOUR. T1 - A genome-wide association study reveals that variants within the HLA region are associated with risk for nonobstructive azoospermia. AU - Zhao, Han. AU - Xu, Jianfeng. AU - Zhang, Haobo. AU - Sun, Jielin. AU - Sun, Yingpu. AU - Wang, Zhong. AU - Liu, Jiayin. AU - Ding, Qiang. AU - Lu, Shaoming. AU - Shi, Rong. AU - You, Li. AU - Qin, Yingying. AU - Zhao, Xiaoming. AU - Lin, Xiaoling. AU - Li, Xiao. AU - Feng, Junjie. AU - Wang, Li. AU - Trent, Jeffrey M.. AU - Xu, Chengyan. AU - Gao, Ying. AU - Zhang, Bo. AU - Gao, Xuan. AU - Hu, Jingmei. AU - Chen, Hong. AU - Li, Guangyu. AU - Zhao, Junzhao. AU - Zou, Shuhua. AU - Jiang, Hong. AU - Hao, Cuifang. AU - Zhao, Yueran. AU - Ma, Jinglong. AU - Zheng, S. Lilly. AU - Chen, Zi Jiang. PY - 2012/5/4. Y1 - 2012/5/4. N2 - A genome-wide association study of Han Chinese subjects was conducted to identify genetic susceptibility loci for nonobstructive azoospermia (NOA). In the discovery stage, 802 azoospermia cases and ...
Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of
Note: Only deletions with sequenced breakpoints are included. Reported deletion junctions may be approximate due to the presence identical repeat sequences at the break points. Alternate junctions may be reported in the cited literature due to the inherent ambiguities of the direct repeats. Other reports of multiple deletions mapped within an individual have been published without specific sequence data for the deletion breakpoints. ...
While the main purpose of DNA is to code for proteins to be built in the cell, we know that a lot of DNA doesnt code for protein after all, such as the repeating region of the C9ORF72 gene. In healthy versions of the gene the repeated region (usually under 30 repeated units) is simply cut out of the RNA copy of the gene before the RNA is exported from the nucleus.. In C9ORF72-MND however, the repeated region is much larger - even up to a thousand repeated units and leads to a build up of the RNA repeats inside the nucleus but also, unexpectedly is made into abnormal toxic constituents in the cell cytoplasm called dipeptide repeat proteins. The discovery of dipeptide repeat proteins was puzzling to scientists as this type of non-protein coding RNA does not normally exit the nucleus to get to where protein can be made.. Dr Hautbergue and colleagues, who have developed expertise in the mechanisms of RNA nuclear export, looked to see how the pathological repeating precursor RNA molecules, that ...
Deutekom, J.C.T. van; Bakker, E.; Lemmers, R.J.L.F.; Wielen, M.J.R. van der; Bik, E.; Hofker, M.H.; Padberg, G.W.A.M. ; Frants, R.R. ...

Genome-wide Hypomethylation in Human Glioblastomas Associated with Specific Copy Number Alteration, Methylenetetrahydrofolate...Genome-wide Hypomethylation in Human Glioblastomas Associated with Specific Copy Number Alteration, Methylenetetrahydrofolate...

... and interspersed repetitive sequences in GBMs. More than one third of DNA methylation in normal tissues occurs in repetitive ... of the human genome, accounts for the majority of 5-methylcytosine loss in human cancers ( 9). Repetitive elements consist of ... Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 2001; 409: 953-8. ... Demethylation of other abundant interspersed repetitive elements, such as the long interspersed nucleotide elements LINE-1, may ...
more infohttp://cancerres.aacrjournals.org/content/66/17/8469

A Hypothesis to Explain How the DNA of Elderly People Is Prone to Damage: Genome-Wide Hypomethylation Drives Genomic...A Hypothesis to Explain How the DNA of Elderly People Is Prone to Damage: Genome-Wide Hypomethylation Drives Genomic...

