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variant calling exome

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https://www.readbyqxmd.com/read/28742119/doestrare-a-statistical-test-to-identify-local-enrichments-in-rare-genomic-variants-associated-with-disease
#1
Elodie Persyn, Matilde Karakachoff, Solena Le Scouarnec, Camille Le Clézio, Dominique Campion, French Exome Consortium, Jean-Jacques Schott, Richard Redon, Lise Bellanger, Christian Dina
Next-generation sequencing technologies made it possible to assay the effect of rare variants on complex diseases. As an extension of the "common disease-common variant" paradigm, rare variant studies are necessary to get a more complete insight into the genetic architecture of human traits. Association studies of these rare variations show new challenges in terms of statistical analysis. Due to their low frequency, rare variants must be tested by groups. This approach is then hindered by the fact that an unknown proportion of the variants could be neutral...
2017: PloS One
https://www.readbyqxmd.com/read/28742110/evaluation-of-exome-variants-using-the-ion-proton-platform-to-sequence-error-prone-regions
#2
Heewon Seo, Yoomi Park, Byung Joo Min, Myung Eui Seo, Ju Han Kim
The Ion Proton sequencer from Thermo Fisher accurately determines sequence variants from target regions with a rapid turnaround time at a low cost. However, misleading variant-calling errors can occur. We performed a systematic evaluation and manual curation of read-level alignments for the 675 ultrarare variants reported by the Ion Proton sequencer from 27 whole-exome sequencing data but that are not present in either the 1000 Genomes Project and the Exome Aggregation Consortium. We classified positive variant calls into 393 highly likely false positives, 126 likely false positives, and 156 likely true positives, which comprised 58...
2017: PloS One
https://www.readbyqxmd.com/read/28736571/evaluation-of-quality-assessment-protocols-for-high-throughput-genome-resequencing-data
#3
REVIEW
Matteo Chiara, Giulio Pavesi
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28722338/hdr-del-a-tool-based-on-hamming-distance-for-prioritizing-pathogenic-chromosomal-deletions-in-exome-sequencing
#4
Atsuko Imai, Masakazu Kohda, Kaori Kobayashi, Tomoko Hirata, Yasushi Sakata, Kei Murayama, Akira Ohtake, Yasushi Okazaki, Akihiro Nakaya, Jurg Ott
High-density oligonucleotide arrays have been widely used to detect pathogenic chromosomal deletions. In addition to high-density oligonucleotide arrays, programs using whole exome sequencing have become available for estimating copy number variations using depth of coverage. Here we propose a new statistical method, HDR-del, to prioritize pathogenic chromosomal deletions based on Hamming distance in exome sequencing. In vcf (Variant Call Format) files generated from exome sequencing, hemizygous chromosomal deletion regions lack heterozygous variants and lead to apparent long runs of homozygosity (ROH)...
July 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28708303/using-medical-exome-sequencing-to-identify-the-causes-of-neurodevelopmental-disorders-experience-of-two-clinical-units-and-216-patients
#5
E Chérot, B Keren, C Dubourg, W Carré, M Fradin, A Lavillaureix, A Afenjar, L Burglen, S Whalen, P Charles, I Marey, S Heide, A Jacquette, D Heron, D Doummar, D Rodriguez, Thierry Billette de Villemeur, M-L Moutard, A Guët, J Xavier, D Périsse, D Cohen, F Demurger, C Quélin, C Depienne, S Odent, C Nava, V David, L Pasquier, C Mignot
Though whole exome sequencing is the gold standard for the diagnosis of neurodevelopmental disorders, it remains expensive for some genetic centers. Commercialized panels comprising all OMIM-referenced genes called "medical exome" constitute an alternative strategy to whole exome sequencing, but its efficiency is poorly known. In this study, we report the experience of two clinical genetic centers using medical exome for diagnosis of neurodevelopmental disorders. We recruited 216 consecutive index patients with neurodevelopmental disorders in two French genetic centers, corresponded to the daily practice of the units and included non-syndromic intellectual disability (n=33), syndromic intellectual disability (n=122), pediatric neurodegenerative disorders (n=7) and autism spectrum disorder (n=54)...
July 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28688840/impact-of-clinical-exomes-in-neurodevelopmental-and-neurometabolic-disorders
#6
Christina Evers, Christian Staufner, Martin Granzow, Nagarajan Paramasivam, Katrin Hinderhofer, Lilian Kaufmann, Christine Fischer, Christian Thiel, Thomas Opladen, Urania Kotzaeridou, Stefan Wiemann, Matthias Schlesner, Roland Eils, Stefan Kölker, Claus R Bartram, Georg F Hoffmann, Ute Moog
Whole exome sequencing (WES) is well established in research and is now being introduced into clinically indicated diagnostics (so-called clinical exomes). We evaluated the diagnostic yield and clinical implications of WES in 72 patients from 60 families with undiagnosed neurodevelopmental disorders (NDD), neurometabolic disorders, and dystonias. Pathogenic or likely pathogenic variants leading to a molecular diagnosis could be identified in 21 of the 60 families (overall 35%, in 36% of patients with NDD, in 43% of patients with neurometabolic disorders, in 25% of patients with dystonias)...
