Comparative Genomic Hybridization: A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.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)Chromosome Aberrations: Abnormal number or structure of chromosomes. Chromosome aberrations may result in CHROMOSOME DISORDERS.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.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.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.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.Chromosome Deletion: Actual loss of portion of a chromosome.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.Gene Amplification: A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. It occurs naturally via the excision of a copy of the repeating sequence from the chromosome and its extrachromosomal replication in a plasmid, or via the production of an RNA transcript of the entire repeating sequence of ribosomal RNA followed by the reverse transcription of the molecule to produce an additional copy of the original DNA sequence. Laboratory techniques have been introduced for inducing disproportional replication by unequal crossing over, uptake of DNA from lysed cells, or generation of extrachromosomal sequences from rolling circle replication.Karyotyping: Mapping of the KARYOTYPE of a cell.DNA, Neoplasm: DNA present in neoplastic tissue.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.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Aneuploidy: The chromosomal constitution of cells which deviate from the normal by the addition or subtraction of CHROMOSOMES, chromosome pairs, or chromosome fragments. In a normally diploid cell (DIPLOIDY) the loss of a chromosome pair is termed nullisomy (symbol: 2N-2), the loss of a single chromosome is MONOSOMY (symbol: 2N-1), the addition of a chromosome pair is tetrasomy (symbol: 2N+2), the addition of a single chromosome is TRISOMY (symbol: 2N+1).Chromosomes, Human, Pair 20: A specific pair of GROUP F CHROMOSOMES of the human chromosome classification.Cytogenetic Analysis: Examination of CHROMOSOMES to diagnose, classify, screen for, or manage genetic diseases and abnormalities. Following preparation of the sample, KARYOTYPING is performed and/or the specific chromosomes are analyzed.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Cytogenetics: A subdiscipline of genetics which deals with the cytological and molecular analysis of the CHROMOSOMES, and location of the GENES on chromosomes, and the movements of chromosomes during the CELL CYCLE.Chromosomes, Human, Pair 8: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Chromosomes, Human, Pair 1: A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.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.Chromosome Disorders: Clinical conditions caused by an abnormal chromosome constitution in which there is extra or missing chromosome material (either a whole chromosome or a chromosome segment). (from Thompson et al., Genetics in Medicine, 5th ed, p429)Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Chromosomes, Human, Pair 3: A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.Intellectual Disability: Subnormal intellectual functioning which originates during the developmental period. This has multiple potential etiologies, including genetic defects and perinatal insults. Intelligence quotient (IQ) scores are commonly used to determine whether an individual has an intellectual disability. IQ scores between 70 and 79 are in the borderline range. Scores below 67 are in the disabled range. (from Joynt, Clinical Neurology, 1992, Ch55, p28)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.Genomic Instability: An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.Loss of Heterozygosity: The loss of one allele at a specific locus, caused by a deletion mutation; or loss of a chromosome from a chromosome pair, resulting in abnormal HEMIZYGOSITY. It is detected when heterozygous markers for a locus appear monomorphic because one of the ALLELES was deleted.Chromosome Duplication: An aberration in which an extra chromosome or a chromosomal segment is made.Chromosomes, Human, Pair 17: A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Chromosomes, Human, Pair 11: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Spectral Karyotyping: The simultaneous identification of all chromosomes from a cell by fluorescence in situ hybridization (IN SITU HYBRIDIZATION, FLUORESCENCE) with chromosome-specific florescent probes that are discerned by their different emission spectra.Chromosomes, Human, Pair 9: A specific pair of GROUP C CHROMSOMES of the human chromosome classification.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Chromosomes, Human, Pair 13: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.Chromosomes, Human, Pair 6: A specific pair GROUP C CHROMSOMES of the human chromosome classification.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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.Chromosomes, Human, Pair 4: A specific pair of GROUP B CHROMOSOMES of the human chromosome classification.Chromosomes, Human, Pair 7: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Chromosomes, Human, Pair 12: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Chromosomes, Human, Pair 16: A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.Genetic Variation: Genotypic differences observed among individuals in a population.Allelic Imbalance: A situation where one member (allele) of a gene pair is lost (LOSS OF HETEROZYGOSITY) or amplified.Chromosome Breakpoints: The locations in specific DNA sequences where CHROMOSOME BREAKS have occurred.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.Chromosomes, Human, Pair 15: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.Abnormalities, MultiplePolar Bodies: Minute cells produced during development of an OOCYTE as it undergoes MEIOSIS. A polar body contains one of the nuclei derived from the first or second meiotic CELL DIVISION. Polar bodies have practically no CYTOPLASM. They are eventually discarded by the oocyte. (from King & Stansfield, A Dictionary of Genetics, 4th ed)Chromosomes, Human, Pair 2: A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.Paraffin Embedding: The infiltrating of tissue specimens with paraffin, as a supporting substance, to prepare for sectioning with a microtome.Chromosomes, Human, Pair 22: A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Chromosome Painting: A technique for visualizing CHROMOSOME ABERRATIONS using fluorescently labeled DNA probes which are hybridized to chromosomal DNA. Multiple fluorochromes may be attached to the probes. Upon hybridization, this produces a multicolored, or painted, effect with a unique color at each site of hybridization. This technique may also be used to identify cross-species homology by labeling probes from one species for hybridization with chromosomes from another species.Chromosome Breakage: A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.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.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Chromosomes, Human, Pair 18: A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.Chromosomal Instability: An increased tendency to acquire CHROMOSOME ABERRATIONS when various processes involved in chromosome replication, repair, or segregation are dysfunctional.Karyotype: The full set of CHROMOSOMES presented as a systematized array of METAPHASE chromosomes from a photomicrograph of a single CELL NUCLEUS arranged in pairs in descending order of size and according to the position of the CENTROMERE. (From Stedman, 25th ed)Genomic Islands: Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".Nucleic Acid Amplification Techniques: Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.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).Translocation, Genetic: A type of chromosome aberration characterized by CHROMOSOME BREAKAGE and transfer of the broken-off portion to another location, often to a different chromosome.Preimplantation Diagnosis: Determination of the nature of a pathological condition or disease in the OVUM; ZYGOTE; or BLASTOCYST prior to implantation. CYTOGENETIC ANALYSIS is performed to determine the presence or absence of genetic disease.Ploidies: The degree of replication of the chromosome set in the karyotype.Chromosomes, Human, Pair 5: One of the two pairs of human chromosomes in the group B class (CHROMOSOMES, HUMAN, 4-5).Mutation: 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.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).Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.Chromosomes, Human, Pair 14: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.Breast Neoplasms: Tumors or cancer of the human BREAST.Chromosomes, Human, X: The human female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in humans.Keratoacanthoma: A benign, non-neoplastic, usually self-limiting epithelial lesion closely resembling squamous cell carcinoma clinically and histopathologically. It occurs in solitary, multiple, and eruptive forms. The solitary and multiple forms occur on sunlight exposed areas and are identical histologically; they affect primarily white males. The eruptive form usually involves both sexes and appears as a generalized papular eruption.Abnormal Karyotype: A variation from the normal set of chromosomes characteristic of a species.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.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)Prognosis: A prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations.Cell Line, Tumor: A cell line derived from cultured tumor cells.Chromosomes, Artificial, P1 Bacteriophage: DNA constructs that are derived from the DNA of BACTERIOPHAGE P1. They can carry large amounts (about 100-300 kilobases) of other sequence for a variety of bioengineering purposes.Ring Chromosomes: Aberrant chromosomes with no ends, i.e., circular.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.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)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.Brucella ovis: A species of the genus BRUCELLA which are pathogenic to SHEEP.Microdissection: The performance of dissections with the aid of a microscope.Hybridization, Genetic: The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.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.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.Formaldehyde: A highly reactive aldehyde gas formed by oxidation or incomplete combustion of hydrocarbons. In solution, it has a wide range of uses: in the manufacture of resins and textiles, as a disinfectant, and as a laboratory fixative or preservative. Formaldehyde solution (formalin) is considered a hazardous compound, and its vapor toxic. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p717)Genetic Testing: Detection of a MUTATION; GENOTYPE; KARYOTYPE; or specific ALLELES associated with genetic traits, heritable diseases, or predisposition to a disease, or that may lead to the disease in descendants. It includes prenatal genetic testing.Fixatives: Agents employed in the preparation of histologic or pathologic specimens for the purpose of maintaining the existing form and structure of all of the constituent elements. Great numbers of different agents are used; some are also decalcifying and hardening agents. They must quickly kill and coagulate living tissue.Carcinoma, Squamous Cell: A carcinoma derived from stratified SQUAMOUS EPITHELIAL CELLS. It may also occur in sites where glandular or columnar epithelium is normally present. (From Stedman, 25th ed)Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.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.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.Leiomyosarcoma: A sarcoma containing large spindle cells of smooth muscle. Although it rarely occurs in soft tissue, it is common in the viscera. It is the most common soft tissue sarcoma of the gastrointestinal tract and uterus. The median age of patients is 60 years. (From Dorland, 27th ed; Holland et al., Cancer Medicine, 3d ed, p1865)Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Trisomy: The possession of a third chromosome of any one type in an otherwise diploid cell.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Chromosomes, Human, Pair 19: A specific pair of GROUP F CHROMOSOMES of the human chromosome classification.Lymphoma, Large B-Cell, Diffuse: Malignant lymphoma composed of large B lymphoid cells whose nuclear size can exceed normal macrophage nuclei, or more than twice the size of a normal lymphocyte. The pattern is predominantly diffuse. Most of these lymphomas represent the malignant counterpart of B-lymphocytes at midstage in the process of differentiation.Facies: The appearance of the face that is often characteristic of a disease or pathological condition, as the elfin facies of WILLIAMS SYNDROME or the mongoloid facies of DOWN SYNDROME. (Random House Unabridged Dictionary, 2d ed)Genes, Tumor Suppressor: Genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check. When tumor suppressor genes are inactivated or lost, a barrier to normal proliferation is removed and unregulated growth is possible.Prenatal Diagnosis: Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Histiocytoma, Benign Fibrous: A benign tumor composed, wholly or in part, of cells with the morphologic characteristics of HISTIOCYTES and with various fibroblastic components. Fibrous histiocytomas can occur anywhere in the body. When they occur in the skin, they are called dermatofibromas or sclerosing hemangiomas. (From DeVita Jr et al., Cancer: Principles & Practice of Oncology, 5th ed, p1747)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)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.Carcinoma in Situ: A lesion with cytological characteristics associated with invasive carcinoma but the tumor cells are confined to the epithelium of origin, without invasion of the basement membrane.Oncogenes: Genes whose gain-of-function alterations lead to NEOPLASTIC CELL TRANSFORMATION. They include, for example, genes for activators or stimulators of CELL PROLIFERATION such as growth factors, growth factor receptors, protein kinases, signal transducers, nuclear phosphoproteins, and transcription factors. A prefix of "v-" before oncogene symbols indicates oncogenes captured and transmitted by RETROVIRUSES; the prefix "c-" before the gene symbol of an oncogene indicates it is the cellular homolog (PROTO-ONCOGENES) of a v-oncogene.Developmental Disabilities: Disorders in which there is a delay in development based on that expected for a given age level or stage of development. These impairments or disabilities originate before age 18, may be expected to continue indefinitely, and constitute a substantial impairment. Biological and nonbiological factors are involved in these disorders. (From American Psychiatric Glossary, 6th ed)Syndrome: A characteristic symptom complex.Ependymoma: Glioma derived from EPENDYMOGLIAL CELLS that tend to present as malignant intracranial tumors in children and as benign intraspinal neoplasms in adults. It may arise from any level of the ventricular system or central canal of the spinal cord. Intracranial ependymomas most frequently originate in the FOURTH VENTRICLE and histologically are densely cellular tumors which may contain ependymal tubules and perivascular pseudorosettes. Spinal ependymomas are usually benign papillary or myxopapillary tumors. (From DeVita et al., Principles and Practice of Oncology, 5th ed, p2018; Escourolle et al., Manual of Basic Neuropathology, 2nd ed, pp28-9)Software: Sequential operating programs and data which instruct the functioning of a digital computer.Uveal Neoplasms: Tumors or cancer of the UVEA.Genes, Bacterial: The functional hereditary units of BACTERIA.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The 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 probe include the radioisotope labels 32P and 125I and the chemical label biotin.Adenocarcinoma: A malignant epithelial tumor with a glandular organization.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Chromosomes, Human, Pair 10: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.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.Skin Neoplasms: Tumors or cancer of the SKIN.Astrocytoma: Neoplasms of the brain and spinal cord derived from glial cells which vary from histologically benign forms to highly anaplastic and malignant tumors. Fibrillary astrocytomas are the most common type and may be classified in order of increasing malignancy (grades I through IV). In the first two decades of life, astrocytomas tend to originate in the cerebellar hemispheres; in adults, they most frequently arise in the cerebrum and frequently undergo malignant transformation. (From Devita et al., Cancer: Principles and Practice of Oncology, 5th ed, pp2013-7; Holland et al., Cancer Medicine, 3d ed, p1082)Gene Fusion: The GENETIC RECOMBINATION of the parts of two or more GENES resulting in a gene with different or additional regulatory regions, or a new chimeric gene product. ONCOGENE FUSION includes an ONCOGENE as at least one of the fusion partners and such gene fusions are often detected in neoplastic cells and are transcribed into ONCOGENE FUSION PROTEINS. ARTIFICIAL GENE FUSION is carried out in vitro by RECOMBINANT DNA technology.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.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Isochromosomes: Metacentric chromosomes produced during MEIOSIS or MITOSIS when the CENTROMERE splits transversely instead of longitudinally. The chromosomes produced by this abnormal division are one chromosome having the two long arms of the original chromosome, but no short arms, and the other chromosome consisting of the two short arms and no long arms. Each of these isochromosomes constitutes a simultaneous duplication and deletion.Metaphase: The phase of cell nucleus division following PROMETAPHASE, in which the CHROMOSOMES line up across the equatorial plane of the SPINDLE APPARATUS prior to separation.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.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Carcinoma, Ductal, Breast: An invasive (infiltrating) CARCINOMA of the mammary ductal system (MAMMARY GLANDS) in the human BREAST.Sensitivity and Specificity: Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)Neoplasm Staging: Methods which attempt to express in replicable terms the extent of the neoplasm in the patient.Gene Order: The sequential location of genes on a chromosome.Disease Progression: The worsening of a disease over time. This concept is most often used for chronic and incurable diseases where the stage of the disease is an important determinant of therapy and prognosis.Mental Retardation, X-Linked: A class of genetic disorders resulting in INTELLECTUAL DISABILITY that is associated either with mutations of GENES located on the X CHROMOSOME or aberrations in the structure of the X chromosome (SEX CHROMOSOME ABERRATIONS).Medulloblastoma: A malignant neoplasm that may be classified either as a glioma or as a primitive neuroectodermal tumor of childhood (see NEUROECTODERMAL TUMOR, PRIMITIVE). The tumor occurs most frequently in the first decade of life with the most typical location being the cerebellar vermis. Histologic features include a high degree of cellularity, frequent mitotic figures, and a tendency for the cells to organize into sheets or form rosettes. Medulloblastoma have a high propensity to spread throughout the craniospinal intradural axis. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, pp2060-1)Brain Neoplasms: Neoplasms of the intracranial components of the central nervous system, including the cerebral hemispheres, basal ganglia, hypothalamus, thalamus, brain stem, and cerebellum. Brain neoplasms are subdivided into primary (originating from brain tissue) and secondary (i.e., metastatic) forms. Primary neoplasms are subdivided into benign and malignant forms. In general, brain tumors may also be classified by age of onset, histologic type, or presenting location in the brain.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.Dermatofibrosarcoma: A sarcoma of the deep layers of the skin. The tumors are locally aggressive tends to recur but rarely metastatic. It can be classified into variants depending on the cell type tumors are derived from or by its characteristics: Pigmented variant from MELANIN-containing DERMAL DENDRITIC CELLS; Myxoid variant, myxoid STROMAL CELLS; Giant cell variant characterized by GIANT CELLS in the tumors; and Fibrosarcomatous variant chracterized by tumor areas histologically indistinguishable from FIBROSARCOMA.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Image Processing, Computer-Assisted: A technique of inputting two-dimensional images into a computer and then enhancing or analyzing the imagery into a form that is more useful to the human observer.Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.Monosomy: The condition in which one chromosome of a pair is missing. In a normally diploid cell it is represented symbolically as 2N-1.Neoplasms, Plasma Cell: Neoplasms associated with a proliferation of a single clone of PLASMA CELLS and characterized by the secretion of PARAPROTEINS.Liver Neoplasms: Tumors or cancer of the LIVER.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.Oligodendroglioma: A relatively slow-growing glioma that is derived from oligodendrocytes and tends to occur in the cerebral hemispheres, thalamus, or lateral ventricle. They may present at any age, but are most frequent in the third to fifth decades, with an earlier incidence peak in the first decade. Histologically, these tumors are encapsulated, relatively avascular, and tend to form cysts and microcalcifications. Neoplastic cells tend to have small round nuclei surrounded by unstained nuclei. The tumors may vary from well-differentiated to highly anaplastic forms. (From DeVita et al., Cancer: Principles and Practice of Oncology, 5th ed, p2052; Adams et al., Principles of Neurology, 6th ed, p655)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.Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.Hernia, Diaphragmatic: Protrusion of abdominal structures into the THORAX as a result of congenital or traumatic defects in the respiratory DIAPHRAGM.Craniofacial Abnormalities: Congenital structural deformities, malformations, or other abnormalities of the cranium and facial bones.Melanoma: A malignant neoplasm derived from cells that are capable of forming melanin, which may occur in the skin of any part of the body, in the eye, or, rarely, in the mucous membranes of the genitalia, anus, oral cavity, or other sites. It occurs mostly in adults and may originate de novo or from a pigmented nevus or malignant lentigo. Melanomas frequently metastasize widely, and the regional lymph nodes, liver, lungs, and brain are likely to be involved. The incidence of malignant skin melanomas is rising rapidly in all parts of the world. (Stedman, 25th ed; from Rook et al., Textbook of Dermatology, 4th ed, p2445)Autistic Disorder: A disorder beginning in childhood. It is marked by the presence of markedly abnormal or impaired development in social interaction and communication and a markedly restricted repertoire of activity and interest. Manifestations of the disorder vary greatly depending on the developmental level and chronological age of the individual. (DSM-V)Genetic Association Studies: The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease.Genetic Heterogeneity: The presence of apparently similar characters for which the genetic evidence indicates that different genes or different genetic mechanisms are involved in different pedigrees. In clinical settings genetic heterogeneity refers to the presence of a variety of genetic defects which cause the same disease, often due to mutations at different loci on the same gene, a finding common to many human diseases including ALZHEIMER DISEASE; CYSTIC FIBROSIS; LIPOPROTEIN LIPASE DEFICIENCY, FAMILIAL; and POLYCYSTIC KIDNEY DISEASES. (Rieger, et al., Glossary of Genetics: Classical and Molecular, 5th ed; Segen, Dictionary of Modern Medicine, 1992)Homozygote: An individual in which both alleles at a given locus are identical.Tissue Array Analysis: The simultaneous analysis of multiple samples of TISSUES or CELLS from BIOPSY or in vitro culture that have been arranged in an array format on slides or microchips.Lymphoma, B-Cell: A group of heterogeneous lymphoid tumors generally expressing one or more B-cell antigens or representing malignant transformations of B-lymphocytes.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.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).Tissue Fixation: The technique of using FIXATIVES in the preparation of cytologic, histologic, or pathologic specimens for the purpose of maintaining the existing form and structure of all the constituent elements.Adenoma: A benign epithelial tumor with a glandular organization.Frozen Sections: Thinly cut sections of frozen tissue specimens prepared with a cryostat or freezing microtome.Supratentorial Neoplasms: Primary and metastatic (secondary) tumors of the brain located above the tentorium cerebelli, a fold of dura mater separating the CEREBELLUM and BRAIN STEM from the cerebral hemispheres and DIENCEPHALON (i.e., THALAMUS and HYPOTHALAMUS and related structures). In adults, primary neoplasms tend to arise in the supratentorial compartment, whereas in children they occur more frequently in the infratentorial space. Clinical manifestations vary with the location of the lesion, but SEIZURES; APHASIA; HEMIANOPSIA; hemiparesis; and sensory deficits are relatively common features. Metastatic supratentorial neoplasms are frequently multiple at the time of presentation.Apraxias: A group of cognitive disorders characterized by the inability to perform previously learned skills that cannot be attributed to deficits of motor or sensory function. The two major subtypes of this condition are ideomotor (see APRAXIA, IDEOMOTOR) and ideational apraxia, which refers to loss of the ability to mentally formulate the processes involved with performing an action. For example, dressing apraxia may result from an inability to mentally formulate the act of placing clothes on the body. Apraxias are generally associated with lesions of the dominant PARIETAL LOBE and supramarginal gyrus. (From Adams et al., Principles of Neurology, 6th ed, pp56-7)Lung Neoplasms: Tumors or cancer of the LUNG.Carcinoma: A malignant neoplasm made up of epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases. It is a histological type of neoplasm but is often wrongly used as a synonym for "cancer." (From Dorland, 27th ed)Clostridium botulinum type B: Subtype of CLOSTRIDIUM BOTULINUM that produces botulinum toxin type B which is neurotoxic to humans and animals.Urinary Bladder Neoplasms: Tumors or cancer of the URINARY BLADDER.Genes, p53: Tumor suppressor genes located on the short arm of human chromosome 17 and coding for the phosphoprotein p53.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.Paraganglioma: A neural crest tumor usually derived from the chromoreceptor tissue of a paraganglion, such as the carotid body, or medulla of the adrenal gland (usually called a chromaffinoma or pheochromocytoma). It is more common in women than in men. (Stedman, 25th ed; from Segen, Dictionary of Modern Medicine, 1992)Genes, myc: Family of retrovirus-associated DNA sequences (myc) originally isolated from an avian myelocytomatosis virus. The proto-oncogene myc (c-myc) codes for a nuclear protein which is involved in nucleic acid metabolism and in mediating the cellular response to growth factors. Truncation of the first exon, which appears to regulate c-myc expression, is crucial for tumorigenicity. The human c-myc gene is located at 8q24 on the long arm of chromosome 8.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.Ovarian Neoplasms: Tumors or cancer of the OVARY. These neoplasms can be benign or malignant. They are classified according to the tissue of origin, such as the surface EPITHELIUM, the stromal endocrine cells, and the totipotent GERM CELLS.Genes, Duplicate: Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Diploidy: The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.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.Genetic Techniques: Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.Cerebellar Neoplasms: Primary or metastatic neoplasms of the CEREBELLUM. Tumors in this location frequently present with ATAXIA or signs of INTRACRANIAL HYPERTENSION due to obstruction of the fourth ventricle. Common primary cerebellar tumors include fibrillary ASTROCYTOMA and cerebellar HEMANGIOBLASTOMA. The cerebellum is a relatively common site for tumor metastases from the lung, breast, and other distant organs. (From Okazaki & Scheithauer, Atlas of Neuropathology, 1988, p86 and p141)