In humans, Phy-RIND-EDSBs are located in the hypermethylated genome. Because the genomes of aging people are hypomethylated, ... Based on this evidence, I hypothesize that in the human Phy-RIND-EDSBs, reduction is a molecular process that mediates the ... genome-wide hypomethylation driving genomic instability, which is a nidus pathogenesis mechanism of human body deterioration in ... Therefore, genome-wide hypomethylation drives genomic instability, causing aging-associated disease phenotypes. However, the ...
more infohttps://www.intechopen.com/books/epigenetics/a-hypothesis-to-explain-how-the-dna-of-elderly-people-is-prone-to-damage-genome-wide-hypomethylation

US6235470B1 - Detection of neoplasia by analysis of saliva 
        - Google PatentsUS6235470B1 - Detection of neoplasia by analysis of saliva - Google Patents

DNA contains unique sequences interspersed with moderately and highly repetitive DNA sequences. Variations in the repetitive ... Microsatellite DNA sequences are an especially common and highly polymorphic class of genomic elements in the human genome. One ... Where a DNA sequence is repetitive, genetic recombination can result in the loss of repeat DNA sequences or the gain of repeat ... where the DNA has a high degree of sequence similarity). Where a DNA sequence is repetitive, the DNA homology is greater. The ...
more infohttps://patents.google.com/patent/US6235470B1/en

Dark Matters in AMD Genetics: Epigenetics and Stochasticity | IOVS | ARVO JournalsDark Matters in AMD Genetics: Epigenetics and Stochasticity | IOVS | ARVO Journals

The haploid human genome contains 29 million CpG residues. Half of these are found in repetitive sequences. 23,24 A large ... a specific subset of short interspersed DNA elements. 24,150 The mouse B family of repetitive sequence elements is related to ... but the total number of such residues for the haploid human genome is 29 million (i.e., 3% surveyed). Intergenic repetitive ... and demethylation of B2 repetitive sequences has also been correlated with age. 152 Demethylation of Alu sequences has ...
more infohttps://iovs.arvojournals.org/article.aspx?articleid=2127002

Immunogenetics of Aging | Springer for Research & DevelopmentImmunogenetics of Aging | Springer for Research & Development

... repetitive elements interspersed on all chromosomes and constituting more than 10% of the human genome. Genomic regions ... Human cytokine gene nucleotide sequence alignments: supplement 1. Eur J Immunogenet 1999; 26:135-223.PubMedCrossRefGoogle ... Human Leukocyte Antigen Cytokine Gene Successful Aging Human Longevity Human Leukocyte Antigen Gene These keywords were added ... Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics ...
more infohttps://rd.springer.com/chapter/10.1007/978-0-387-76842-7_13

Study of viral integration of HPV-16 in young patients with LSIL | Journal of Clinical PathologyStudy of viral integration of HPV-16 in young patients with LSIL | Journal of Clinical Pathology

24 or in interspersed repetitive sequences of DNA.25 Nevertheless, it has not been possible to demonstrate a specific and ... preferred integration site in the human genome. From the viral perspective, the integration produces, first of all, a small ... Structural and transcriptional analysis of human papillomavirus type 16 sequences in cervical carcinoma cell lines. J Virol1987 ... IARC monographs on the evaluation of carcinogenic risks to humans. Human papillomaviruses. Lyon: IARC Scientific Publication 64 ...
more infohttp://jcp.bmj.com/content/56/7/532

Nucleotide Sequences Homologous to a Cloned Repeated Human DNA Fragment in Human Leukemic DNAs | SpringerLinkNucleotide Sequences Homologous to a Cloned Repeated Human DNA Fragment in Human Leukemic DNA's | SpringerLink

... contains repetitive nucleotide sequences that are in part organized in blocks in the heterochromatin and partly interspersed ... The human genome contains repetitive nucleotide sequences that are in part organized in blocks in the heterochromatin and ... Nelli L.C., Corneo G. (1984) Nucleotide Sequences Homologous to a Cloned Repeated Human DNA Fragment in Human Leukemic DNAs. ... Nucleotide Sequences Homologous to a Cloned Repeated Human DNA Fragment in Human Leukemic DNAs. ...
more infohttps://link.springer.com/chapter/10.1007/978-1-4684-4856-6_29

DNA Tests Determine Whether 2013s Injured Hawks Came From Bird Cams Nest | All About BirdsDNA Tests Determine Whether 2013's Injured Hawks Came From Bird Cams Nest | All About Birds

... repetitive sequences interspersed throughout otherwise complex genomes," Steve explains. "Humans, Red-tailed Hawks, plants, and ... Like humans, birds receive one copy of their DNA from each of their parents. By lining up the peaks in the graphs, its clear ... Finding a set of specific markers that can be used as a basis for comparison is the same technique used to identify human crime ... from Big Red and another from Ezra at each microsatellite locus-just as humans inherit one copy of each parents DNA. Any ...
more infohttps://www.allaboutbirds.org/dna-tests-determine-whether-2013s-injured-hawks-came-from-bird-cams-nest/

Mouse euchromatin specific genome-painting with a LINE probe: A rapid method for identification and mapping of human...Mouse euchromatin specific 'genome-painting' with a LINE probe: A rapid method for identification and mapping of human...