June 30, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28659176/isown-accurate-somatic-mutation-identification-in-the-absence-of-normal-tissue-controls
#7
Irina Kalatskaya, Quang M Trinh, Melanie Spears, John D McPherson, John M S Bartlett, Lincoln Stein
BACKGROUND: A key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a variety of common scenarios in which matched normal tissue is not available for comparison. RESULTS: In this work, we describe an algorithm to distinguish somatic single nucleotide variants (SNVs) in next-generation sequencing data from germline polymorphisms in the absence of normal samples using a machine learning approach...
June 29, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#8
Ruibang Luo, Michael C Schatz, Steven L Salzberg
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy for calling indels as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT...
June 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28594829/mendel-md-a-user-friendly-open-source-web-tool-for-analyzing-wes-and-wgs-in-the-diagnosis-of-patients-with-mendelian-disorders
#9
Raony G C C L Cardenas, Natália D Linhares, Raquel L Ferreira, Sérgio D J Pena
Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28589114/unexpected-findings-in-a-child-with-atypical-hemolytic-uremic-syndrome-an-example-of-how-genomics-is-changing-the-clinical-diagnostic-paradigm
#10
Eleanor G Seaby, Rodney D Gilbert, Gaia Andreoletti, Reuben J Pengelly, Catherine Mercer, David Hunt, Sarah Ennis
CBL is a tumor suppressor gene on chromosome 11 encoding a multivalent adaptor protein with E3 ubiquitin ligase activity. Germline CBL mutations are dominant. Pathogenic de novo mutations result in a phenotype that overlaps Noonan syndrome (1). Some patients with CBL mutations go on to develop juvenile myelomonocytic leukemia (JMML), an aggressive malignancy that usually necessitates bone marrow transplantation. Using whole exome sequencing methods, we identified a known mutation in CBL in a 4-year-old Caucasian boy with atypical hemolytic uremic syndrome, moyamoya phenomenon, and dysmorphology consistent with a mild Noonan-like phenotype...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/28586236/inspecting-targeted-deep-sequencing-of-whole-genome-amplified-dna-versus-fresh-dna-for-somatic-mutation-detection-a-genetic-study-in-myelodysplastic-syndrome-patients
#11
Laura Palomo, Francisco Fuster-Tormo, Daniel Alvira, Vera Ademà, María Pilar Armengol, Paula Gómez-Marzo, Nuri de Haro, Mar Mallo, Blanca Xicoy, Lurdes Zamora, Francesc Solé
Whole genome amplification (WGA) has become an invaluable method for preserving limited samples of precious stock material and has been used during the past years as an alternative tool to increase the amount of DNA before library preparation for next-generation sequencing. Myelodysplastic syndromes (MDS) are a group of clonal hematopoietic stem cell disorders characterized by presenting somatic mutations in several myeloid-related genes. In this work, targeted deep sequencing has been performed on four paired fresh DNA and WGA DNA samples from bone marrow of MDS patients, to assess the feasibility of using WGA DNA for detecting somatic mutations...
June 6, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28566479/targeted-exome-sequencing-identifies-pbx1-as-involved-in-monogenic-congenital-anomalies-of-the-kidney-and-urinary-tract
#12
Laurence Heidet, Vincent Morinière, Charline Henry, Lara De Tomasi, Madeline Louise Reilly, Camille Humbert, Olivier Alibeu, Cécile Fourrage, Christine Bole-Feysot, Patrick Nitschké, Frédéric Tores, Marc Bras, Marc Jeanpierre, Christine Pietrement, Dominique Gaillard, Marie Gonzales, Robert Novo, Elise Schaefer, Joëlle Roume, Jelena Martinovic, Valérie Malan, Rémi Salomon, Sophie Saunier, Corinne Antignac, Cécile Jeanpierre
Congenital anomalies of the kidney and urinary tract (CAKUT) occur in three to six of 1000 live births, represent about 20% of the prenatally detected anomalies, and constitute the main cause of CKD in children. These disorders are phenotypically and genetically heterogeneous. Monogenic causes of CAKUT in humans and mice have been identified. However, despite high-throughput sequencing studies, the cause of the disease remains unknown in most patients, and several studies support more complex inheritance and the role of environmental factors and/or epigenetics in the pathophysiology of CAKUT...