Carotenoid biosynthesis in cyanobacteria: structural and evolutionary scenarios based on comparative genomics. (1/1533)

Carotenoids are widely distributed pigments in nature and their biosynthetic pathway has been extensively studied in various organisms. The recent access to the overwhelming amount genomic data of cyanobacteria has given birth to a novel approach called comparative genomics. The putative enzymes involved in the carotenoid biosynthesis among the cyanobacteria were determined by similarity-based tools. The reconstruction of biosynthetic pathway was based on the related enzymes. It is interesting to find that nearly all the cyanobacteria share quite similar pathway to synthesize beta-carotene except for Gloeobacter violaceus PCC 7421. The enzymes, crtE-B-P-Qb-L, involved in the upstream pathway are more conserved than the subsequent ones (crtW-R). In addition, many carotenoid synthesis enzymes exhibit diversity in structure and function. Such examples in the families of zeta -carotene desaturase, lycopene cylases and carotene ketolases were described in this article. When we mapped these crt genes to the cyanobacterial genomes, the crt genes showed great structural variation among species. All of them are dispersed on the whole chromosome in contrast to the linear adjacent distribution of the crt gene cluster in other eubacteria. Moreover, in unicellular cyanobacteria, each step of the carotenogenic pathway is usually catalyzed by one gene product, whereas multiple ketolase genes are found in filamentous cyanobacteria. Such increased numbers of crt genes and their correlation to the ecological adaptation were carefully discussed.  (+info)

A family of human microRNA genes from miniature inverted-repeat transposable elements. (2/1533)

While hundreds of novel microRNA (miRNA) genes have been discovered in the last few years alone, the origin and evolution of these non-coding regulatory sequences remain largely obscure. In this report, we demonstrate that members of a recently discovered family of human miRNA genes, hsa-mir-548, are derived from Made1 transposable elements. Made1 elements are short miniature inverted-repeat transposable elements (MITEs), which consist of two 37 base pair (bp) terminal inverted repeats that flank 6 bp of internal sequence. Thus, Made1 elements are nearly perfect palindromes, and when expressed as RNA they form highly stable hairpin loops. Apparently, these Made1-related structures are recognized by the RNA interference enzymatic machinery and processed to form 22 bp mature miRNA sequences. Consistent with their origin from MITEs, hsa-mir-548 genes are primate-specific and have many potential paralogs in the human genome. There are more than 3,500 putative hsa-mir-548 target genes; analysis of their expression profiles and functional affinities suggests cancer-related regulatory roles for hsa-mir-548. Taken together, the characteristics of Made1 elements, and MITEs in general, point to a specific mechanism for the generation of numerous small regulatory RNAs and target sites throughout the genome. The evolutionary lineage-specific nature of MITEs could also provide for the generation of novel regulatory phenotypes related to species diversification. Finally, we propose that MITEs may represent an evolutionary link between siRNAs and miRNAs.  (+info)

Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach. (3/1533)

Inverted repeats have been found to occur in both prokaryotic and eukaryotic genomes. Usually they are short and some have important functions in various biological processes. However, long inverted repeats are rare and can cause genome instability. Analyses of C. elegans genome identified long, nearly-perfect inverted repeat sequences involving both divergently and convergently oriented homologous gene pairs and complete intergenic sequences. Comparisons with the orthologous regions from the genomes of C. briggsae and C. remanei show that the inverted repeat structures are often far more conserved than the sequences. This observation implies that there is an active mechanism for maintaining the inverted repeat nature of the sequences.  (+info)

Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes. (4/1533)

BACKGROUND: Lineage-specific, or taxonomically restricted genes (TRGs), especially those that are species and strain-specific, are of special interest because they are expected to play a role in defining exclusive ecological adaptations to particular niches. Despite this, they are relatively poorly studied and little understood, in large part because many are still orphans or only have homologues in very closely related isolates. This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein. METHODOLOGY/PRINCIPAL FINDINGS: We have developed "QIPP" ("Quality Index for Predicted Proteins"), an index that scores the "quality" of a protein based on non-homology-based criteria. QIPP can be used to assign a value between zero and one to any protein based on comparing its features to other proteins in a given genome. We have used QIPP to rank the predicted proteins in the proteomes of Bacteria and Archaea. This ranking reveals that there is a large amount of variation in QIPP scores, and identifies many high-scoring orphans as potentially "authentic" (expressed) orphans. There are significant differences in the distributions of QIPP scores between orphan and non-orphan genes for many genomes and a trend for less well-conserved genes to have lower QIPP scores. CONCLUSIONS: The implication of this work is that QIPP scores can be used to further annotate predicted proteins with information that is independent of homology. Such information can be used to prioritize candidates for further analysis. Data generated for this study can be found in the OrphanMine at http://www.genomics.ceh.ac.uk/orphan_mine.  (+info)

Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. (5/1533)

BACKGROUND: Array Comparative Genomic Hybridization (a-CGH) is a powerful molecular cytogenetic tool to detect genomic imbalances and study disease mechanism and pathogenesis. We report our experience with the clinical implementation of this high resolution human genome analysis, referred to as Chromosomal Microarray Analysis (CMA). METHODS AND FINDINGS: CMA was performed clinically on 2513 postnatal samples from patients referred with a variety of clinical phenotypes. The initial 775 samples were studied using CMA array version 4 and the remaining 1738 samples were analyzed with CMA version 5 containing expanded genomic coverage. Overall, CMA identified clinically relevant genomic imbalances in 8.5% of patients: 7.6% using V4 and 8.9% using V5. Among 117 cases referred for additional investigation of a known cytogenetically detectable rearrangement, CMA identified the majority (92.5%) of the genomic imbalances. Importantly, abnormal CMA findings were observed in 5.2% of patients (98/1872) with normal karyotypes/FISH results, and V5, with expanded genomic coverage, enabled a higher detection rate in this category than V4. For cases without cytogenetic results available, 8.0% (42/524) abnormal CMA results were detected; again, V5 demonstrated an increased ability to detect abnormality. Improved diagnostic potential of CMA is illustrated by 90 cases identified with 51 cryptic microdeletions and 39 predicted apparent reciprocal microduplications in 13 specific chromosomal regions associated with 11 known genomic disorders. In addition, CMA identified copy number variations (CNVs) of uncertain significance in 262 probands; however, parental studies usually facilitated clinical interpretation. Of these, 217 were interpreted as familial variants and 11 were determined to be de novo; the remaining 34 await parental studies to resolve the clinical significance. CONCLUSIONS: This large set of clinical results demonstrates the significantly improved sensitivity of CMA for the detection of clinically relevant genomic imbalances and highlights the need for comprehensive genetic counseling to facilitate accurate clinical correlation and interpretation.  (+info)

Epigenetic natural variation in Arabidopsis thaliana. (6/1533)

Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F(2) families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.  (+info)

ADaCGH: A parallelized web-based application and R package for the analysis of aCGH data. (7/1533)