We describe the use of a long interspersed repetitive sequence (mCPE1.51) for mouse euchromatin specific genome-painting. In ... N2 - We describe the use of a long interspersed repetitive sequence (mCPE1.51) for mouse euchromatin specific genome-painting ... AB - We describe the use of a long interspersed repetitive sequence (mCPE1.51) for mouse euchromatin specific genome-painting ... abstract = "We describe the use of a long interspersed repetitive sequence (mCPE1.51) for mouse euchromatin specific genome- ...
more infohttps://hungary.pure.elsevier.com/en/publications/mouse-euchromatin-specific-genome-painting-with-a-line-probe-a-ra

Genome survey sequence - WikipediaGenome survey sequence - Wikipedia

... in mammalian genome. There are about 300 to 500 thousand copies of Alu repetitive element in human genome, which means one Alu ... Alu repetitive element is member of Short Interspersed Elements (SINE) ... Genome survey sequencing is a new way to map the genome sequences since it is not dependent on mRNA. Current genome sequencing ... "ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)." Bmc Bioinformatics 9.1 (2008): 366. ...
more infohttps://en.wikipedia.org/wiki/Genome_survey_sequence

Microsatellite repeats - definition of Microsatellite repeats by The Free DictionaryMicrosatellite repeats - definition of Microsatellite repeats by The Free Dictionary

n. 1. A short sequence of DNA consisting of multiple repetitions of a set of two to nine base pairs, used as a genetic marker ... and Brazil describe the repetitive content of eukaryotic genomes and the impact on genome structure, function, and evolution; ... the evolutionary dynamics of transposable elements in eukaryotic genomes; short interspersed elements (SINEs) in genome ... Related to Microsatellite repeats: Simple Sequence Repeat mi·cro·sat·el·lite. (mī′krō-săt′l-īt′). n.. 1. A short sequence of ...
more infohttp://www.thefreedictionary.com/Microsatellite+repeats

The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14 | The EMBO JournalThe crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14 | The EMBO Journal

... cytoplasmic 7S RNA is complementary to the dominant interspersed middle repetitive DNA sequence family in the human genome. ... domain known as the Alu domain due to the homology of the RNA sequences with the Alu family of repetitive DNA sequences and the ... Larsen N and Zwieb C (1991) SRP‐RNA sequence alignment and secondary structure. Nucleic Acids Res, 19, 209-215. ... Walter P and Johnson AE (1994) Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. Annu ...
more infohttp://emboj.embopress.org/content/16/13/3757

Replication independent DNA double-strand break retention may prevent genomic instability | Molecular Cancer | Full TextReplication independent DNA double-strand break retention may prevent genomic instability | Molecular Cancer | Full Text

Interestingly, the most significant differences between EDSBs and genomes were observed when cells were cultured in the absence ... Consequently, spontaneous mutations in hypomethylated genome are produced at faster rates because unmethylated EDSBs are unable ... and found that those sites have a higher level of methylation than the rest of the genome. ... Complete or partial methylation of CpG dinucleotides in the human genome commonly occurs at interspersed repetitive sequences [ ...
more infohttps://molecular-cancer.biomedcentral.com/articles/10.1186/1476-4598-9-70

Metagenomes obtained by deep sequencing - what do they tell about the enhanced biological phosphorus removal communities? |...Metagenomes obtained by 'deep sequencing' - what do they tell about the enhanced biological phosphorus removal communities? |...

