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  • 2001
  • 2001) showing near total congruence of mtDNA-based and nuclear-based trees when such sequences were excluded, some authors continued to produce misleading trees (Arnason et al. (wikipedia.org)
  • 2001). "Prediction of the coding sequences of unidentified human genes. (wikipedia.org)
  • tumor
  • Also discussed are important recent diagnostic applications of DNA sequencing in cancer, including analysis of tumor derived cell free DNA and exosomes that are present in body fluids. (frontiersin.org)
  • Sequencing Analysis of Tumor DNA: Is It All in the Plasma? (ascopost.com)
  • Circulating tumor DNA (ctDNA) in plasma comprises a fraction of cfDNA, and is believed to be shed in the bloodstream by cancer cells through apoptosis, necroptosis, or secretion (eg, exosomes) not only from the primary tumor, but also metastatic lesions and minimal residual disease. (ascopost.com)
  • As the amount of ctDNA in cfDNA varies (and is often low in patients with low tumor burden), de novo discovery of mutations by plasma DNA analysis is not trivial. (ascopost.com)
  • In fact, there is evidence to suggest that these techniques may be useful for disease monitoring in cases where the primary tumor has been previously subjected to sequencing or for patients with tumor types characterized by the presence of highly recurrent mutations, as well as for the identification of emerging mutations already known to result in therapy resistance. (ascopost.com)
  • Whether sequencing of ctDNA will render tumor biopsies redundant remains to be determined, particularly because of the strong association between ctDNA yield and disease burden and the technologic and bioinformatic developments required for de novo discovery of mutations based solely on ctDNA analysis. (ascopost.com)
  • loci
  • In particular, the invention relates to analysis of defined CpG loci that are coordinately methylated in DNAs from cancer and adenoma samples, methods for identifying coordinately methylated loci, and methods of using analysis of coordinately methylated loci in one or more marker regions in the design of assays for adenoma and cancer. (patentsencyclopedia.com)
  • 6. The method of claim 1, wherein said determining the methylation status of said defined set of CpG loci comprises treating DNA from said samples with bisulfite. (patentsencyclopedia.com)
  • 7. The method of claim 1, wherein said determining the methylation status of said defined set of CpG loci comprises digital analysis of each of a plurality of CpG loci in a plurality of individual copies of a marker nucleic acid. (patentsencyclopedia.com)
  • 12. The method of claim 10, wherein said determining comprises analysis of said CpG loci in a nucleic acid detection assay configured to determine the methylation status of each of said loci in a single nucleic acid detection assay. (patentsencyclopedia.com)
  • Synthesizer
  • Caruthers and Leroy Hood at the California Institute of Technology constructed the first automated DNA Synthesizer which the MBCF successfully tested after discussions with Don Taylor. (wikipedia.org)
  • Molecular
  • Molecular analysis of the patient isolate allowed the classification of the strain to B. lusitaniae, a genospecies previously thought to be nonpathogenic in humans The woman had a weak serological response, which is present in a high percentage of patients with unspecific and long-lasting skin manifestations. (wikipedia.org)
  • BPC) The Molecular Biology Core Facilities has had a continuous web presence since 1992 and began receiving primer sequence for high throughput DNA synthesis by web forms in 1995 when new high volume DNA synthesizers were brought on-line. (wikipedia.org)
  • detection
  • The sequencing techniques currently available for the detection of known or "hotspot" mutations, however, offer incredibly high levels of sensitivity. (ascopost.com)
  • 14. The method of claim 10, wherein said nucleic acid detection assay comprises at least one assay selected from the group consisting of a primer extension assay, a nucleic acid amplification assay, a nucleic acid sequencing assay, a structure-specific cleavage assay, 5' nuclease cleavage assay, an invasive cleavage assay, and a ligation assay. (patentsencyclopedia.com)
  • synthetic
  • Typically, synthetic oligonucleotides are single-stranded DNA or RNA molecules around 15-25 bases in length. (wikipedia.org)
  • synthesis
  • It appears that most spontaneously arising mutations result from error prone replication (trans-lesion synthesis) past a DNA damage in the template strand. (wikipedia.org)
  • bacteria
  • The sequence data were finally used for scanning data libraries containing the corresponding sequences of present-day bacteria, to infer the putative ecophysiology of the ancient ones. (calpoly.edu)
  • microarray
  • And, for those experiments where you are looking for concordance between your RNA-Seq and Microarray data, shouldn't you have the concordance in your analysis software as well? (genecodes.com)
  • next-gen
  • An Illumina MiSeq was evaluated on multiple projects and now a series of three MiSeqs have been streamlined for fast analysis of Next Gen samples. (wikipedia.org)
  • software
  • I ran enrichment analysis side by side with the PRO and Basic versions of the software with the exact same input dataset and parameters. (omictools.com)