BACKGROUND: Copy number alterations (CNAs) in genomic DNA have been associated with complex human diseases, including cancer. One of the most common techniques to detect CNAs is array-based comparative genomic hybridization (aCGH). The availability of aCGH platforms and the need for identification of CNAs has resulted in a wealth of methodological studies. METHODOLOGY/PRINCIPAL FINDINGS: ADaCGH is an R package and a web-based application for the analysis of aCGH data. It implements eight methods for detection of CNAs, gains and losses of genomic DNA, including all of the best performing ones from two recent reviews (CBS, GLAD, CGHseg, HMM). For improved speed, we use parallel computing (via MPI). Additional information (GO terms, PubMed citations, KEGG and Reactome pathways) is available for individual genes, and for sets of genes with altered copy numbers. CONCLUSIONS/SIGNIFICANCE: ADACGH represents a qualitative increase in the standards of these types of applications: a) all of the best performing algorithms are included, not just one or two; b) we do not limit ourselves to providing a thin layer of CGI on top of existing BioConductor packages, but instead carefully use parallelization, examining different schemes, and are able to achieve significant decreases in user waiting time (factors up to 45x); c) we have added functionality not currently available in some methods, to adapt to recent recommendations (e.g., merging of segmentation results in wavelet-based and CGHseg algorithms); d) we incorporate redundancy, fault-tolerance and checkpointing, which are unique among web-based, parallelized applications; e) all of the code is available under open source licenses, allowing to build upon, copy, and adapt our code for other software projects.  (+info)

Detection of novel amplicons in prostate cancer by comprehensive genomic profiling of prostate cancer cell lines using oligonucleotide-based arrayCGH. (8/1533)

BACKGROUND: The purpose of this study was to prove the feasibility of a longmer oligonucleotide microarray platform to profile gene copy number alterations in prostate cancer cell lines and to quickly indicate novel candidate genes, which may play a role in carcinogenesis. METHODS/RESULTS AND FINDINGS: Genome-wide screening for regions of genetic gains and losses on nine prostate cancer cell lines (PC3, DU145, LNCaP, CWR22, and derived sublines) was carried out using comparative genomic hybridization on a 35,000 feature oligonucleotide microarray (arrayCGH). Compared to conventional chromosomal CGH, more deletions and small regions of gains, particularly in pericentromeric regions and regions next to the telomeres, were detected. As validation of the high-resolution of arrayCGH we further analyzed a small amplicon of 1.7 MB at 9p13.3, which was found in CWR22 and CWR22-Rv1. Increased copy number was confirmed by fluorescence in situ hybridization using the BAC clone RP11-165H19 from the amplified region comprising the two genes interleukin 11 receptor alpha (IL11-RA) and dynactin 3 (DCTN3). Using quantitative real time PCR (qPCR) we could demonstrate that IL11-RA is the gene with the highest copy number gain in the cell lines compared to DCTN3 suggesting IL11-RA to be the amplification target. Screening of 20 primary prostate carcinomas by qPCR revealed an IL11-RA copy number gain in 75% of the tumors analyzed. Gain of DCTN3 was only found in two cases together with a gain of IL11-RA. CONCLUSIONS/SIGNIFICANCE: ArrayCGH using longmer oligonucleotide microarrays is feasible for high-resolution analysis of chomosomal imbalances. Characterization of a small gained region at 9p13.3 in prostate cancer cell lines and primary prostate cancer samples by fluorescence in situ hybridization and quantitative PCR has revealed interleukin 11 receptor alpha gene as a candidate target of amplification with an amplification frequency of 75% in prostate carcinomas. Frequent amplification of IL11-RA in prostate cancer is a potential mechanism of IL11-RA overexpression in this tumor type.  (+info)