... deep sequencing - what do they tell about the enhanced biological phosphorus removal communities?. Metagenomics enables ... Now, CRISPR-Cas9 has facilitated robust genome editing in virtually any organism including: human cells, rat, mice, zebra fish ... of sequenced Bacteria. CRISPR arrays consist of interspersed identical REPEAT sequences (21-48bp) and several unique invader- ... CRISPR is a ubiquitous family of clustered repetitive DNA elements present in 90% of Archaea and 40% ...
more infohttps://www.environmental-expert.com/articles/metagenomes-obtained-by-deep-sequencing-what-do-they-tell-about-the-enhanced-biological-phosphorus-r-401420

Molecular Biology Structures - Overview | CourseraMolecular Biology Structures - Overview | Coursera

The genome, Writing a DNA sequence, Central dogma, ... ... The genome, Writing a DNA sequence, Central dogma, ... We also have interspersed repeats which really just means the same idea, repetitive sequence thats identical or near identical ... So a typical human messenger RNA, which is what we get our proteins from, looks like this. We have some sequence which is shown ... And if you have a very short sequence, remember when we read DNA sequences were only reading a few hundred base pairs at a ...
more infohttps://www.coursera.org/lecture/introduction-genomics/molecular-biology-structures-VugcH?authMode=signup

Long non-coding RNA - WikipediaLong non-coding RNA - Wikipedia

February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. doi:10.1038/35057062. PMID ... The short interspersed nuclear (SINE) Alu elements in humans and analogous B1 and B2 elements in mice have succeeded in ... The ability to quickly mediate global changes is also apparent in the rapid expression of non-coding repetitive sequences. ... Large-scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate ...
more infohttps://en.wikipedia.org/wiki/Long_non-coding_RNA

Bioinformatics PapersBioinformatics Papers

The origin of interspersed repeats in the human genome. Smit AF. * Ancestral, mammalian-wide subfamilies of LINE-1 repetitive ... Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Hardison RC, ... Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. ... A comparison of expressed sequence tags (ESTs) to human genomic sequences. Wolfsberg TG, Landsman D * A computer program for ...
more infohttp://globin.cse.psu.edu/courses/spring2000/papers.html

Bioinformatics PapersBioinformatics Papers

The origin of interspersed repeats in the human genome. Smit AF. * Ancestral, mammalian-wide subfamilies of LINE-1 repetitive ... Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Hardison RC, ... Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. ... A comparison of expressed sequence tags (ESTs) to human genomic sequences. Wolfsberg TG, Landsman D * A computer program for ...
more infohttp://globin.cse.psu.edu/courses/fall2000/papers.html

Diagnosis of Tuberculosis in Three Zoo Elephants and a Human Contact - Oregon, 2013Diagnosis of Tuberculosis in Three Zoo Elephants and a Human Contact - Oregon, 2013

Elephant Cs isolate was not whole genome sequenced; all of this elephants human contacts were the same as those of elephant B ... and found that they differed by only one locus in the 24-locus mycobacterial interspersed repetitive units (MIRU) pattern ( ... Isolates from patient A and elephant A were analyzed at CDC using whole genome sequencing. Comparison of the assembled genomes ... Whole-genome sequencing revealed that one elephants M. tuberculosis isolate identically matched the isolate of a person with ...
more infohttps://www.cdc.gov/mmwr/preview/mmwrhtml/mm6452a2.htm?s_cid=mm6452a2_w

Repetitive elements shape embryonic chromatin landscape - Healthcanal.com : Healthcanal.comRepetitive elements shape embryonic chromatin landscape - Healthcanal.com : Healthcanal.com

Retrotransposons are repetitive elements that form almost half of the mammalian genome. Even though they are so common, they ... Retrotransposons are repetitive elements that form almost half of the mammalian genome. Even though they are so common, they ... L1 elements account for approximately 17 percent of the genetic material in humans and up to 40 percent in other mammals.. ... The term "retrotransposons" refers to a class of transposable DNA sequences that is structurally very similar to the ...
more infohttps://www.healthcanal.com/pregnancy-childbirth/240147-repetitive-elements-shape-embryonic-chromatin-landscape.html

Mobile DNA | ArticlesMobile DNA | Articles

Long interspersed nuclear element-1 (LINE-1 or L1) is a dominant repetitive sequence in the human genome. Besides mediating its ... Alu pair exclusions in the human genome The human genome contains approximately one million Alu elements which comprise more ... In some species, such as humans, these elements are the most abundant genome sequence and continue to replicate to th... ... Endogenous retroviruses (ERVs) and ERV-like sequences comprise 8% of the human genome. A hitherto unknown proportion of ERV ...
more infohttps://mobilednajournal.biomedcentral.com/articles?searchType=journalSearch&sort=PubDate&page=6

Investigation of Global Methylation in Peripheral Blood from Breast Cancer PatientsInvestigation of Global Methylation in Peripheral Blood from Breast Cancer Patients