  • human
  • In addition, the Human Genome Project facilitated the development of technologies for high throughput sequencing of DNA and enhanced methods for DNA sequence analysis. (frontiersin.org)
  • Capabilities for characterizing human DNA sequence variations, including sequence variations that led to human diseases were thus facilitated. (frontiersin.org)
  • The results are discussed in light of what is known about the preservation of microbial DNA at the Iceman's site and of previous parasitological studies performed on the Iceman himself and on human coprolites. (calpoly.edu)
  • Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. (sciencemag.org)
  • The automated DNA sequencer was an enabling technology for the Human Genome Project. (wikipedia.org)
  • mutations
  • DNA sequence information gathered from healthy and diseased tissues is highly valuable in the medical field as mutations can be identified, individualized medical care can be administered, and organisms identified and cataloged. (wikipedia.org)
  • However, some DNA damages remain and give rise to mutations. (wikipedia.org)
  • Thus it seems that DNA damages are the underlying cause of most spontaneous mutations, either because of error-prone replication past damages or error-prone repair of damages. (wikipedia.org)
  • search
  • By consequence, many computational biologists have intensified studies in order to understand the content of these sequences and, in some cases, to search for association to disease. (springer.com)
  • results
  • Had I not done the side-by-side analysis I easily could have tried to publish false results showing that there were no significantly enriched GO categories in my dataset, and I never would have known otherwise. (omictools.com)
  • multiple
  • Despite multiple papers pointing out that some mitochondrial sequences showed unusual properties (particularly murid rodents and hedgehogs) and were likely distorting the overall tree (Sullivan and Swofford 1997, Waddell et al. (wikipedia.org)
  • cell free
  • Although the presence of circulating DNA in plasma has long been known, circulating cell-free plasma DNA (cfDNA) is detected in normal individuals, and its measure is of limited utility in oncology. (ascopost.com)
  • initial analysis
  • This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics. (sciencemag.org)
  • proteins
  • Phage display is a laboratory technique for the study of protein-protein, protein-peptide, and protein-DNA interactions that uses bacteriophages (viruses that infect bacteria) to connect proteins with the genetic information that encodes them. (wikipedia.org)
  • These displaying phages can then be screened against other proteins, peptides or DNA sequences, in order to detect interaction between the displayed protein and those other molecules. (wikipedia.org)
  • Phage eluted in the final step can be used to infect a suitable bacterial host, from which the phagemids can be collected and the relevant DNA sequence excised and sequenced to identify the relevant, interacting proteins or protein fragments. (wikipedia.org)
  • For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three-dimensional arrangement of amino acids which may not be adjacent. (wikipedia.org)
  • Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
  • For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. (wikipedia.org)
  • Later in the 2000's, post-genomic research in his laboratory established signature proteins in halophilic Archaea, and the function of many genes and genetic elements, including multiple replication origins, general transcription factors, and DNA repair systems. (wikipedia.org)
  • These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. (wikipedia.org)
  • species
  • Drosophila sechellia has significantly distinct mitochondrial DNA, further emphasizing the evolutionary differences between the three species. (wikipedia.org)
  • nuclear
  • Phylogenetic studies in the Commelinaceae subfamily Commelinoideae inferred from nuclear ribosomal and chloroplast DNA sequences. (wikipedia.org)
  • Bulbeck (2013) likewise noted that the Andamanese's nuclear DNA clusters with that of other Andamanese Islanders, as they carry Haplogroup D-M174 and maternal mitochondrial Haplogroup M unique to their own. (wikipedia.org)
  • mechanism
  • Applications of phage display technology include determination of interaction partners of a protein (which would be used as the immobilised phage "bait" with a DNA library consisting of all coding sequences of a cell, tissue or organism) so that the function or the mechanism of the function of that protein may be determined. (wikipedia.org)
  • To compensate, they have evolved a sophisticated DNA repair mechanism. (wikipedia.org)
  • methods
  • Sequenom is the exclusive licensee of U.S. Patent No. 6,258,540, which claims methods of using cell-free fetal DNA (cffDNA) circulating in maternal plasma (cell-free blood) to diagnose fetal abnormalities. (wikipedia.org)
  • The point of the invention is that the inventors discovered in 1996 that fetal DNA might be floating around in the mother's blood (not just in the blood of the fetus, which was accessible only by invasive methods, such as amniocentesis , that created risks of miscarriage). (wikipedia.org)