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 chromosome (BAC) clones ...
Recent genome-wide microarray-based research investigations have revealed a high frequency of submicroscopic copy number alterations (CNAs) in the myelodysplastic syndromes (MDS), suggesting microarray-based comparative genomic hybridization (aCGH) has the potential to detect new clinically relevant genomic markers in a diagnostic laboratory. We performed an exploratory study on 30 cases of MDS, myeloproliferative neoplasia (MPN) or evolving acute myeloid leukemia (AML) (% bone marrow blasts ≤ 30%, range 0-30%, median, 8%) by aCGH, using a genome-wide bacterial artificial chromosome (BAC) microarray. The sample data were compared to corresponding cytogenetics, fluorescence in situ hybridization (FISH), and clinical-pathological findings. Previously unidentified imbalances, in particular those considered submicroscopic aberrations (| 10 Mb), were confirmed by FISH analysis. CNAs identified by aCGH were concordant with the cytogenetic/FISH results in 25/30 (83%) of the samples tested. aCGH revealed new
Comparative genomic hybridization analysis of adrenocortical tumors.: Comparative genomic hybridization (CGH) is a molecular cytogenetic technique that allows t
TY - JOUR. T1 - Molecular and clinical characterization of a recurrent cryptic unbalanced t(4q;18q) resulting in an 18q deletion and 4q duplication. AU - Horbinski, Craig. AU - Carter, Erika M.. AU - Heard, Patricia L.. AU - Sathanoori, Malini. AU - Hu, Jie. AU - Vockley, Jerry. AU - Gunn, Shelly. AU - Hale, Daniel. AU - Surti, Urvashi. AU - Cody, Jannine D.. PY - 2008/11/15. Y1 - 2008/11/15. N2 - Recurrent constitutional non-Robertsonian translocations are very rare. We present the third instance of cryptic, unbalanced translocation between 4q and 18q. This individual had an apparently normal karyotype; however, after subtelomere fluorescence in situ hybridization (FISH), he was found to have a cryptic unbalanced translocation between 4q and 18q [ish der(18)t(4;18)(q35;q23) (4qtel+, 18qtel-)]. Oligonucleotide array comparative genomic hybridization (aCGH) refined the breakpoints in this child and in the previously reported child and indicated that the breakpoints were within 20 kb of each ...
Lim, G., J. Karaskova, et al. (2005). "An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage-fusion-bridge cycle events in osteosarcoma." Genes Chromosomes Cancer 42(4): 392-403. Coe, B. P., L. J. Henderson, et al. (2005). "High-resolution chromosome arm 5p array CGH analysis of small cell lung carcinoma cell lines." Genes Chromosomes Cancer 42(3): 308-13. Garnis, C., B. Coe, et al. (2004). "Construction and optimization of chromosome arm-specific comparative genomic hybridization arrays for identifying genetic alterations in preinvasive lung cancers." Chest 125(5 Suppl): 104S-5S. Garnis, C., B. P. Coe, et al. (2004). "Overexpression of LRP12, a gene contained within an 8q22 amplicon identified by high-resolution array CGH analysis of oral squamous cell carcinomas." Oncogene 23(14): 2582-6. de Leeuw, R. J., J. J. Davies, et al. (2004). "Comprehensive whole genome array CGH ...
Background: When abnormalities are found during the anatomy scan most patients are offered amniocentesis and conventional karyotyping, using Giemsa (G)-banding of metaphase chromosomes to detect aneuploidies and large structural changes in the prenatal diagnosis. The use of fluorescent in situ hybridization (FISH) reduces the time to obtain a result because culture is not necessary, but can only detect a limited number of prespecified targets. Small studies have shown that array comparative genomic hybridization (aCGH) can detect all unbalanced chromosomal abnormalities as well as smaller deletions and duplications that cannot be detected with routine cytogenetic analysis. Should aCGH screening be used instead of karyotyping to diagnose prenatal chromosomal abnormalities in pregnant patients with abnormal ultrasound? Methods: An exhaustive search of available medical literature from the past 5 years was conducted using Medline-OVID, CINAHL, Web of Science. Key words included: comparative genomic
Uveal melanomas (UM) are aggressive ocular tumours of adults that are typically characterized by chromosomal aberrations such as loss of 1p, 3, 6q, and gain 6p, and 8q. Of these monosomy 3 (M3) and 8q+ are powerful predictors of prognosis. The relationship of changes affecting chromosome 6 is however more ambivalent, having been linked to both good and poor prognosis, and yet both regions have not been well defined, which suggest the presence of one or more oncogenes in 6p and tumour suppressor gene in 6q. Therefore, different chromosome 6 alterations may have a variable impact on the prognosis of UM, and ultimately contain genes that contribute to the development and metastasis of this disease. It is likely that these changes can act as moderators to the tumour outcome. Although UM disseminates haematogenous with high propensity for the liver, and hepatic involvement reported in over 90% of patients, infrequently some patients will however initially present with metastases in sites other than ...
Abnormal genomic losses detected by array comparative genomic hybridization are prevalent in adults with unexplained intellectual disability. Our data showing abnormalities in 22% and 17% of overall patients and of cases with normal karyotypes, respectively, suggest that the yield of array comparati …
Detection of submicroscopic genomic copy number variation is now considered the first-tier clinical test-in place of standard G-banded karyotyping-in the evaluation of children with unexplained developmental delay, intellectual disability, autism spectrum disorders, or congenital anomalies. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variants (CNVs), but microarray-based comparative genomic hybridization (array CGH) has a much higher diagnostic yield for these patients when compared to traditional cytogenetic methods such as karyotype and FISH. This unit focuses on oligonucleotide arrays, including updated information about detection of long contiguous stretches of homozygosity (LCSH) through inclusion of single-nucleotide polymorphism (SNP) probes. Most clinical laboratories now offer arrays with some level of probe coverage throughout the genome, and many are offering detection of LCSH. Updated guidelines for array design
TY - JOUR. T1 - Overlay analysis of the oligonucleotide array gene expression profiles and copy number abnormalities as determined by array comparative genomic hybridization in medulloblastomas. AU - Lo, Ken C.. AU - Rossi, Michael R.. AU - Burkhardt, Tania. AU - Pomeroy, Scott L.. AU - Cowell, John K.. PY - 2007/1/1. Y1 - 2007/1/1. N2 - Combined analysis of gene expression array data and array-based comparative genomic hybridization data have been used in a series of 26 pediatric brain tumors to define up- and downregulated genes that coincide with losses, gains, and amplifications involving specific chromosome regions. Frequent losses were defined in chromosome arms 3q, 6q, 8p, 10q, 16q, 17p, and gains were identified in chromosome 7, and chromosome arms 9p and 17q. Amplification of a 2p region was seen in only one tumor, which corresponded to increased expression of the MYCN and DDX1 genes. To facilitate the analysis of the two data sets, we have developed a custom overlay tool that defines ...
Br J Haematol. 2010 Nov;151(4):336-45. doi: 10.1111/j.1365-2141.2010.08341.x. Epub 2010 Aug 31. Comparative Study; Multicenter Study; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Govt
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 candidate genes associated with this ...
Background: Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence. Results: We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the ...
The Cytogenetics Laboratory performs chromosome analysis, fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (array CGH) on cells prepared from a wide variety of tissues including amniotic fluid, chorionic villi, products of conception, peripheral blood leukocytes, bone marrow, lymph node, and skin/muscle biopsy.. Learn more. ...
Leukaemia is often associated with genetic alterations such as translocations, amplifications and deletions, and recurrent chromosome abnormalities are used as markers of diagnostic and prognostic relevance. However, a proportion of acute myeloid leukaemia (AML) cases have an apparently normal karyotype despite comprehensive cytogenetic analysis. Based on conventional cytogenetic analysis of banded chromosomes, we selected a series of 23 paediatric patients with acute myeloid leukaemia and performed whole genome array comparative genome hybridization (aCGH) using DNA samples derived from the same patients. Imbalances involving large chromosomal regions or entire chromosomes were detected by aCGH in seven of the patients studied. Results were validated by fluorescence in situ hybridization (FISH) to both interphase nuclei and metaphase chromosomes using appropriate bacterial artificial chromosome (BAC) probes. The majority of these copy number alterations (CNAs) were confirmed by FISH and found ...
There is merit in each of these predictions. For example, profiling has re-emerged in clinical testing in the form of protein, tissue and nucleic acid arrays (e.g., cytokine profiles, array comparative genomic hybridization analysis) [49-52]. Computers and automation have played an increasingly important role in improving the efficiency and effectiveness of testing. More recently, pharmacogenetics, popularized by the slogan "right patient, right drug, right time" [53], has moved into mainstream testing (e.g., CYP2C9 for warfarin dosing) [54]. Since 1969, there have been many predictions and views of the future development of laboratory medicine and its sub-specialties. A summary of these predictions is provided in Table 1 [12-48]. A number of common themes and buzz-words can be identified in the prognostications such as nanotechnology, biosensors, microchips, genomics, and proteomics. These topics, together with the more specific predictions, are discussed in greater detail below. ...
BACKGROUND: Currently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with amplification or deletion. The correlation as well as the discriminative power of these platforms has never been compared statistically on a significant set of human patient samples. RESULTS: In this paper, we present an exhaustive comparison between the two CGH platforms, undertaken at two independent sites using the same batch of DNA from 19 advanced prostate cancers. The comparison was performed directly on the raw data and a significant correlation was found between the two platforms. The correlation was greatly improved when the data were averaged over large chromosomic regions using a segmentation algorithm. In addition, this analysis has enabled the development of a statistical model to discriminate BAC
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Background: Mental retardation can be caused by copy number variations (deletions, insertions, duplications), ranging in size from 1 kb to several megabases. Array based comparative genomic hybridisation (array-CGH) allows detection of an increasing number of genomic alterations.. Methods: A series of 46 patients with mental retardation and congenital abnormalities (previously screened for subtelomeric rearrangements) were evaluated for cryptic chromosomal imbalances by array-CGH. This array contains 6465 large-insert BAC/PAC clones, representing sequences uniformly distributed throughout the human genome. The results were confirmed by alternative techniques.. Results: Four pathogenic rearrangements were detected: two of them were novel, a deletion at 2q31.2 and a duplication at 8q12 band; the other two have been previously reported-a duplication of the Williams-Beuren region and a deletion of 3q29. By adding the subtelomeric alterations previously identified, a total rate of 18% of pathogenic ...
The new whitepaper explains how utilising a range of available tools builds a more complete picture of inherently complex genetic disorders, providing the insights necessary to drive novel discoveries and research into potential therapeutic strategies. At the forefront of this approach is Professor Madhuri Hegde, Professor of Human Genetics at Emory Genetics Laboratory (EGL, Atlanta, USA), whose success in applying such an integrated strategy is also explored. The paper highlights that while targeted DNA sequencing presents a valuable approach for genomic analysis, it is unable to detect copy number variations (CNV) with certainty. In contrast, comparative genomic hybridisation arrays (aCGH) are the gold-standard for CNV detection and the 60-mer oligonucleotide probes utilised by OGTs aCGH platform have been shown to deliver superior CNV detection compared with alternative platforms.. In collaboration with experts at EGL, OGT has designed a range of molecular arrays that are the ideal ...
Chromosomal abnormalities are diagnostic and prognostic key factors in acute myeloid leukemia (AML) patients, as they play a central role for risk stratification algorithms. High hyperdiploidy (HH), a rare cytogenetic abnormality seen commonly in elder male AML patients, is normally categorized under AML with complex karyotype (CK). Accordingly, patients with HH generally are associated with low remission rates and a short overall survival. Here we report a case of 21-year-old female, diagnosed with a de novo AML-M1 according to WHO classification and a CK at diagnosis. Cytogenetic, molecular cytogenetic approaches (standard fluorescence in situ hybridization (FISH), array-proven multicolor banding (aMCB)) and high resolution array comparative genomic hybridization (aCGH) analyses revealed a unique complex but still near diploid karyotype involving eleven chromosomes was identified. It included pentasomy 4, three yet unreported chromosomal aberrations t(1;2)(p35;p22), t(1;3)(p36.2;p26.2), and t(10;12)
In countries where comparative genomic hybridization arrays (aCGH) and next generation sequencing are not widely available due to accessibility and economic constraints, conventional 400-500-band karyotyping is the first-line choice for the etiological diagnosis of patients with congenital malformations and intellectual disability. Conventional karyotype analysis can rule out chromosomal alterations greater than 10 Mb. However, some large structural abnormalities, such as derivative chromosomes, may go undetected when the analysis is performed at less than a 550-band resolution and the size and banding pattern of the interchanged segments are similar. Derivatives frequently originate from inter-chromosomal exchanges and sometimes are inherited from a parent who carries a reciprocal translocation. We present two cases with derivative chromosomes involving a 9.1 Mb 5p deletion/14.8 Mb 10p duplication in the first patient and a 19.9 Mb 5p deletion/ 18.5 Mb 9p duplication in the second patient. These long
Understanding tumors as evolutionary systems is an important area of study with far-reaching implications in diagnostic and treatment paradigms. Computational phylogenetics is a valuable method for inferring tumor evolution in terms of evolutionary trees, phylogenies, where paths in a tree correspond to possible tumor progression pathways. The location of specific cell-types and patient samples in the tree provide information on tumor sub-types and development of heterogeneity. We previously developed a tumor phylogeny inference pipeline for array comparative genome hybridization (aCGH)-based tumor copy number profiles. Steps in the pipeline included extraction of robust progression markers from the data, which could differentiate stages of tumor evolution or the different paths in the tree, and assigning amplification states to the inferred markers in those stages. We introduced a novel multi-sample model for amplicon identification and calling, HMMCNA, which jointly extracted markers from and ...
Comparative genomic hybridization (CGH) is a modern genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether t
Comparative genomic hybridization is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells. The aim of this technique is to quickly and efficiently compare two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole chromosomes or subchromosomal regions (a portion of a whole chromosome). This technique was originally developed for the evaluation of the differences between the chromosomal complements of solid tumor and normal tissue, and has an improved resoIution of 5-10 megabases compared to the more traditional cytogenetic analysis techniques of giemsa banding and fluorescence in situ hybridization (FISH) which are limited by the resolution of the microscope utilized. This is achieved through the use of competitive ...
Comparative genomic hybridization (CGH) is a technique used to detect unbalanced chromosome rearrangements based on the use o f in situ hybridization of differentially labeled DNA. This technique can be used to analyze complex clinical cases which have constitutional chromosomal abnormalities that do not lend themselves to routine chromosomal analysis. CGH was examined in order to develop a reliable and reproducible protocol that can be used as an additional diagnostic tool in Shodair Hospitals clinical lab. CGH involves the isolation o f both test and reference DNA and the differentially labeling o f the different DNA with fluorescent probes. Then those samples o f DNA were hybridized onto a normal metaphase spread. The slide was examined under a fluorescent microscope and analyzed using Perceptive Scientific Instruments MacProbe fluorescent imaging software. It appears that a slightly modified version o f the published Vysis Protocol (1998) yields the best CGH results in our clinical diagnostic
臺大位居世界頂尖大學之列,為永久珍藏及向國際展現本校豐碩的研究成果及學術能量,圖書館整合機構典藏(NTUR)與學術庫(AH)不同功能平台,成為臺大學術典藏NTU scholars。期能整合研究能量、促進交流合作、保存學術產出、推廣研究成果。. To permanently archive and promote researcher profiles and scholarly works, Library integrates the services of "NTU Repository" with "Academic Hub" to form NTU Scholars.. ...
Chromosome abnormalities are common in oocytes derived from patients undergoing IVF treatment. The proportion of oocytes displaying aneuploidy is closely related to maternal age and may exceed 60% in patients over 40 years old. However, little information currently exists concerning the incidence of such anomalies in oocytes derived from young fertile women. A total of 121 metaphase II oocytes and their corresponding first polar bodies (PB) were analysed with the use of a comprehensive cytogenetic method, comparative genomic hybridization (CGH). The oocytes were donated from 13 young women (average age 22 years) without any known fertility problems. All oocytes were mature at the time of retrieval and were unexposed to spermatozoa. A low aneuploidy rate (3%) was detected. These results clearly indicate that meiosis I segregation errors are not frequent in oocytes of young fertile women. The higher aneuploidy rates reported in embryos derived from donor oocytes could be due to aggressive hormonal
Chromosome abnormalities are common in oocytes derived from patients undergoing IVF treatment. The proportion of oocytes displaying aneuploidy is closely related to maternal age and may exceed 60% in patients over 40 years old. However, little information currently exists concerning the incidence of such anomalies in oocytes derived from young fertile women. A total of 121 metaphase II oocytes and their corresponding first polar bodies (PB) were analysed with the use of a comprehensive cytogenetic method, comparative genomic hybridization (CGH). The oocytes were donated from 13 young women (average age 22 years) without any known fertility problems. All oocytes were mature at the time of retrieval and were unexposed to spermatozoa. A low aneuploidy rate (3%) was detected. These results clearly indicate that meiosis I segregation errors are not frequent in oocytes of young fertile women. The higher aneuploidy rates reported in embryos derived from donor oocytes could be due to aggressive hormonal