... of the entire genome [24,25]. Alu is a short interspersed repetitive sequence that contributes almost 11% of the human genome [ ... are rich in repetitive sequences that account for approximately half of the human genome and those repetitive DNA sequences are ... There are several different categories of repetitive sequences dispersed throughout the genome, such as long interspersed ... 2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921. ...
more infohttps://www.omicsonline.org/open-access/investigation-of-global-methylation-in-peripheral-blood-from-breast-cancer-patients-2155-9929-S2-037-96330.html

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes | ScienceExtensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes | Science

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome ... Tumor genomes are peppered with mobile repeat sequences that carry along adjacent DNA when they insert into new genomic sites. ... The human genome is peppered with mobile repetitive elements called long interspersed nuclear element-1 (L1) retrotransposons. ... 6Human Genome Laboratory, Department of Human Genetics, VIB and KU Leuven, Leuven, Belgium. ...
more infohttp://science.sciencemag.org/content/345/6196/1251343

Protocols and Video Articles Authored by Christina A. Pacak (Translated to Swedish)Protocols and Video Articles Authored by Christina A. Pacak (Translated to Swedish)

... that integrated rAAV vector sequences could be amplified using primers specific for mouse interspersed repetitive sequences (B1 ... Vector genome quantification showed an increase in genome copy numbers in cardiac tissue for several weeks following ... Here, we describe a 3-h method to isolate COL1 from rabbit, lamb, and human skin in sufficient quantities for fabrication of ... One day old alpha sarcoglycan knockout mice (sgca-/-) were injected with 1 x 10(11) vector genomes of rAAV2/1-tMCK-sgca in one ...
more infohttps://www.jove.com/author/Christina+A._Pacak?language=Swedish

The human genome: a multifractal analysis | BMC Genomics | Full TextThe human genome: a multifractal analysis | BMC Genomics | Full Text