  • interaction
  • The study of this interaction has been dominated by the analysis of artifacts such as carnelian beads and marine shell, along with limited textual evidence. (blogspot.com)
  • primer
  • These DNA primer pairs were designed by prioritizing the gene regions most commonly found in transcript variants. (bio-rad.com)
  • protein
  • In the case of M13 filamentous phage display, the DNA encoding the protein or peptide of interest is ligated into the pIII or pVIII gene, encoding either the minor or major coat protein, respectively. (wikipedia.org)
  • If a "phagemid" vector is used (a simplified display construct vector) phage particles will not be released from the E. coli cells until they are infected with helper phage, which enables packaging of the phage DNA and assembly of the mature virions with the relevant protein fragment as part of their outer coat on either the minor (pIII) or major (pVIII) coat protein. (wikipedia.org)
  • By immobilizing a relevant DNA or protein target(s) to the surface of a microtiter plate well, a phage that displays a protein that binds to one of those targets on its surface will remain while others are removed by washing. (wikipedia.org)
  • The technique is also used to determine tumour antigens (for use in diagnosis and therapeutic targeting) and in searching for protein-DNA interactions using specially-constructed DNA libraries with randomised segments. (wikipedia.org)
  • formation
  • Their age at the moment of death has been determined in both cases on the basis of multi-feature analysis of changes occurring in formation of particular morphologic features of skeleton and teeth. (blogspot.com)
  • cell
  • Cell routine evaluation After removal of methanol, cells had been treated having a Coulter DNA-Prep reagent package (Beckman-Coulter, France). (cancercurehere.com)
  • The primary role of bacterioruberin in the cell is to protect against DNA damage incurred by UV light. (wikipedia.org)
  • identify
  • Then, they could reliably identify fetal DNA, which would in turn allow them to diagnose certain fetal genetic conditions such as Down Syndrome , which can be detected by observing presence of extra chromosomes. (wikipedia.org)
  • Accurate
  • Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
  • repair
  • This allows H. salinarum to repair damage to DNA faster and more efficiently than other organisms and allows them to be much more UV tolerant. (wikipedia.org)
  • example
  • It appears that dots represent identity with the reference sequence, so for example M201 has a dot for skeleton 1 which indicates a T at position 15,027,529 (GRCh37) which is the position where this mutation has occurred. (blogspot.com)
  • conditions
  • H. salinarum is polyploid and highly resistant to ionizing radiation and desiccation, conditions that induce DNA double-strand breaks. (wikipedia.org)
  • high
  • Analysis of morphological characters in Commelinaceae indicate Geogenanthus is closely related to Dichoriscantieae and Siderasis, but Geogenanthus is placed as the sister to Dichoriscantieae and Siderasis in the cladogram from the combined morphology and sequence analysis, with high bootstrap value supporting the placement. (wikipedia.org)
  • potential
  • Ancient DNA has the potential of resolving this issue, because if L3*(xM, N) in Eurasia is really recent (e.g., associated with Islamic/Arab dispersals spanning Africa and Eurasia), then it ought to be missing from the earliest genetic layers. (blogspot.com)
  • rather
  • Then they realized that they could selectively amplify the fetal DNA by focusing on the paternally inherited portion of its DNA (rather than the maternally inherited DNA). (wikipedia.org)
  • Bacterioruberin protects the DNA by acting as an antioxidant, rather than directly blocking UV light. (wikipedia.org)
  • sample
  • The claim itself has two simple and conventional steps: first amplifying (by polymerase chain reaction , PCR) and then detecting the paternally inherited DNA from the plasma sample. (wikipedia.org)
  • There was a problem, however, of how to ascertain which DNA in the sample was that of the fetus and which was the mother's (which greatly outnumbered the fetal DNA in the sample). (wikipedia.org)
  • elements
  • The fundamental idea behind all these notations is the matching principle, which assigns a meaning to a sequence of elements of the pattern notation: a sequence of elements of the pattern notation matches a sequence of amino acids if and only if the latter sequence can be partitioned into subsequences in such a way that each pattern element matches the corresponding subsequence in turn. (wikipedia.org)
  • shown
  • Through the analysis of cytoplasmic incompatibility and similar mitochondrial DNA, it has been shown that D. simulans and D. mauritiana are more closely related to each other than to D. sechellia. (wikipedia.org)
  • known
  • The phage gene and insert DNA hybrid is then inserted (a process known as "transduction") into Escherichia coli (E. coli) bacterial cells such as TG1, SS320, ER2738, or XL1-Blue E. coli. (wikipedia.org)
  • individuals
  • Based on this distribution of values, it would appear from our preliminary analysis that almost half of the individuals sampled from the Harappa cemetery have isotope values outside the local baseline (0.7158-0.7189). (blogspot.com)