Patrick Buckley graduated with a Bsc. Hons in Biochemistry and Molecular Biology from DIT. In 2005, he completed a PhD in Clinical Genetics entitled "Development and Application of Microarray-Based Comparative Genomic Hybridization - Analysis of Neurofibromatosis Type-2, Schwannomatosis and related tumours" in the group of Professor Jan Dumanski at the Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden.. Moving back to Ireland, he spent two years in the Medical Devices Department within the Irish Medicines Board (now HPRA), before moving to the Department of Cancer Genetics at The Royal College of Surgeons in Ireland. Patrick received an Irish Research Council for Science, Engineering and Technology (IRCSET) Post-Doctoral Fellowship in 2007 and was appointed to a lecturering position in the Department of Molecular and Cellular Therapeutics, RCSI in 2010.. In 2011, Patrick moved to Beaumont Hospital to establish the Molecular Pathology Laboratory, which is now an ...
4183 Array comparative genomic hybridization (CGH) is a high-resolution technique that allows a genome-wide screen to identify regions of genomic imbalances. The technique has been widely used to characterize recurrent genomic copy number alterations in cancers, typically detected through the application of gain and loss thresholds. However, to date, the effect of sample ploidy on the detection accuracy of these thresholds towards single copy alterations (SCAs) has not been evaluated. Here, we describe a method to evaluate the detection accuracy of thresholds towards SCAs in array CGH data. Through the application of a Hidden Markov Model based method, we segment array CGH data from well-karyotyped cell lines, and generate ploidy-specific sensitivity-specificity plots, from which we identify optimum thresholds relevant to sample ploidy. We demonstrate that commonly used non-ploidy-specific thresholds are sub-optimal in their ability to call SCAs, partic ularly when applied to tetraploid samples ...
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 genome, were identified. Interestingly, 87% of the detected CNV regions overlapped with known genes ...
Array-based comparative genomic hybridization analysis was performed on 21 malignant mesothelioma (MM) samples (16 primary cell cultures and 5 cell lines) and two reactive mesothelial hyperplasia (RM) primary cell cultures. The RM samples did not have any genomic losses or gains. In MM samples, deletions in 1p, 3p21, 4q, 9p21, 16p13 and 22q were detected frequently. We focused on 3p21 because this deletion was specific to the epithelioid type. Especially, a deletion in 3p21.1 region carrying seven genes including SEMA3G was found in 52% of MM samples (11 of 14 epithelioid samples). The allele loss of 3p21.1 might be a good marker for the epithelioid MM. A homozygous deletion in this region was detected in two MM primary cell cultures. A heterozygous deletion detected in nine samples contained the 3p21.1 region and 3p21.31 one carrying the candidate tumor suppressor genes such as semaphorin 3F (SEMA3F), SEMA3B and Ras association (RalGDS/AF-6) domain family member 1 (RASSF1A). SEMA3B, 3F and 3G ...
Array-based comparative genomic hybridization (aCGH) is a powerful tool to detect genomic imbalances in the human genome. The analysis of aCGH data sets has revealed the existence of a widespread technical artifact termed as waves, characterized by an undulating data profile along the chromosome.
Crete Fertility Centre is one of the very few centres in Greece which perform the new method, Array-CGH (Array Comparative Genomic Hybridization), with excellent results.. Array CGH is the only method able to detect unbalanced chromosomal abnormalities. This is because balanced chromosomal abnormalities such as reciprocal translocations, inversions or ring chromosomes do not affect copy number, which is what is detected by CGH technologies. CGH enables the exploration of all 46 human chromosomes in single test and the discovery of deletions and duplications, even on microscopic scale which may lead to the identification of candidate genes to be further explored by other cytological techniques.. Array CGH can help in cases of advanced maternal age, multiple miscarriages and failed embryo transfers.. Humans generally have 46 chromosomes that come as 23 pairs, one of each pair from our Mum and one of each from our Dad. Problems arise when an embryo misses out on a chromosome or picks up an extra ...
Paulette Mhawech-Fauceglia, Tanja Pejovic, Daniel Dim, Xueping Fang, Jeffrey Conroy, Shashikant Lele, Richard Cheney, and Kunle Odunsi. Array-based comparative genomic hybridization (aCGH) analysis is a useful tool for distinguishing primary pulmonary from metastatic neuroendocrine carcinoma to the lung. Applied Immunohistochemistry and Molecular Morphology. 2008 May; 16(3): 291-5 ...
Gain a deeper understanding of array comparative genomic hybridization, how it works and how it is being applied in clinical research today.
(2005) Lai et al. Bioinformatics. MOTIVATION: Array Comparative Genomic Hybridization (CGH) can reveal chromosomal aberrations in the genomic DNA. These amplifications and deletions at the DNA level are important in the pathogenesi...
Current models suggest that colon cancer initiation and progression are secondary to both the activation of oncogenes and the deletion of tumor suppressor genes. The role of each, however, is still poorly understood, particularly with regard to the induction of metastasis. We hypothesized that genetic differences exist between tumors that metastasize distantly and those that do not, and that oncogenes and tumor suppressor genes participate equally in this process. To address this hypothesis, human tumor specimens from localized [tumor-node-metastasis (TNM) stage I-III] and primary colon cancers (n = 10) were directly compared with metastatic (TNM stage IV) lesions (n = 10) using comparative genomic hybridization analysis. Although several alterations were shared equally between primary tumors and metastases (+7q, +19q, and +20q), two patterns of distinguishing alterations were observed: (a) alterations that were more extensive in liver metastases than in primary tumors (+8q, +13q, -4p, -8p, ...
The biomedical literature is an incredibly rich resource for researchers. Information obtained from previous scientific studies helps researchers focus their own efforts. To obtain the maximal benefit from studies in genetics and genomics there is a need to link this data with the information available in the associated biomedical literature. In particular, microarray gene expression, comparative genomic hybridization, and genetic mapping studies depend on an integrated pool of information to drive output analysis. In mining the literature to find regions previously associated with Prostate Cancer, one can define focus points for future research efforts. Subsequent analytical methods include actual placement of gene expression patterns on metabolic pathways, and the use of comparative genomic hybridization information along with genetic mapping data to determine localized genomic structure. The latter approach promises the added benefit of associating differential gene expression profiles with ...
In the present study, we examined DNA copy number alterations in 106 invasive cancers using 4 × 44K Agilent arrays. Our CGH analysis correctly identified clinical HER-2 amplification status with 96% to 99% accuracy, depending on the cutoff value used to determine HER-2 status by our CGH data. In addition, we report that 3,007 genes presented a significant correlation between copy number and mRNA levels. Interestingly, a high number of molecular targets (HER-2, EGFR, PTEN, VEGFA, AURKA, CHEK, AKT…) currently under investigation presented such correlation. Altogether, these two data suggest that (a) the occurrence of a DNA gain and/or lost leads to an unregulated overexpression or underexpression of mRNA and (b) high-resolution CGH array is a reliable technology to assess such copy number anomalies. CGH array, as complement to other technologies, could be an interesting approach in clinical practice to identify some subsets of patients who are candidates to targeted therapies.. We could ...
SANTA CLARA, Calif., July 28, 2016 Agilent Technologies Inc. (NYSE: A) today announced that scientists using the companys comparative genomic hybridization (CGH) technology have shown that cancer cell lines, which are broadly used in all aspects of biomedical research, may have vast differences in their genetic makeup, even when grown in the same batch.. As a result, the scientists have recommended that cell culture banks use advanced genomic technologies, such as array CGH, to ensure the consistency of the cells they provide to the research community.. Researchers have long been aware that some popular cell lines are not stable. That is, their biological properties and genetic makeup change as cultures are propagated in laboratories. While standard precautions and quality assurance methods are being used to control such changes and validate authenticity of the cell lines, they may not be sufficient, according to a paper published July 26 in Scientific Reports, an online journal from the ...
Comparative genomic analysis is the only way to determine the authenticity of industrial biotechnology in misappropriation litigation.
Scientists using Agilent Technologies comparative genomic hybridization CGH technology have shown that cancer cell lines, which are broadly used in all aspects of biomedical research, may have vast differences in their genetic makeup, even when grown in the same batch. As a result, the scientists have recommended that cell culture banks use...
Develop molecular markers that will facilitate accurate diagnosis (including prenatal diagnosis) and permit correlation of phenotypic variation with specific mutations by localizing the gene(s) for CDH to specific chromosomal segments using linkage analysis in familial cases. In sporadic cases, characterize the role of somatic mutations in CDDs by using a candidate gene approach, and comparative genomic hybridization (CGH) arrays ...
A comparison of the conceptual steps in aCGH and CNV-seq methods. 1. Starting material in both cases is genomic fragments from two genomes. 2. In CNV-seq the fr
Supervised clustering of the minimal recurrent regions revealed the association of the gain at 1q23.3- q24.1 with histopathologic variables. The genomic profile
Looking for online definition of comparative genomic hybridization in the Medical Dictionary? comparative genomic hybridization explanation free. What is comparative genomic hybridization? Meaning of comparative genomic hybridization medical term. What does comparative genomic hybridization mean?
Nasopharyngeal carcinoma (NPC) is a distinct geographical disease with high incidence in Southeast Asia. Previous CGH studies have located multiple regions of chromosomal gains and losses in NPC. To elucidate the regions of gain and amplification, a high-resolution array comparative genomic hybridization (array CGH) was applied to characterize the common amplicons in NPC cell lines and xenografts. Consistent with our previous CGH findings, frequent gains at chromosomes 1q, 3q, 7, 8, 9q, 12q and 20q were detected. High incidence of gains were identified on chromosome 3q and 12q. The findings were further confirmed by FISH analysis. Using 16 BAC clones on 3q26-28 and 6 BAC clones on 12q13, the smallest regions of gain at 3q and 12q were defined on five NPC cell lines. Chromosome 3q26.33 (RP11-510K16) and 12q13.2-q13.3 (RP11-183H16) showed the highest amplification frequency in FISH analysis with 100 and 66.7%, respectively. PIK3CA, a candidate oncogene located at 3q26.32 adjacent to this 3q ...
OBJECTIVE: During IVF, non-transferred embryos are usually selected for cryopreservation on the basis of morphological criteria. This investigation evaluated an application for array comparative genomic hybridization (aCGH) in assessment of surplus embryos prior to cryopreservation. METHODS: First-time IVF patients undergoing elective single embryo transfer and having at least one extra non-transferred embryo suitable for cryopreservation were offered enrollment in the study. Patients were randomized into two groups: Patients in group A (n=55) had embryos assessed first by morphology and then by aCGH, performed on cells obtained from trophectoderm biopsy on post-fertilization day 5. Only euploid embryos were designated for cryopreservation. Patients in group B (n=48) had embryos assessed by morphology alone, with only good morphology embryos considered suitable for cryopreservation. RESULTS: Among biopsied embryos in group A (n=425), euploidy was confirmed in 226 (53.1%). After fresh single embryo
TY - JOUR. T1 - Olfactory copy number association with age at onset of Alzheimer disease. AU - Shaw, C. A.. AU - Li, Y.. AU - Wiszniewska, J.. AU - Chasse, S.. AU - Zaidi, S. N.Y.. AU - Jin, W.. AU - Dawson, B.. AU - Wilhelmsen, K.. AU - Lupski, J. R.. AU - Belmont, J. W.. AU - Doody, R. S.. AU - Szigeti, K.. PY - 2011/4/12. Y1 - 2011/4/12. N2 - Objectives: Copy number variants (CNVs) have been recognized as a source of genetic variation that contributes to disease phenotypes. Alzheimer disease (AD) has high heritability for occurrence and age at onset (AAO). We performed a cases-only genome-wide CNV association study for age at onset of AD. Methods: The discovery case series (n = 40 subjects with AD) was evaluated using array comparative genome hybridization (aCGH). A replication case series (n = 507 subjects with AD) was evaluated using Affymetrix array (n = 243) and multiplex ligation-dependent probe amplification (n = 264). Hazard models related onset age to CNV. Results: The discovery ...
Torenbeek, R., Hermsen, M.A., Meijer, G.A., Baak, J.P. and Meijer, C.J. (1999) Analysis by Comparative Genomic Hybridization of Epithelial and Spindle Cell Components in Sarcomatoid Carcinoma and Carcinosarcoma Histogenetic Aspects. Journal of Pathology, 189, 338-343.
Background: Previous data implicating genetic and epigenetic events on chromosome 9, including the CDKN2A/2B locus, as molecular predictors of Wilms tumour relapse, have been conflicting. Aims: To clarify this using genome-wide and focused molecular genetic analysis. Methods: Microarray-based comparative genomic hybridisation (aCGH) using genome-wide coverage was applied to 76 favourable histology Wilms tumours. Additional investigation of the 9p21 locus was carried out using loss of heterozygosity (LOH) and fluorescence in situ hybridisation (FISH), as well as immunohistochemistry for CDKN2A/p16INK4a on a paediatric renal tumour tissue microarray. Results: Approximately half of the tumours were found to show chromosome 9 copy number changes. Those cases which harboured alterations comprised at least four distinct patterns: gain of the entire chromosome, loss of 9p, gain of 9q34, or a more complex combination of gains/losses. None of these tumour groups showed any statistically significant ...
This example shows how to use a Bayesian hidden Markov model (HMM) technique to identify copy number alteration in array-based comparative genomic hybridization (CGH) data.
Early gastric carcinoma (GC) is considered to be a curable cancer, as it progresses to the advanced stage following varying durations. Understanding the early stage of GC may provide an insight into its pathogenesis and contribute to reducing the mortality rate of this disease. To investigate the genomic aberrations associated with 22 cases of early GC, high-density microarray comparative genomic hybridization was performed in the present study. The most notable finding was copy number gains (log2 ratio >0.25) on the long arm of chromosome 8, which occurred in 77.3% (17/22) of GC cases, and the delineated minimal common region was 8q22.1-q24.3. More specifically, two amplified (log2 ratio >1) loci in the 8q22.1-q24.3 region were detected in 18.2% (4/22) of GC cases. The first loci covered a region of 102.4-107.9 kb, mapping on 8q22.3-q23.1, and comprised the transcription factor CP2-like 3 gene. The second loci, spanning 128.7-145.7 kb on 8q24.21-q24.3, comprised the representative oncogene of ...
TY - JOUR. T1 - Genome-wide aberrations in pancreatic adenocarcinoma. AU - Nowak, Norma J.. AU - Gaile, Daniel. AU - Conroy, Jeffrey M.. AU - McQuaid, Devin. AU - Cowell, John Kenneth. AU - Carter, Randy. AU - Goggins, Michael G.. AU - Hruban, Ralph H.. AU - Maitra, Anirban. PY - 2005/8/1. Y1 - 2005/8/1. N2 - Chromosomal instability, manifesting as copy number alterations (CNAs), is characteristic of pancreatic adenocarcinoma. We used bacterial artificial chromosome (BAC) array-based comparative genomic hybridization (aCGH) to examine the pancreatic adenocarcinoma genome for submicroscopic amplifications and deletions. Profiles of 33 samples (17 first-passage xenografts and 16 cell lines) identified numerous chromosomal regions with CNAs, including losses at 1p36.33∼p34.3, 1p13.3∼p13.2, 3p26, 3p25.2∼p22.3, 3p22.1∼p14.1, 4q28.3, 4q31, 4q35.1, 5q14.3, 6p, 6q, 8p23.3∼p12, 9p, 9q22.32∼q31.1, 13q33.2, 15q11.2, 16p13.3, 17p, 18q11.21∼q23 , 19p13.3∼p13.12, 19q13.2, 21p, 21q, and 22p, ...
CGH stands for comparative genome hybridisation, which aims to compare the presence / absence / number of similar genes in 2 genomes (i.e. its a survey of genetic differences between 2 organisms). So, a CGH experiment might compare gemomic DNA from 2 closely related bacterial species or strains. The difference between CGH array experiments and gene expression array experiments is just the target which is hybridised to the array: labelled genomic DNA for CGH; labelled cDNA (or cRNA - derived from mRNA in either case) for gene expression. You can use exactly the same arrays for both types of experiment, although the objective of CGH is normally genome-wide comparison of 2 genomes, so CGH normally uses whole-genome microarrays (for prokaryotes, at least). In general, you can use any genomic array for either gene expression or CGH ...
Formalin-fixed paraffin-embedded (FFPE) archival clinical specimens are invaluable in discovery of prognostic and therapeutic targets for diseases such as cancer. However, the suitability of FFPE-derived genetic material for array-based comparative genomic hybridization (array-CGH) studies is underexplored. In this study, genetic profiles of matched FFPE and fresh-frozen specimens were examined to investigate DNA integrity differences between these sample types and determine the impact this may have on genetic profiles. Genomic DNA was extracted from three patient-matched FFPE and fresh-frozen clinical tissue samples. T47D breast cancer control cells were also grown in culture and processed to yield a fresh T47D sample, a fresh-frozen T47D sample and a FFPE T47D sample. DNA was extracted from all the samples; array-CGH conducted and genetic profiles of matched samples were then compared. A loss of high molecular weight DNA was observed in the FFPE clinical tissues and FFPE T47D samples. A dramatic
