Results 21 to 30 of about 215,208 (174)

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Nature Communications, 2020
With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes
Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. Simpson, Mark B. Gerstein, Li Ding, PCAWG Consortium   +20 more
doaj   +1 more source

Novel genotyping algorithms for rare variants significantly improve the accuracy of Applied Biosystems™ Axiom™ array genotyping calls: Retrospective evaluation of UK Biobank array data.

PLoS ONE, 2022
The UK Biobank genotyped about 500k participants using Applied Biosystems Axiom microarrays. Participants were subsequently sequenced by the UK Biobank Exome Sequencing Consortium. Axiom genotyping was highly accurate in comparison to sequencing results,
Orna Mizrahi-Man, Marcos H Woehrmann, Teresa A Webster, Jeremy Gollub, Adrian Bivol, Sara M Keeble, Katherine H Aull, Anuradha Mittal, Alan H Roter, Brant A Wong, Jeanette P Schmidt   +10 more
doaj   +1 more source

TrAp: a Tree Approach for Fingerprinting Subclonal Tumor Composition [PDF]

Nucl. Acids Res. 41 (2013) e165, 2013
Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide an overview of an aggregate of numerous cells, rather than subclonal-specific quantification of aberrations such as single ...
arxiv   +1 more source

Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation

Nature Communications, 2023
The short lengths of short-read sequencing reads challenge the analysis of paralogous genomic regions in exome and genome sequencing data. Most genetic variants within these homologous regions therefore remain unidentified in standard analyses.
Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen   +12 more
doaj   +1 more source

Detecting somatic mutations in genomic sequences by means of Kolmogorov-Arnold analysis [PDF]

Royal Society Open Science, 2, 150143, 2015, 2015
The Kolmogorov-Arnold stochasticity parameter technique is applied for the first time to the study of cancer genome sequencing, to reveal mutations. Using data generated by next generation sequencing technologies, we have analyzed the exome sequences of brain tumor patients with matched tumor and normal blood.
arxiv   +1 more source

Whole Exome Sequencing Identifies Novel Genetic Alterations in Patients with Pheochromocytoma/Paraganglioma [PDF]

Endocrinology and Metabolism, 2020
Background Pheochromocytoma and paragangliomas (PPGL) are known as tumors with the highest level of heritability, approximately 30% of all cases. Clinical practice guidelines of PPGL recommend genetic testing for germline variants in all patients.
Soo Hyun Seo, Jung Hee Kim, Man Jin Kim, Sung Im Cho, Su Jin Kim, Hyein Kang, Chan Soo Shin, Sung Sup Park, Kyu Eun Lee, Moon-Woo Seong   +9 more
doaj   +1 more source

Effect of Next-Generation Exome Sequencing Depth for Discovery of Diagnostic Variants [PDF]

Genomics & Informatics, 2015
Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields ...
Kyung Kim, Moon-Woo Seong, Won-Hyong Chung, Sung Sup Park, Sangseob Leem, Won Park, Jihyun Kim, KiYoung Lee, Rae Woong Park, Namshin Kim   +9 more
doaj   +1 more source

Genotype–Phenotype Correlations of Dystrophic Epidermolysis Bullosa in India: Experience from a Tertiary Care Centre

Acta Dermato-Venereologica, 2018
Recent advances in the field of genomics have seen the successful implementation of whole exome sequencing as a rapid and efficient diagnostic strategy in several genodermatoses.
Vamsi K. Yenamandra, Shamsudheen K. Vellarikkal, Madhumita R. Chowdhury, Rijith Jayarajan, Ankit Verma, Vinod Scaria, Sridhar Sivasubbu, Subrata Basu Ray, Amit K. Dinda, Madhulika Kabra, Vinod K. Sharma, Gomathy Sethuraman   +11 more
doaj   +1 more source

Identification of Two Cases of Ciliopathy-Associated Diabetes and Their Mutation Analysis Using Whole Exome Sequencing [PDF]

Diabetes & Metabolism Journal, 2015
BackgroundAlström syndrome and Bardet-Biedl syndrome are autosomal recessively inherited ciliopathies with common characteristics of obesity, diabetes, and blindness.
Min Kyeong Kim, Soo Heon Kwak, Shinae Kang, Hye Seung Jung, Young Min Cho, Seong Yeon Kim, Kyong Soo Park   +6 more
doaj   +1 more source

In Silico Derivation of HLA-Specific Alloreactivity Potential from Whole Exome Sequencing of Stem Cell Transplant Donors and Recipients: Understanding the Quantitative Immuno-biology of Allogeneic Transplantation [PDF]

Frontiers in Immunology 2014. 5:529, 2014
Donor T cell mediated graft vs. host effects may result from the aggregate alloreactivity to minor histocompatibility antigens (mHA) presented by the HLA in each donor-recipient pair (DRP) undergoing stem cell transplantation (SCT). Whole exome sequencing has demonstrated extensive nucleotide sequence variation in HLA-matched DRP. Non-synonymous single
arxiv   +1 more source