May 31, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28552987/contribution-of-systemic-and-somatic-factors-to-clinical-response-and-resistance-to-pd-l1-blockade-in-urothelial-cancer-an-exploratory-multi-omic-analysis
#13
Alexandra Snyder, Tavi Nathanson, Samuel A Funt, Arun Ahuja, Jacqueline Buros Novik, Matthew D Hellmann, Eliza Chang, Bulent Arman Aksoy, Hikmat Al-Ahmadie, Erik Yusko, Marissa Vignali, Sharon Benzeno, Mariel Boyd, Meredith Moran, Gopa Iyer, Harlan S Robins, Elaine R Mardis, Taha Merghoub, Jeff Hammerbacher, Jonathan E Rosenberg, Dean F Bajorin
BACKGROUND: Inhibition of programmed death-ligand 1 (PD-L1) with atezolizumab can induce durable clinical benefit (DCB) in patients with metastatic urothelial cancers, including complete remissions in patients with chemotherapy refractory disease. Although mutation load and PD-L1 immune cell (IC) staining have been associated with response, they lack sufficient sensitivity and specificity for clinical use. Thus, there is a need to evaluate the peripheral blood immune environment and to conduct detailed analyses of mutation load, predicted neoantigens, and immune cellular infiltration in tumors to enhance our understanding of the biologic underpinnings of response and resistance...
May 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28516087/dna-sequence-analysis-in-clinical-medicine-proceeding-cautiously
#14
REVIEW
Moyra Smith
Delineation of underlying genomic and genetic factors in a specific disease may be valuable in establishing a definitive diagnosis and may guide patient management and counseling. In addition, genetic information may be useful in identification of at risk family members. Gene mapping and initial genome sequencing data enabled the development of microarrays to analyze genomic variants. The goal of this review is to consider different generations of sequencing techniques and their application to exome sequencing and whole genome sequencing and their clinical applications...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28508493/exome-sequencing-reveals-novel-genetic-loci-influencing-obesity-related-traits-in-hispanic-children
#15
Aniko Sabo, Pamela Mishra, Shannon Dugan-Perez, V Saroja Voruganti, Jack W Kent, Divya Kalra, Shelley A Cole, Anthony G Comuzzie, Donna M Muzny, Richard A Gibbs, Nancy F Butte
OBJECTIVE: To perform whole exome sequencing in 928 Hispanic children and identify variants and genes associated with childhood obesity. METHODS: Single-nucleotide variants (SNVs) were identified from Illumina whole exome sequencing data using integrated read mapping, variant calling, and an annotation pipeline (Mercury). Association analyses of 74 obesity-related traits and exonic variants were performed using SeqMeta software. Rare autosomal variants were analyzed using gene-based association analyses, and common autosomal variants were analyzed at the SNV level...
May 16, 2017: Obesity
https://www.readbyqxmd.com/read/28499414/hlascan-genotyping-of-the-hla-region-using-next-generation-sequencing-data
#16
Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung
BACKGROUND: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. RESULTS: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28481730/next-generation-sequencing-reveals-novel-mutations-in-x-linked-intellectual-disability
#17
Babylakshmi Muthusamy, Lakshmi Dhevi N Selvan, Thong T Nguyen, Jesna Manoj, Eric W Stawiski, Bijay S Jaiswal, Weiru Wang, Remya Raja, Vedam Laxmi Ramprasad, Ravi Gupta, Sakthivel Murugan, Jayarama S Kadandale, T S Keshava Prasad, Kavita Reddy, Andrew Peterson, Akhilesh Pandey, Somasekar Seshagiri, Satish Chandra Girimaji, Harsha Gowda
Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next-generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28453708/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#18
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C L Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28420412/intersect-then-combine-approach-improving-the-performance-of-somatic-variant-calling-in-whole-exome-sequencing-data-using-multiple-aligners-and-callers
#19
Maurizio Callari, Stephen-John Sammut, Leticia De Mattos-Arruda, Alejandra Bruna, Oscar M Rueda, Suet-Feung Chin, Carlos Caldas
Bioinformatic analysis of genomic sequencing data to identify somatic mutations in cancer samples is far from achieving the required robustness and standardisation. In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28409725/genetic-landscape-of-sporadic-vestibular-schwannoma
#20
Aril Løge Håvik, Ove Bruland, Erling Myrseth, Hrvoje Miletic, Mads Aarhus, Per-Morten Knappskog, Morten Lund-Johansen
OBJECTIVE Vestibular schwannoma (VS) is a benign tumor with associated morbidities and reduced quality of life. Except for mutations in NF2, the genetic landscape of VS remains to be elucidated. Little is known about the effect of Gamma Knife radiosurgery (GKRS) on the VS genome. The aim of this study was to characterize mutations occurring in this tumor to identify new genes and signaling pathways important for the development of VS. In addition, the authors sought to evaluate whether GKRS resulted in an increase in the number of mutations...
April 14, 2017: Journal of Neurosurgery
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