Leukemic non-nodal mantle cell lymphoma (lMCL) is a particular subtype of mantle cell lymphoma (MCL), characterized by leukemic non-nodal disease and slow progression. Recognition of this entity is relevant to avoid overtreatment. Despite indolent clinical behaviour, lMCL might transform to a more aggressive disease. The purpose of this study was to compare lMCL with classical MCL (cMCL) and aggressive MCL (aMCL) using immunohistochemistry, interphase fluorescence in situ hybridization (FISH), and array-based comparative genomic hybridization, in order to identify biomarkers for lMCL diagnosis and prognosis. Seven lMCL patients were included. All had bone marrow involvement without lymphadenopathy. An lMCL phenotype was distinct from that of cMCL and aMCL: SOX11-, ATM+, PARP1+/-, and low KI67 (average 2 %). Beyond the t(11;14) translocation, fewer secondary cytogenetic alterations were found in lMCL compared to cMCL and aMCL, including deletion of PARP1 and 13q14. At last follow-up, one patient with
1. Raish M, Khurshid M, Ansari MA. et al. Analysis of molecular cytogenetic alterations in uterine leiomyosarcoma by array-based comparative genomic hybridization. J Cancer Res Clin Oncol. 2012;138:1173-1186 2. Dash DP, Silvestri G, Hughes AE. Fine mapping of the keratoconus with cataract locus on chromosome 15q and candidate gene analysis. Mol Vis. 2006;12:499-505 3. Birkenkamp-Demtroder K, Maghnouj A, Mansilla F. et al. Repression of KIAA1199 attenuates wnt-signalling and decreases the proliferation of colon cancer cells. Br J Cancer. 2011;105:552-561 4. He QY, Liu XH, Li Q. et al. G8: A novel domain associated with polycystic kidney disease and non-syndromic hearing loss. Bioinformatics. 2006;22:2189-2191 5. Yoshida H, Nagaoka A, Nakamura S. et al. N-terminal signal sequence is required for cellular trafficking and hyaluronan-depolymerization of KIAA1199. FEBS Lett. 2014;588:111-116 6. Abe S, Usami S, Nakamura Y. Mutations in the gene encoding KIAA1199 protein, an inner-ear protein expressed ...
To validate segments selected as rare CNVs according to our density score we automate the process of a manual validation of segments based on UCSC [29], i.e. the protocol by which geneticians usually act. Lastly, we compare resulting sets of segments with the set produced manually by geneticists from IMC.. Manual validation by geneticists involves inspecting reported CNVs segments, overlaying them on UCSC tracks. This purposes to filter out known polymorphisms and, by interrogation of all known syndrome regions, to try to narrow down the segment set to only those clinically relevant. This step is followed by FISH or PCR confirmation of the CNVs existence in patients DNA [30, 31].. For the automated process we decided to focus on three main databases storing the information related to genomic variations and diseases resulting from it: ISCA, DGV and GAD.. ISCA is a group of clinical cytogenetics laboratories committed to improve the quality of patients care related to clinical genetic testing ...
Introduction: Lung carcinoids comprise a group of smoking-unrelated neuroendocrine tumors, which can be classified in typical (TC) and atypical (AC) carcinoids. Classification is complex and its accuracy to predict disease outcome is variable. In a previous array comparative genomic hybridization (arrayCGH) study, we showed that the average number of chromosomal alterations (≥ 1Mb) was significantly higher in ACs than in TCs (512 v. 226 per tumor) and that the most common region of chromosome loss was 11q21-q25 (Neuroendocrinology 2009;90:136-137 ...
237 total publications from NE-1334 Project participants 2013-2017. *= 33 cooperative publications among 2 or more project participants. *Abernathy, J., X. Li, X. Jia, W. Chou, S. J. Lamont, R. Crooijmans, and H. Zhou, H. 2014. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Anim. Genet. 45:400-411.. *Banat, G. R., S. Tkalcic, J. A. Dzielawa, M. W. Jackwood, M. D. Saggese, L. Yates, R. Kopulos, W. Briles, and E. W. Collisson. 2013. Association of the chicken MHC B haplotypes with resistance to avian coronavirus. Dev. Comp. Immunol. 39:430-437.. *Bauer, M. M., M. M. Miller, W. E. Briles, and K. M. Reed. 2013. Genetic variation at the MHC in a population of introduced wild turkeys. Animal biotechnology 24:210-228.. *Coble, D. J., E. E. Sandford, T. Ji, J. Abernathy, D. Fleming, H. Zhou, and S. J. Lamont. 2013. Impacts of Salmonella enteritidis infection on liver transcriptome in broilers. Genesis 51:357-364. *Da Silva A. P., Hauck R., ...
A number of results of array-CGH analysis of breast tumours and breast cancer cell lines have been published [19, 21, 22, 25, 27, 80-88] (Table 1). Some of these results, together with large amounts of conventional CGH, FISH and SKY data of breast cancer, are freely available through the Progenetix repository [89, 90]; NCI and NCBIs SKY/M-FISH and CGH Database (2001) [91]; Charité, Berlin University [92]; and in the supplementary data of many individual publications. Cytogenetic data has been described [53, 54] and is available for more then 1000 cases at NCBI. The following discussion illustrates the use and usefulness of array-CGH for various breast cancer genomes.. A detailed study of 31 advanced archival breast tumours conducted by Nessling and coworkers [47] elegantly demonstrates how specificity, sensitivity and resolution are increased in (matrix) array-CGH compared with conventional CGH by using the same samples on both platforms. They identified 44 genes by array-CGH and verified all ...
In Vitro Fertilization (IVF) $7,950. Anesthesia $350. *Intra-Cytoplasmic Sperm Injection (ICSI) $1,500. *Assisted Hatching (AH) $450. *First year freezing & Cryopreservation $650. Array Comparative Genomic Hybridization (aCGH) including Preimplantation Genetic Diagnosis (PGD) and family balancing - $3750. *Fees apply if deemed medically necessary. All fees in effect as of July 2016.. ...
Systematic forward genetics using somatic cell mutants is a powerful tool in elucidating biochemical pathways [1]. However, it is often difficult to identify the genetic loci responsible for a particular somatic cell mutant phenotype. Map-based positional cloning strategies can be used in somatic cell hybrids to analyze mutants with recessive phenotypes. By tracking DNA sequence variants that co-segregate with heritable traits, the genes accounting for these traits can be localized to specific chromosomal locations [2]. Recent advances in genome sequencing have facilitated the assembly of physical maps of candidate regions, but fine mapping and narrowing of candidate regions is still often tedious and remains a major obstacle in somatic cell genetics. Consequently, there is a need to efficiently map the positions of genes in somatic cell mutants.. We previously established a method to enrich for human genes that complement rodent somatic cell mutants [3]. The mutant rodent cells are fused with ...
Vulvar squamous cell carcinoma (VSCC) is a rare disease that has a high mortality rate (∼40%). However, little is known about its molecular signature. Therefore, an integrated genomics approach, based on comparative genome hybridization (aCGH) and genome-wide expression (GWE) array, was performed to identify driver genes in VSCC. To achieve that, DNA and RNA were extracted from frozen VSCC clinical specimens and examined by aCGH and GWE array, respectively. On the basis of the integration of data using the CONEXIC algorithm, PLXDC2 and GNB3 were validated by RT-qPCR. The expression of these genes was then analyzed by IHC in a large set of formalin-fixed paraffin-embedded specimens. These analyses identified 47 putative drivers, 46 of which were characterized by copy number gains that were concomitant with overexpression and one with a copy number loss and downregulation. Two of these genes, PLXDC2 and GNB3, were selected for further validation: PLXDC2 was downregulated and GNB3 was ...
Comparative genomic hybridizations have been used to examine genetic relationships between bacteria. The microarrays used in these experiments may have open reading frames from one or more reference strains, or they may be composed of random DNA fragments from a large number of strains (mixed-genome microarrays; MGM). Herein both experimental and virtual arrays are analyzed to assess the validity of genetic inferences from these experiments with a focus on MGMs. Empirical data is analyzed from an Enterococcus MGM while a virtual MGM is constructedin silico using sequenced genomes (Streptococcus). On average a small MGM is capable of correctly deriving phylogenetic relationships between seven species of Enterococcus with 100% (n=100 probes) and 95% (n=46 probes) accuracy; more probes are required for intra-specific differentiation. Compared to multilocus sequence methods and whole-genome microarrays, MGM provides additional discrimination between closely related strains and offers the possibility ...
Oxford Gene Technology this week launched a new microarray that can be used to screen embryos for chromosomal abnormalities prior to implantation during an in vitro fertilization cycle.
GenomePlex® Single Cell WGA Kit CGH Data. The GenomePlex Single Cell WGA (WGA-4) provides accurate and unbiased amplification that preserves the original genome representation.
We have some time ahead of us to finish developing the product to the point where it can be put in someone elses lab," he said. "We are still working on the instrument format, but we are aiming at something that will be very available and accessible to users - not requiring something too sophisticated or exotic ...
TY - JOUR. T1 - Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. AU - Snijders, Antoine M.. AU - Schmidt, Brian. AU - Fridlyand, Jane. AU - Dekker, Nusi. AU - Pinkel, Daniel. AU - Jordan, Richard C K. AU - Albertson, Donna. PY - 2005/6/16. Y1 - 2005/6/16. N2 - Genomes of solid tumors are characterized by gains and losses of regions, which may contribute to tumorigenesis by altering gene expression. Often the aberrations are extensive, encompassing whole chromosome arms, which makes identification of candidate genes in these regions difficult. Here, we focused on narrow regions of gene amplification to facilitate identification of genetic pathways important in oral squamous cell carcinoma (SCC) development. We used array comparative genomic hybridization (array CGH) to define minimum common amplified regions and then used expression analysis to identify candidate driver genes in amplicons that spanned ,3Mb. We found genes involved ...
Copy number analysis usually refers to the process of analyzing data produced by a test for DNA copy number variation in patients sample. Such analysis helps detect chromosomal copy number variation that may cause or may increase risks of various critical disorders. Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, comparative genomic hybridization and with high-resolution array-based tests based on array comparative genomic hybridization (or aCGH), SNP array technologies and high resolution microarrays that include copy number probes as well an SNPs. Array-based methods have been accepted as the most efficient in terms of their resolution and high-throughput nature and the highest coverage (choose an array with over 2 million probes) and they are also referred to as Virtual Karyotype. Data analysis for an array-based DNA copy number test can be very challenging though due to very high volume of data that come out of an array platform. ...
Deregulation of the EGFR signaling pathway is one of the most frequently observed genetic abnormalities that drives cancer development. Although mutations in the downstream components of the EGFR signaling pathway, including KRAS, BRAF and PIK3CA, have been reported in numerous cancers, extensive mutation and copy number analysis of these genes in clinical samples has not been performed for head and neck squamous cell carcinoma (HNSCC). We examined the mutations and copy number alterations of KRAS, BRAF and PIK3CA in 115 clinical specimens of HNSCC obtained from surgically treated patients. We used DNA sequencing to detect mutations and the copy number changes were evaluated by qPCR and array comparative genomic hybridization (CGH) analysis. We examined the mutations and copy number alterations of KRAS, BRAF and PIK3CA in 115 clinical specimens of HNSCC obtained from surgically treated patients. We identified 3 mutations (2.6%) in K-RAS and 3 mutations (2.6%) in PIK3CA. Copy number amplification was
Oncogenic point mutations in KIT or PDGFRA are recognized as the primary events responsible for the pathogenesis of most gastrointestinal stromal tumors (GIST), but additional genomic alterations are frequent and presumably required for tumor progression. The relative contribution of such alterations for the biology and clinical behavior of GIST, however, remains elusive. In the present study, somatic mutations in KIT and PDGFRA were evaluated by direct sequencing analysis in a consecutive series of 80 GIST patients. For a subset of 29 tumors, comparative genomic hybridization was additionally used to screen for chromosome copy number aberrations. Genotype and genomic findings were cross-tabulated and compared with available clinical and follow-up data. We report an overall mutation frequency of 87.5%, with 76.25% of the tumors showing alterations in KIT and 11.25% in PDGFRA. Secondary KIT mutations were additionally found in two of four samples obtained after imatinib treatment. Chromosomal imbalances
Translocations affecting chromosome subband 6p25.3 containing the IRF4 gene have been recently described as characteristic alterations in a molecularly distinct subset of germinal center B-cell-derived lymphomas. Secondary changes have yet only been described in few of these lymphomas. Here, we performed array-comparative genomic hybridization and molecular inversion probe microarray analyses on DNA from 12 formalin-fixed paraffin-embedded and two fresh-frozen IRF4 translocation-positive lymphomas, which together with the previously published data on nine cases allowed the extension of copy number analyses to a total of 23 of these lymphomas. All except one case carried chromosomal imbalances, most frequently gains in Xq28, 11q22.3-qter, and 7q32.1-qter and losses in 6q13-16.1, 15q14-22.31, and 17p. No recurrent copy-neutral losses of heterozygosity were observed. TP53 point mutations were detected in three of six cases with loss of 17p. Overall this study unravels a recurrent pattern of ...
Abstract: Resistance to chemotherapeutic agents and radiotherapy has kept surgery the primary treatment of uterine leiomyosarcoma (ULMS). In search of leads for potential therapeutic targets, array CGH (aCGH) was used to obtain a genomewide pattern of ULMS-specific genetic imbalances and to define the affected biological processes. Fine-resolution genomewide aCGH analysis was performed using customised 16K cDNA microarrays on 18 primary ULMS cases. Furthermore, patterns of DNA copy number changes were assessed for associations with clinical parameters, i.e., tumour grade, tumour size and patient status at last follow-up. Our aCGH results demonstrated extensive DNA copy number changes in all chromosomes. Of the 10,590 gene loci included in the analysis, 4,387 were found to be affected by DNA copy number gains and 4,518 by DNA copy number losses in at least one case. Further analyses revealed that 231 of these were commonly gained, and 265 lost in at least 20% of the cases. The gains affected loci ...
CMA-Expanded utilizes array-based comparative genomic hybridization (aCGH) and contains 400,000 oligonucleotides for copy number analysis and SNP probes for all chromosomes for detection of uniparental disomy (UPD) and consanguinity. SNP probes are also useful for the detection of triploidy. This expanded prenatal array offers exon-by-exon coverage of over 1,700 genes. It is recommended for providers and patients who want the highest level of detection possible. This option may be the best choice for fetal evaluations assessing possible copy number changes at breakpoints of de novo apparently balanced rearrangements. CMA is limited to detection of gains and losses of genomic material and will not detect low-level mosaicism, balanced translocations, inversions or point mutations in specific genes ...
article{7b211b82-b7cf-45eb-9b6c-526d9db736a8, abstract = {Chemotherapy resistance remains a major obstacle to successful treatment of ovarian cancer patients. Therefore, increased knowledge of underlying mechanisms and identification of predictive factors are of great importance. Standard treatment for ovarian carcinoma is surgery followed by platinum-based chemotherapy. In this study, we aimed to search for genes or genomic regions involved in platinum resistance in ovarian carcinoma. Array-based comparative genomic hybridization (CGH) was used to identify genetic alterations in 32 early-stage epithelial ovarian carcinomas homogeneously treated with single-agent carboplatin. The arrays contain 33,370 bacterial artificial chromosome (BAC) clones and form a contiguous and tiling coverage of the human genome with an average resolution of similar to 100 kb. We found certain genetic changes associated with carboplatin response. Gains in 1q25.1-q41 were significantly more frequent in ...
Urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC) strains. In contrast to many enteric E. coli pathogroups, no genetic signature has been identified for UPEC strains. We conducted a high-resolution comparative genomic study using E. coli isolates collected from the urine of women suffering from frequent recurrent UTIs. These isolates were genetically diverse and varied in their urovirulence, that is, their ability to infect the bladder in a mouse model of cystitis. We found no set of genes, including previously defined putative urovirulence factors (PUFs), that were predictive of urovirulence. In addition, in some patients, the E. coli strain causing a recurrent UTI had fewer PUFs than the supplanted strain. In competitive experimental infections in mice, the supplanting strain was more efficient at colonizing the mouse bladder than the supplanted strain. Despite the lack of a clear genomic signature for urovirulence, comparative transcriptomic and phenotypic ...
Grey zone. Structural genomic variants or copy number variations (CNV) can be reliably assessed using array comparative genomic hybridization (array CGH) or Single Nucleotide Polymorphism (SNP) arrays. However, for deletions or duplications smaller than 50-100 kB, these technologies have a poor detection rate with many false positive and false negative findings unless platforms are used that target specific candidate regions. Exome analysis, on the other hand, is capable of assessing genetic variation reliably on the single base-pair level. Between both technologies, there is a grey zone of structural genomic variants that are difficult to detect; CNVs smaller than 50 kB are often difficult to assess, and the extent and pathogenic role of these small CNVs is unclear. Now, a recent paper in the American Journal of Human Genetics manages to detect small CNVs through exome data. Their analysis in patients with autism, parents, and unaffected siblings suggests a contribution of small inherited CNVs ...
NSCLC-associated EGFR mutations are most frequently heterozygous. However, Paez et al. (18) reported one mutation involving exon 19 that appeared to be homozygous, and we detected two such cases. Interpretation of mutational status solely from DNA sequencing can be problematic. On the one hand, contaminating normal cells with wild-type EGFR could account for apparent heterozygosity; on the other hand, amplification of mutant EGFR, as occurs in lung cancer (23), could account for detection of only mutant sequences. Mouse models expressing mutant EGFR proteins in the lung and analysis of mutant-positive NSCLCs by fluorescence in situ hybridization and/or array-based comparative genomic hybridization may help address these issues. Interestingly, in one of these tumors (G3), we detected a heterozygous intronic polymorphism downstream of exon 19 (data not shown). In this case, it is probable that a gene conversion event occurred, encompassing the area of deletion in exon 19.. Five of 17 reported ...