We report here multifractality in the human genome sequence. This behavior correlates strongly on the presence of Alu elements ... Based on these findings, we propose a descriptive non-linear model for the structure of the human genome, with some biological ... Here we investigate the possibility that the human genome shows a similar behavior to that observed in the nematode. ... Given the role of Alu sequences in gene regulation, genetic diseases, human genetic diversity, adaptation and phylogenetic ...
more infohttps://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-506
  • Independent of DNA replication, the eukaryotic genome retains a certain amount of endogenous DNA double-strand breaks (EDSBs), called physiologic replication-independent EDSBs (Phy-RIND-EDSBs), that possess physiological function. (intechopen.com)
  • Three mechanisms by which hypomethylation contributes to malignancy have been proposed, including oncogene activation, loss of imprinting, and promoting genomic instability via unmasking of repetitive elements. (aacrjournals.org)
  • Therefore, genome-wide hypomethylation drives genomic instability, causing aging-associated disease phenotypes. (intechopen.com)
  • Genomic instability, a hallmark of cancer and aging, is defined as a high frequency of mutations within the genome [ 1 , 2 ]. (intechopen.com)
  • Recent studies analyzing the role of nuclear organization in DNA repair and factors that suppress non-allelic homologous recombination (NAHR) have provided insights into how genome stability is maintained in eukaryotes. (nih.gov)
  • DNA transposons usually move by a mechanism analogous to cut and paste, rather than copy and paste, using an enzyme called transposase, which recognizes the ends of an element, cuts it out, and reinserts it elsewhere in the genome. (n-equals-one.com)
  • 3) Because LINE's move by copying themselves (instead of moving, as transposons do), they enlarge the genome. (n-equals-one.com)
  • Assuming that Homo sapiens is not an exception to this order, many studies over the last few years have been focused on these evolutionarily conserved pathways in order understand the genetics of human aging and longevity. (springer.com)
  • Here, we report that global hypomethylation is common in primary human glioblastomas [glioblastoma multiforme (GBM)] and can affect up to an estimated 10 million CpG dinucleotides per haploid tumor genome. (aacrjournals.org)
  • Localized hypermethylation of gene-associated CpG islands and a more extensive genome-wide reduction in 5-methylcytosine are epigenetic alterations that typify many cancers ( 3 - 5 ). (aacrjournals.org)
  • In this chapter we will review the data on the role of HLA and cytokine gene polymorphisms in human longevity and comment on the future directions in this field. (springer.com)
  • There have been several attempts to delineate the different categories of selection signatures seen amongst lncRNAs including: lncRNAs with strong sequence conservation across the entire length of the gene, lncRNAs in which only a portion of the transcript (e.g. 5' end, splice sites) is conserved, and lncRNAs that are transcribed from syntenic regions of the genome but have no recognizable sequence similarity. (wikipedia.org)
  • Analysis of EST-driven gene annotation in human genomic sequence. (psu.edu)
  • Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. (psu.edu)
  • Prediction of complete gene structures in human genomic DNA. (psu.edu)
  • Given the role of Alu sequences in gene regulation, genetic diseases, human genetic diversity, adaptation and phylogenetic analyses, these quantifications are especially useful. (biomedcentral.com)
  • This highly regionalized structure introduces complex patterns for understanding the gene structure and repetitive DNA sequence composition and its role in human development, physiology, medicine and phylogeny. (biomedcentral.com)
  • The somatic theory explains aging in terms of accumulation of mutations in the genome of somatic cells leading to cell senescence, cell death or transformation, as well as loss of function. (springer.com)
  • In the process, they can cause mutations and change the amount of DNA in the genome. (n-equals-one.com)
  • Interestingly, the most significant differences between EDSBs and genomes were observed when cells were cultured in the absence of serum. (biomedcentral.com)
  • However, further investigations into vertebrate lncRNAs revealed that while lncRNAs are conserved in sequence, they are not conserved in transcription. (wikipedia.org)
  • In other words, even when the sequence of a human lncRNA is conserved in another vertebrate species, there is often no transcription of a lncRNA in the orthologous genomic region. (wikipedia.org)
  • While the turnover of lncRNA transcription is much higher than initially expected, it is important to note that still, hundreds of lncRNAs are conserved at the sequence level. (wikipedia.org)
  • Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% i. (biomedcentral.com)
  • This is the common missing heritability problem of complex disease, 6 often referred to as the dark matter of the genome . (arvojournals.org)
  • SRP recognizes the signal sequence of the nascent polypeptide chain emerging from the ribosome, and targets the ribosome-nascent chain-SRP complex to the rough endoplasmic reticulum. (embopress.org)
  • Metagenomics enables studies of the genomic potential of complex microbial communities by sequencing bulk genomic DNA directly from the environment. (environmental-expert.com)
  • Genomic sequences within these transcriptional foci are often shared within a number of different coding and non-coding transcripts in the sense and antisense directions giving rise to a complex hierarchy of overlapping isoforms. (wikipedia.org)
  • In 2013, public health officials in Multnomah County, Oregon, started an investigation of a tuberculosis (TB) outbreak among elephants and humans at a local zoo. (cdc.gov)
  • The investigation ultimately identified three bull elephants with active TB and 118 human contacts of the elephants. (cdc.gov)
  • Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. (psu.edu)
  • (A) Repetitive sequences form secondary structures that block progression of the replication fork and induce fork reversal which can result in sequence duplications. (nih.gov)
  • In addition to higher tissue specificity, lncRNAs are characterized by higher developmental stage specificity, and cell subtype specificity in heterogeneous tissues, such as human neocortex. (wikipedia.org)
  • The GENCODE consortium has collated and analysed a comprehensive set of human lncRNA annotations and their genomic organisation, modifications, cellular locations and tissue expression profiles. (wikipedia.org)
  • The three bulls were isolated and treated (elephants with TB typically are not euthanized) to prevent infection of other animals and humans, and persons with latent infection were offered treatment. (cdc.gov)
  • You'll also get an introduction to the key concepts in computing and data science that you'll need to understand how data from next-generation sequencing experiments are generated and analyzed. (coursera.org)
  • To investigate the physical status of human papillomavirus 16 (HPV-16) in low grade squamous intraepithelial lesions (LSILs) as a means of determining the percentage of viral integration. (bmj.com)
  • Here we investigate the possibility that the human genome shows a similar behavior to that observed in the nematode. (biomedcentral.com)
  • The Alu domain of SRP mediates the specific pause(s) in the synthesis of nascent ER‐targeted proteins whose signal sequence has been bound by SRP54 ( Siegel and Walter, 1988 ). (embopress.org)
  • Recently, we used a multifractal approach to study the genetic information content of the Caenorhabditis elegans genome. (biomedcentral.com)
  • Given that all these genomic variations produce a regionalized genomic landscape in the human genome, we thought fractal geometry could be an appropriate approach to studying how the genetic information content is fragmented. (biomedcentral.com)