A 3-month-old boy presented with decreased appetite, fatigue, and a nosebleed. Initial workup revealed hemoglobin 2.6 g/dL (10.2-12.7), hematocrit 7.7% (30.9-37.9), mean corpuscular volume 104 fL (71.3-82.6), white blood cell count 4200/μL (240 absolute neutrophil count), platelets 50 000/μL (140-400), and reticulocyte count 1.31% (1.55-2.7). Bone marrow revealed hypercellularity with cytoplasmic vacuolization of myeloid and erythroid precursors (panels A-B; original magnification ×1000, Wright-Giemsa stain). Iron staining of marrow biopsy revealed numerous ringed sideroblasts (panels C-D; original magnification ×1000, Prussian blue stain). DNA was examined by array-based comparative genomic hybridization and revealed a 4.9-kb deletion, m.11027_15950del4923, consistent with mitochondrial DNA deletion syndrome, also known as Pearson syndrome. Fecal elastase was initially normal, but now it is ,15 μg/g (normal ,200), consistent with severe pancreatic insufficiency. We have begun pancreatic ...
STUDY QUESTION: Can next-generation sequencing (NGS) techniques be used reliably for comprehensive aneuploidy screening of human embryos from patients undergoing IVF treatments, with the purpose of identifying and selecting chromosomally normal embryos for transfer?. SUMMARY ANSWER: Extensive application of NGS in clinical preimplantation genetic screening (PGS) cycles demonstrates that this methodology is reliable, allowing identification and transfer of euploid embryos resulting in ongoing pregnancies.. WHAT IS KNOWN ALREADY: The effectiveness of PGS is dependent upon the biology of the early embryo and the limitations of the technology. Fluorescence in situ hybridization, used to test for a few chromosomes, has largely been superseded by microarray techniques that test all 24 chromosomes. Array comparative genomic hybridization (array-CGH) has been demonstrated to be an accurate PGS method and has become the de facto gold standard, but new techniques, such as NGS, continue to emerge.. STUDY ...
Importantly, when creating the mimicked data sets we did not generate any simulated ratio values; rather, we formed different selections of values using real experimental data. We believe that this use of real experimental data is of significance for aCGH data. This belief is founded on that, in contrast to expression levels, copy number levels are restricted to a, by comparison, moderate dynamic range. Therefore, when a genomic region is subjected to gain or amplification, the increase of genomic material is relatively substantial. Thus, we reasoned that probes for regions of gain would yield comparably higher average intensities than those for regions of normal copy number and that this, in turn, would result in a correlation between M and A: probes measuring ratios of gain will have higher average intensities. The opposite relationship would apply for probes measuring ratios of loss. Consequently, utilizing normalization strategies based on Lowess would possibly correct for correlations ...
DNA copy number variants represent the greatest source of genetic variability in humans [1] and are the underlying cause of many human diseases. Array CGH is recognized as a first-tier test for DNA copy number variants (CNV) [2] and accordingly, many laboratories have already established their pipelines for pre-processing of array CGH data and CNV calling. In many cases these pipelines are based on software packages provided by the companies selling DNA microarrays or scanners such as BlueFuse [3], CytoSure [4] or CytoGenomics [5]. Yet, the scope of these tools is focused on the identification of CNVs and their evaluation in the context of gene content and frequency of a given variant in the healthy population. Comparative analysis, which integrates data obtained from multiple patients, or other experiment types are hardly supported, in particular when they are based on different array platforms or NGS technology.. Such kind of meta-analysis needs the implementation of additional commercial or ...
Manjegowda, D. S. and Karunakar, P. and Ramachandra, N. B. (2015) Effect of structural changes in proteins derived from GATA4 nonsynonymous single nucleotide polymorphisms in congenital heart disease. Indian Journal of Pharmaceutical Sciences, 77 (6). pp. 735-741. Avinash, M. V. and Megha, N. Murthy and Sangeetha, V. and Kusuma, L. and Suresh, R. V. and Nachappa, S. A. and Prashali, Nelchi and Sangeetha, N. Y. and Manjula, A. S. and Manjegowda, D. S. and Seshachalam, K. B. and Ramachandra, N. B. (2014) Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression. Plosone, 9 (2). Veerappa, Avinash M. and Vishweswaraiah, S. and Kusuma, L. and Megha, N. Murthy and Manjegowda, D. S. and Radhika Nayaka, and Ramachandra, N. B. (2013) Unravelling the Complexity of Human Olfactory Receptor Repertoire by Copy Number Analysis across Population Using High Resolution Arrays. PLOS ONE, 8 (7). pp. 1-14. ...
Roche NimbleGen, Inc. has launched NimbleGen Comparative Genomic Hybridization (CGH) microarrays in a 12x135K format for analysis of DNA copy number v
Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six i(7)(q10)-positive HSTL cases, including HSTL-derived cell line (DERL-2), and three cases with ring 7 [r(7)], the recently identified rare variant aberration. Using high resolution array CGH, we profiled all cases and mapped the common deleted region (CDR) at 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp) and the common gained region (CGR) at 7q22.11q31.1 (38.77 Mb; 86259620-124892276 bp). Interestingly, CDR spans a smaller region of 13 Mb (86259620-99271246 bp) constantly amplified in cases with r(7). In addition, we found that TCRG (7p14.1) and TCRB (7q32) are involved in formation of r(7), which seems to be a byproduct of illegitimate somatic rearrangement of both loci. Further transcriptomic ...
View the review history for Comparative genomic analysis of the PKS genes in five species and expression analysis in upland cotton
Bioconductor version: Release (3.6) The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.. Author: Lei Song, Krithika Bhuvaneshwar, Yue Wang, Yuanjian Feng, Ie-Ming Shih, Subha Madhavan, Yuriy Gusev Maintainer: Yuriy Gusev ,yg63 at georgetown.edu, ...
Copy number variants (CNVs) on the Breakpoint 1 to Breakpoint 2 region Ki8751 at 15q11. of publically obtainable expression data identified a relationship between expression of mRNA and FOXP2 in mind. We suggest that changed medication dosage through aberrant patterning from the lh.SMG may donate to language-related Mouse monoclonal to CD11b.4AM216 reacts with CD11b, a member of the integrin a chain family with 165 kDa MW. which is expressed on NK cells, monocytes, granulocytes and subsets of T and B cells. It associates with CD18 to form CD11b/CD18 complex.The cellular function of CD11b is on neutrophil and monocyte interactions with stimulated endothelium; Phagocytosis of iC3b or IgG coated particles as a receptor; Chemotaxis and apoptosis. Ki8751 issues connected with BP1-2 CNVs. Even more generally this process may be useful in clarifying the contribution Ki8751 of individual genes at CNV risk loci. Introduction Rare multi-gene copy number variants (CNVs) are well established to increase ...
Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We developed a method we call Sector-Ploidy-Profiling to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization. Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that ...
Integrative and conjugative elements (ICEs) of the ICESa2603 family have been isolated from several species of Streptococcus spp.; however, the comparative genomic and evolutionary analyses of these particular ICEs are currently only at their initial stages. By investigating 13 ICEs of the ICESa2603 family and two ICESa2603 family-like ICEs derived from diverse hosts and locations, we have determined that ICEs comprised a backbone of 30 identical syntenic core genes and accessory genes that were restricted to the intergenic sites or the 3-end of the non-conserved domain of core genes to maintain its function. ICESa2603 family integrase IntICESa2603 specifically recognized a 15-bp att sequence (TTATTTAAGAGTAAC) at the 3-end of rplL, which was highly conserved in genus Streptococcus. Phylogenetic analyses suggest that extensive recombination/insertion and the occurrence of a hybrid/mosaic in the ICESa2603 family were responsible for the significant increase in ICE diversity, thereby broadening its host
Dr. Dobyns leads a broad-based research program investigating the nature and causes of a wide range of human developmental brain disorders. These include malformations of the forebrain, mid-hindbrain (brainstem and cerebellum) and cerebral cortex, as well as a wide spectrum of developmental disabilities including autism, intellectual disability, early childhood developmental forms of epilepsy, and complex developmental disorders combining several of the above. His work includes recognition and delineation of specific conditions, identification of numerous underlying genes, and detailed phenotype and genotype-phenotype analysis. The methods used in his lab include most standard molecular genetics methods plus fluorescence in situ hybridization, chromosome microarrays (comparative genome hybridization), RNA expression arrays, methylation-sensitive assays for X inactivation, standard (Sanger) sequencing, and most recently high-throughput exome sequencing.. ...
The incidence of adenocarcinoma of the lung is increasing in the United States, however, the difficulties in obtaining lung cancer families and representative samples of early to late stages of the disease have lead to the intense study of mouse models for lung cancer. We used Spectral Karyotyping (SKY), mapping with fluorescently labeled genomic clones (FISH), comparative genomic hybridization (C
The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed h
TY - JOUR. T1 - A hibridizáció és alkalmazása DNS-array rendszerekben. AU - Gyorffy, András. AU - Gyorffy, Balázs. AU - Molnár, Béla. AU - Tulassay, Zsolt. PY - 2005/12/1. Y1 - 2005/12/1. N2 - DNA hybridization arrays measure simultaneously the expression of several genes. First, a known DNA sequence (probe) is fixed on a firm basis. Then the complementer sequence (target sequence) is linked to it during the hybridization process. The target sequence extracted from biological samples is fluorescently, enzimatically or radioactivelly labeled before detection. Higher expression results in higher signal in the detection system. Unlabeled DNA strands can also be detected, as the electronical and optical characteristics of the DNA is altered after complementer hybridization. In this review we summarize the basics of hybridisation and its newest application area in the DNA array systems.. AB - DNA hybridization arrays measure simultaneously the expression of several genes. First, a known DNA ...
Intrahepatic cholangiocarcinoma (ICC) is an aggressive, highly lethal tumors and lacks of effective chemo and targeted therapies. Cell lines and animal models, even partially reflecting tumor characteristics, have limits to study ICC biology and drug response. In this work, we created and characterized a novel ICC patient-derived xenograft (PDX) model of Italian origin. Seventeen primary ICC tumors derived from Italian patients were implanted into NOD (Non-Obese Diabetic)/Shi-SCID (severe combined immunodeficient) mice. To verify if the original tumor characteristics were maintained in PDX, immunohistochemical (cytokeratin 7, 17, 19, and epithelial membrane antigen) molecular (gene and microRNA expression profiling) and genetic analyses (comparative genomic hybridization array, and mutational analysis of the kinase domain of EGFR coding sequence, from exons 18 to 21, exons 2 to 4 of K-RAS, exons 2 to 4 of N-RAS, exons 9 and 20 of PI3KCA, and exon 15 of B-RAF) were performed after tumor stabilization.
Structural variation is thought to play a major etiological role in the development of autism spectrum disorders (ASDs), and numerous studies documenting the relevance of copy number variants (CNVs) in ASD have been published since 2006. To determine if large ASD families harbor high-impact CNVs that may have broader impact in the general ASD population, we used the Affymetrix genome-wide human SNP array 6.0 to identify 153 putative autism-specific CNVs present in 55 individuals with ASD from 9 multiplex ASD pedigrees. To evaluate the actual prevalence of these CNVs as well as 185 CNVs reportedly associated with ASD from published studies many of which are insufficiently powered, we designed a custom Illumina array and used it to interrogate these CNVs in 3,000 ASD cases and 6,000 controls. Additional single nucleotide variants (SNVs) on the array identified 25 CNVs that we did not detect in our family studies at the standard SNP array resolution. After molecular validation, our results demonstrated
We report on a 4-year-old girl who presented with microcephaly, multiple minor anomalies of face and limbs, congenital heart defect, hypotonia, neuropsychomotor delay, deafness and seizures. A GTG-banded karyotype identified an additional fragment of unknown origin on the terminal region of 4p. Parental karyotypes were normal. FISH analysis using a whole chromosome paint probe for chromosome 4 and subtelomere probes showed a signal on the entire add (4) chromosome and loss of the 4p subtelomere region, respectively. Additional analysis using microsatellite markers for chromosome 4 and whole-genome array comparative genomic hybridization (array-CGH) identified a duplication of the region 4p13 4p16.3. Her karyotype was thus interpreted as an inverted duplication with terminal deletion of 4p: 46,XX,der(4)(:p13 p16.3::p16.3 qter). The clinical features of our patient differed from those typically observed in Wolf-Hirschhorn syndrome and were more compatible with duplication 4(p14 p16.3), with ...
Abstract: Cutaneous squamous cell carcinoma (SCC) occurs commonly and can metastasize. Identification of specific molecular aberrations and mechanisms underlying the development and progression of cutaneous SCC may lead to better prognostic and therapeutic approaches and more effective chemoprevention strategies. To identify genetic changes associated with early stages of cutaneous SCC development, we analyzed a series of 40 archived skin tissues ranging from normal skin to invasive SCC. Using high-resolution array-based comparative genomic hybridization, we identified deletions of a region on chromosome 10q harboring the INPP5A gene in 24% of examined SCC tumors. Subsequent validation by immunohistochemistry on an independent sample set of 71 SCC tissues showed reduced INPP5A protein levels in 72% of primary SCC tumors. Decrease in INPP5A protein levels seems to be an early event in SCC development, as it also is observed in 9 of 26 (35%) examined actinic keratoses, the earliest stage in SCC ...
TY - JOUR. T1 - Breakpoint localization using array-CGH in three siblings with an unbalanced 4q;16q translocation and childhood apraxia of speech (CAS). AU - Shriberg, Lawrence D.. AU - Jakielski, Kathy J.. AU - El-Shanti, Hatem. PY - 2008/9/1. Y1 - 2008/9/1. N2 - We report clinical, cytogenetic, and comparative genomic hybridization findings for three siblings with an unbalanced 4q;16q translocation, minor malformations, and cognitive abnormalities, including childhood apraxia of speech, a rare, severe motor speech disorder. Breakpoint findings indicate that in addition to possible contributions from duplicated genes on chromosome 16, haploinsufficiency of one or more of 11 genes deleted in the telomeric region of the long arm of chromosome 4 is the likely cause of the speech disorder, the associated impairments in cognition and language, and the dysmorphic features. The present findings are the first to document childhood apraxia of speech in a multiplex family using contemporary speech ...
RODERIC (Repositori dObjectes Digitals per a lEnsenyament la Recerca i la Cultura) es el repositorio institucional de la Universitat de València. Se concibe como una ventanilla única para el acceso y la difusión de la producción digital de la Universitat. RODERIC responde al compromiso de la Universitat con el movimiento de acceso abierto al conocimiento adquirido con su adhesión a la Declaración de Berlín (30 Septiembre de 2008).
Expression profile and molecular genetic regulation of cyclin D1 expression in epithelioid sarcoma Epithelioid sarcoma is a distinctive, aggressive soft tissue tumor typically presenting as a subcutaneous or deep dermal mass in the distal extremities of young adults. Molecular genetic data of well-characterized cases of epithelioid sarcoma are sparse. A recent cytogenetic study of epithelioid sarcoma by conventional metaphase comparative genomic hybridization reported recurrent gains at chromosome 11q13, a region containing many genes, including the cyclin D1 gene. Cyclin D1 is a positive cell cycle regulator that is overexpressed in a variety of neoplasms, including mantle cell lymphoma and breast carcinoma. The objective of this study was to examine cyclin D1 expression in epithelioid sarcoma. Of 24 cases evaluated, 23 (96%) displayed cyclin D1 nuclear expression using immunohistochemical evaluation. Eight cases, which expressed cyclin D1 by immunohistochemistry, were evaluated by fluorescence ...
"Array comparative genomic hybridization in male infertility". Human Reproduction. 27 (3): 921-9. doi:10.1093/humrep/der440. ...
... detected both by comparative genomic hybridization (CGH),[32] and array CGH,[38]) and karyotypic variations including ... "Interglandular cytogenetic heterogeneity detected by comparative genomic hybridization in pancreatic cancer". Cancer Res. 62 (3 ... "Inferring tree models for oncogenesis from comparative genome hybridization data". J. Comput. Biol. 6 (1): 37-51. doi:10.1089/ ... 2007). "The genomic landscapes of human breast and colorectal cancers". Science. 318 (5853): 1108-1113. doi:10.1126/science. ...
... comparative genomic hybridization and with high-resolution array-based tests based on array comparative genomic hybridization ( ... Array comparative genomic hybridization Bioinformatics DNA microarray Virtual Karyotype Sebat, J.; et al. (2007). "Strong ... Bassem A. Bejjani and Lisa G. Shaffer (2006). "Application of Array-Based Comparative Genomic Hybridization to Clinical ... Copy number variation can be detected with various types of tests such as fluorescent in situ hybridization, ...
... using oligo-microarray comparative genomic hybridization (aCGH)". Am. J. Med. Genet. A 149A (7): 1431-7. ... Heard PL, Carter EM, Crandall AC, Sebold C, Hale DE, Cody JD (July 2009). "High resolution genomic analysis of 18q- ...
Seven astroblastoma cases of comparative genomic hybridization, a molecular technique analyzing chromosomal changes in DNA ... "Astroblastoma: Clinicopathologic Features and Chromosomal Abnormalities Defined by Comparative Genomic Hybridization." Brain ... These genomic features are responsible for widespread proliferation, tumorigenesis, and deregulation of pathways associated ...
... can be detected through array comparative genomic hybridization (aCGH). Some symptoms can be managed ...
2006). "Bladder cancer stage and outcome by array-based comparative genomic hybridization". Clin. Cancer Res. 11 (19 Pt 1): ...
"Preimplantation genetic diagnosis and chromosome analysis of blastomeres using comparative genomic hybridization". Hum. Reprod ...
"Diagnostic yield of array comparative genomic hybridization in adults with autism spectrum disorders". Genetics in Medicine. 16 ... "Genomic characterization of primary central nervous system lymphoma". Acta Neuropathologica. 131 (6): 865-875. doi:10.1007/ ...
... using oligo-microarray comparative genomic hybridization (aCGH)". Am. J. Med. Genet. A. 149A (7): 1431-7. doi:10.1002/ajmg.a. ... Heard PL, Carter EM, Crandall AC, Sebold C, Hale DE, Cody JD (July 2009). "High resolution genomic analysis of 18q- ...
"High resolution genomic analysis of 18q- using oligo-microarray comparative genomic hybridization (aCGH)". Am. J. Med. Genet. A ...
Microarray comparative genomic hybridization (array CGH) shows changes in small amounts DNA on chromosomes. Therapy can help ... Techniques used to diagnose this disorder are fluorescence in situ hybridization (FISH) and microarrays. FISH uses fluorescent ...
"Characterization of the Genome Composition of Bartonella koehlerae by Microarray Comparative Genomic Hybridization Profiling". ...
"Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization". Proceedings of the ... at 20q13.2 in tissue samples of human gastric adenocarcinomas by high-resolution microarray comparative genomic hybridization ... c-MYC and ZNF217 gene amplification during breast cancer progression using fluorescence in situ hybridization". Oncology ...
... and amplification of genomic material in rhabdomyosarcoma analyzed by comparative genomic hybridization". Cancer Research. 56 ( ...
CNVs are detected by fluorescence in situ hybridization (FISH) or comparative genomic hybridization (CGH). To detect the ... specific breakpoints at which a deletion occurs, or to detect genomic lesions introduced by a duplication or amplification ...
Genomic balance in Xp22 and Xq26 may also be analyzed through array comparative genomic hybridization. Due to the high ...
A Comparative Genomic Hybridization Study". Modern Pathology. 13 (10): 1092-6. doi:10.1038/modpathol.3880203. PMID 11048803. ... Molecular cytogenetic characterization by use of spectral karyotyping and comparative genomic hybridization". International ...
Comprehensive chromosome analysis methods include array-comparative genomic hybridization (aCGH), quantitative PCR and SNP ... A major drawback of genomic profiling for embryo quality is that the results generally rely on the assessment of a single cell ...
Ethical implications of array comparative genomic hybridization in complex phenotypes: points to consider in research. Genet ... Genomic imprinting models have been proposed; one of their strengths is explaining the high male-to-female ratio in ASD. One ... Comparative analysis of neurological disorders focuses genome-wide search for autism genes. Genomics. 2008;93(2):120-9. doi: ... The comorbidity of autism with the genomic disorders of chromosome 15q11.2-q13. Neurobiol Dis. 2008;38(2):181-91. doi:10.1016/j ...
April 2004). "Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and ... a novel clinically recognisable genetic condition identified by array comparative genomic hybridisation". J. Med. Genet. 46 (9 ... DECIPHER is a web-based resource and database of genomic variation data from analysis of patient DNA. It documents ...
This may be done through karyotyping or comparative genomic hybridization (CGH) to detect chromosomal abnormalities. Sequencing ... Nov 2015). "Integrated genomic characterization of IDH1-mutant glioma malignant progression". Nature Genetics. 48: 59-66. doi: ... The acquisition of mutations is random as a result of increased genomic instability with each successive generation. The long- ... A more common source is genomic instability, which often arises when key regulatory pathways are disrupted in the cells. Some ...
"Comparison of genomic abnormalities between BRCAX and sporadic breast cancers studied by comparative genomic hybridization". ...
Other chip-based methods such as comparative genomic hybridization can detect genomic gains or deletions leading to LOH. SNP ... A detection system that records and interprets the hybridization signal.. The ASO probes are often chosen based on sequencing ... These are the convergence of DNA hybridization, fluorescence microscopy, and solid surface DNA capture. The three mandatory ... "Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations". Genome Biology. 17 ( ...
Olshen, A. B.; Venkatraman, E. S. (2002). "Change-point analysis of array-based comparative genomic hybridization data". ... "Array comparative genomic hybridization and its applications in cancer" (PDF). Nature Genetics 37. Páxs. S11-S17.. ... "Comparative Genomics" (PDF). PLoS Biology 1 (2). Páxs. 156-160.. *↑ Eriksen, N. (2003). "Combinatorial methods in comparative ... The Institute for Genomic Research, TIGR, hoxe J. Craig Venter Institute) para secuenciar o primeiro xenoma bacteriano, o de ...
"Customized oligonucleotide array-based comparative genomic hybridization as a clinical assay for genomic profiling of chronic ... such as array comparative genomic hybridization (arrayCGH) and SNP arrays. Conceptually, the arrays are composed of hundreds to ... Some consider all platforms to be a type of array comparative genomic hybridization (arrayCGH), while others reserve that term ... The main methods used for creating virtual karyotypes are array-comparative genomic hybridization and SNP arrays. A karyotype ( ...
Anderson, Richard L. (2004). Calliope's Sisters: A Comparative Study of Philosophies of Art. 2nd edition. Pearson. ... Hybridization with the subspecies that evolved southwestwards of its range, S. c. massaicus, has apparently been prevented from ... Baker, A. J.; Haddrath, O.; McPherson, J. D.; Cloutier, A. (2014). "Genomic Support for a Moa-Tinamou Clade and Adaptive ... Marshall, Alan John (1960). Biology and Comparative Physiology of Birds. Academic Press. p. 446.. ...
Array-based comparative genomic hybridization (aCGH) tracks chromosome deletions and or amplifications using fluorescent dyes ... PMC 1867615 . Peng, H.H., & Van den Veyyer, I.B. "HOW DOES ARRAY-BASED COMPARATIVE GENOMIC HYBRIDIZATION WORK?", 2008 N/A, " ... FISH is a screening test that uses multicolour probes or comparative genomic hybridization to find any chromosome ... fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA), array comparative genomic ...
... and profiling genomes using comparative genomic hybridization. Breast carcinomas display two classes of genomic structural ... We therefore developed a method to quantify genomic copy number in single cells using next-generation sequencing. This method, ... SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, ...
We report clinical, cytogenetic, and comparative genomic hybridization findings for three siblings with an unbalanced 4q;16q ... N2 - We report clinical, cytogenetic, and comparative genomic hybridization findings for three siblings with an unbalanced 4q; ... AB - We report clinical, cytogenetic, and comparative genomic hybridization findings for three siblings with an unbalanced 4q; ... abstract = "We report clinical, cytogenetic, and comparative genomic hybridization findings for three siblings with an ...
However, the hybridization pattern for GGA 4 in A. roseicollis and M. undulatus is in sharp contrast to the most common pattern ... However, their genome organization, evolution and genomic relation with other birds are poorly understood. Chromosome painting ... In contrast, the smaller GGA macrochromosomes 6, 7 and 8 displayed a complex hybridization pattern: two or three of these ... Chromosome repatterning in three representative parrots (Psittaciformes) inferred from comparative chromosome painting ...
Array comparative genomic hybridization (also microarray-based comparative genomic hybridization, matrix CGH, array CGH, aCGH) ... Comparative genomic hybridization. Molecular Pathology 52:243-251. [3] Pinkel D, Albertson DG (2005) Comparative genomic ... based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes, Chromosomes and Cancer 20:399-407. ... Lee CN, Lin SY, Lin CH, Shih JC, Lin TH, Su YN (2012) Clinical utility of array comparative genomic hybridization for prenatal ...
... Lorena Rodrigo,1 ... Comprehensive Chromosome Screening by Array Comparative Genomic Hybridization," BioMed Research International, vol. 2014, ...
Standard array-comparative genomic hybridization experiments, including a simultaneous blind analysis of a set of clinical ... arrays used clinically in comparative genomic hybridization experiments to detect constitutional copy number changes in genomic ... This custom 44K oligo array consists of probes localized to the genomic positions of ,1400 fluorescence in situ hybridization- ... Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A 2004; 101: ...
Novel deletion of RPL15 identified by array-comparative genomic hybridization in Diamond-Blackfan anemia.. Landowski M1, ... Novel deletion of RPL15 identified by array-comparative genomic hybridization in Diamond-Blackfan anemia ... Novel deletion of RPL15 identified by array-comparative genomic hybridization in Diamond-Blackfan anemia ... Novel deletion of RPL15 identified by array-comparative genomic hybridization in Diamond-Blackfan anemia ...
Comparative genomic hybridization study of primary neuroblastoma tumors. United Kingdom Childrens Cancer Study Group.. ... Twenty primary tumors were studied by comparative genomic hybridization (CGH), and abnormalities were found in 19. While these ...
... were analysed by comparative genomic hybridization (CGH), to screen for changes in copy-number of DNA sequences. Chromosomal ... and amplifications of genomic materials in primary gastric cancers analyzed by comparative genomic hybridization. Genes ... Detection and mapping of amplified DNA sequences in breast cancer by comparative genomic hybridization. Proc Natl Acad Sci USA ... Comparative genomic hybridization analysis of human sarcomas: II. Identification of novel amplicons at 6p and 17p in ...
Here, we used comparative genomic hybridization (CGH) to screen for DNA sequence copy number changes along all chromosomes in ... Genetic Changes in Primary and Recurrent Prostate Cancer by Comparative Genomic Hybridization. Tapio Visakorpi, Anne H. ... Genetic Changes in Primary and Recurrent Prostate Cancer by Comparative Genomic Hybridization ... Genetic Changes in Primary and Recurrent Prostate Cancer by Comparative Genomic Hybridization ...
Notes: Sales, means the sales volume of Comparative Genomic Hybridization... ... 119 Pages Report] Check for Discount on United States Comparative Genomic Hybridization Market Report 2016 report by QYResearch ... 2.4.1 Comparative Genomic Hybridization Market Concentration Rate 2.4.2 Comparative Genomic Hybridization Market Share of Top 3 ... 1 Comparative Genomic Hybridization Overview 1.1 Product Overview and Scope of Comparative Genomic Hybridization 1.2 ...
Solinas-Toldo S, Lampel S, Stilgenbauer S, et al Matrix-based comparative genomic hybridization: biochips to screen for genomic ... as analyzed by comparative genomic hybridization and fluorescence in situ hybridization. Genes Chromosomes Cancer, 25: 82-90, ... Array Comparative Genomic Hybridization Analysis of Colorectal Cancer Cell Lines and Primary Carcinomas. Eleanor J. Douglas, ... Array comparative genomic hybridization, with a genome-wide resolution of ∼1 Mb, has been used to investigate copy number ...
New Genes Involved in Molecular Etiology of Rett Syndrome Through DNA Microarray Comparative Genomic Hybridization (RETT). The ... Search for New Genes Involved in Molecular Etiology of Rett Syndrome Through Comparative Genomic Hybridization on DNA ... Search for pathogenic chromosomal imbalance through comparative genomic hybridization (aCGH) on DNA microarrays will be done in ... Analysis of chromosomal imbalances through comparative genomic hybridization on DNA microarrays [ Time Frame: up to 12 months ] ...
Comparative genomic hybridizations indicated distinct lineages for each subspecies where the closest genomic relatedness ... Comparative genomic hybridization of M. avium subspecies by use of DNA microarrays. A) PCR confirmation of the identity of the ... Whole-Genome Plasticity among Mycobacterium avium Subspecies: Insights from Comparative Genomic Hybridizations. Chia-wei Wu, ... Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from ...
... comparative genomic hybridization explanation free. What is comparative genomic hybridization? Meaning of comparative genomic ... hybridization medical term. What does comparative genomic hybridization mean? ... Looking for online definition of comparative genomic hybridization in the Medical Dictionary? ... comparative genomic hybridization. Also found in: Acronyms, Encyclopedia, Wikipedia. comparative genomic hybridization. a ...
Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the ... Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants. doi: 10.3791/51718 Published ... Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants. J. Vis. Exp. (96), e51718, ... Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants. J. Vis. Exp. (96), e51718, ...
Array comparative genomic hybridization (array CGH) has been applied to study copy number alterations and genomic imbalances ... Rabin KR,Man TK,Yu A,Folsom MR,Zhao YJ,Rao PH,Plon SE,Naeem RC,Clinical utility of array comparative genomic hybridization for ... Dawson A,Yanofsky R,Vallente R,Bal S,Schroedter I,Liang L,Mai S,Array comparative genomic hybridization and cytogenetic ... A high resolution 244K array-based Comparative Genomic Hybridization (array-CGH) was used to study eleven ETV6/RUNX1-positive ...
Validation of array comparative genomic hybridization FISH and chromosome comparative genomic hybridization. Brain tumor cell ... Comparing chromosome comparative genomic hybridization and array comparative genomic hybridization. Chromosome CGH was done as ... Chromosome comparative genomic hybridization and array comparative genomic hybridization comparisons.Table 2 compares CNAs ... Array Comparative Genomic Hybridization Identifies Genetic Subgroups in Grade 4 Human Astrocytoma. Anjan Misra, Malgorzata ...
The input strain DNA was then compared with the selected strains using comparative DNA hybridization (CGH) on an E. coli ... The input strain DNA was then compared with the selected strains using comparative DNA hybridization (CGH) on an E. coli ... This study aimed to identify genomic regions of EHEC O157:H7 that contribute to colonization and multiplication at this site. A ... To verify the library, clones containing a complete locus of enterocyte effacement (LEE) were identified by DNA hybridization. ...
Genomic alterations in sporadic synchronous primary breast cancer using array and metaphase comparative genomic hybridization. ... Comparative genomic hybridisation as a supportive tool in diagnostic pathology. J Clin Pathol 2003;56:522-7. ... Genetic alterations in lobular breast cancer by comparative genomic hybridization. Int J Cancer 1997;74:513-7. ... Genetic changes in bilateral breast cancer by comparative genomic hybridisation. Clin Exp Med 2007;7:1-5. ...
... comparative genomic hybridization (CGH) and array-based CGH have described secondary genomic alterations in BL.6-13 One of the ... Comparative genomic hybridization. CGH was performed using a commercially available CGH kit provided by Vysis (Downers Grove, ... 2006) Combined spectral karyotyping, comparative genomic hybridization, and in vitro apoptyping of a panel of Burkitts ... Chromosomal alterations detected by comparative genomic hybridization in subgroups of gene expression-defined Burkitts ...
Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants. J. Vis. Exp. (96), e51718, ... Ahn, J. W., et al. Validation and implementation of array comparative genomic hybridisation as a first line test in place of ...
Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray ... On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem ... via heterologous hybridization). Our results showed that the current microarray platform for A. palmata is able to provide ... The hybridization of gDNA to a cDNA microarray is an example of a comparative genomic hybridization (CGH). In this case gDNA ...
We used microarray-based comparative genomic hybridization to explore genome-wide profiles of chromosomal aberrations in 26 ... in head and neck squamous cell carcinomas in Norwegian and Sudanese populations by array comparative genomic hybridization. * ... in head and neck squamous cell carcinomas in Norwegian and Sudanese populations by array comparative genomic hybridization. ... in head and neck squamous cell carcinomas in Norwegian and Sudanese populations by array comparative genomic hybridization. ...
  • SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization. (suny.edu)
  • Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. (suny.edu)
  • We report clinical, cytogenetic, and comparative genomic hybridization findings for three siblings with an unbalanced 4q;16q translocation, minor malformations, and cognitive abnormalities, including childhood apraxia of speech, a rare, severe motor speech disorder. (elsevier.com)
  • We therefore developed a method to quantify genomic copy number in single cells using next-generation sequencing. (suny.edu)
  • ArrayCGH data have been deposited in the Database of Genomic Variants (accession ID estd228) and the DECIPHER database ( decipher.sanger.ac.uk ). (plos.org)
  • As only a relatively small proportion of the CNV regions overlap with regions found in other studies, the current total of more than 6,000 CNVs detailed in the Database of Genomic Variants ( http://projects.tcag.ca/variation/ ) is most likely an underestimate. (pubmedcentralcanada.ca)
  • Comparative genomic hybridization and high-resolution single nucleotide polymorphism (SNP) array profiling showed that gains/amplifications of the BCL2 gene locus in 18q were restricted to the t(14;18)-positive FL subgroup. (bloodjournal.org)
  • A total of 121 metaphase II oocytes and their corresponding first polar bodies (PB) were analysed with the use of a comprehensive cytogenetic method, comparative genomic hybridization (CGH). (ox.ac.uk)
  • This platform can be used in conjunction with conventional karyotyping and will provide rapid and accurate diagnoses for the targeted genomic regions while eliminating the need to interpret clinically-uncertain genomic regions. (biomedcentral.com)
  • 3: Key words: aneuploidy, comparative genomic hybridization, PGD, blastocyst INTRODUCTION Chromosomal aneuploidy is a recognised significant contributing factor in spontaneous miscarriages with approximately two thirds of miscarriages being due to aneuploidy . (docplayer.net)
  • paratuberculosis isolates, those from wildlife animals displayed the highest level of genomic rearrangements that were not observed in other isolates. (asm.org)
  • DNA rearrangements are responsible for genomic diversity in microbial systems and usually contribute to the fitness of a pathogen in specific microenvironments ( 24 ). (asm.org)
  • Using comparative genomic hybridizations, we examined several isolates belonging to the MAC group to better understand the changes responsible for adaptation to different microenvironments and to identify possible genomic rearrangements that could explain their divergent phenotypes. (asm.org)
  • There follows a cleanup step to remove unincorporated nucleotides before the labeled DNAs are mixed and resuspended in a hybridization buffer and applied to an array comprising ~60,000 oligonucleotide probes from loci across the genome, with high probe density in clinically important areas. (jove.com)
  • The aim of the project was to detect genomic regions that were normal, duplicated or deleted in these cell lines for transcription factors NFKBp50, NFkBp65, HIF1a and FAS gene which we studied. (datamed.org)
  • This approach involves the isolation and enumeration of short sequence tags from specific genomic loci. (pnas.org)
  • This study aimed to identify genomic regions of EHEC O157:H7 that contribute to colonization and multiplication at this site. (frontiersin.org)