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variant calling exome

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https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28408746/novel-metrics-to-measure-coverage-in-whole-exome-sequencing-datasets-reveal-local-and-global-non-uniformity
#14
Qingyu Wang, Cooduvalli S Shashikant, Matthew Jensen, Naomi S Altman, Santhosh Girirajan
Whole Exome Sequencing (WES) is a powerful clinical diagnostic tool for discovering the genetic basis of many diseases. A major shortcoming of WES is uneven coverage of sequence reads over the exome targets contributing to many low coverage regions, which hinders accurate variant calling. In this study, we devised two novel metrics, Cohort Coverage Sparseness (CCS) and Unevenness (UE) Scores for a detailed assessment of the distribution of coverage of sequence reads. Employing these metrics we revealed non-uniformity of coverage and low coverage regions in the WES data generated by three different platforms...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28407084/comparative-analysis-of-de-novo-assemblers-for-variation-discovery-in-personal-genomes
#15
Shulan Tian, Huihuang Yan, Eric W Klee, Michael Kalmbach, Susan L Slager
Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data...
April 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28395282/expanding-genetic-and-functional-diagnoses-of-igf1r-haploinsufficiencies
#16
Paula Ocaranza, Marjorie C Golekoh, Shayne F Andrew, Michael H Guo, Paul Kaplowitz, Howard Saal, Ron G Rosenfeld, Andrew Dauber, Fernando Cassorla, Philippe F Backeljauw, Vivian Hwa
BACKGROUND: The growth-promoting effects of IGF-I is mediated through the IGF-I receptor (IGF1R), a widely expressed cell-surface tyrosine kinase receptor. IGF1R copy number variants (CNV) can cause pre- and postnatal growth restriction or overgrowth. METHODS: Whole exome sequence (WES), chromosomal microarray, and targeted IGF1R gene analyses were performed on 3 unrelated children who share features of small for gestational age, short stature, and elevated serum IGF-I, but otherwise had clinical heterogeneity...
April 10, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/28391287/identification-of-2-potentially-relevant-gene-mutations-involved-in-strabismus-using-whole-exome-sequencing
#17
Xiangrong Min, Haiying Fan, Guiqiu Zhao, Guixiang Liu
BACKGROUND The etiology of strabismus has a genetic component. Our study aimed to localize the candidate causative gene mutant in a Chinese family with strabismus and to describe its underlying etiology. MATERIAL AND METHODS Genomic DNA was extracted from the affected individual and his parents in a Chinese pedigree with strabismus. The resulting exomes were sequenced by whole-exome sequencing. After variant calling and filtering, the candidate causative gene mutations were selected for the rarity and predicted damaging effect, which complied with the model of recessive disease transmission...
April 9, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28388302/genome-wide-association-and-replication-study-of-hepatotoxicity-induced-by-antiretrovirals-alone-or-with-concomitant-anti-tuberculosis-drugs
#18
Zelalem Petros, Ming Ta Michael Lee, Atsushi Takahashi, Yanfei Zhang, Getnet Yimer, Abiy Habtewold, Ina Schuppe-Koistinen, Taisei Mushiroda, Eyasu Makonnen, Michiaki Kubo, Eleni Aklillu
Drug-induced hepatotoxicity (DIH) is a common adverse event that is associated with both antiretroviral (ARV) and anti-tuberculosis drugs (ATD). Moreover, the genetic variations predisposing ARV- and ARV-ATD-induced liver toxicity in African populations are not well investigated, despite the two diseases being the major global health problems in sub-Saharan Africa. We performed a genome-wide association study (GWAS) and replication study to identify the genetic variants linked to the risk of developing DIH due to ARV drugs alone, and ARV-ATD co-treatment in Ethiopian HIV-positive patients...
April 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28361668/gatk-hard-filtering-tunable-parameters-to-improve-variant-calling-for-next-generation-sequencing-targeted-gene-panel-data
#19
Simona De Summa, Giovanni Malerba, Rosamaria Pinto, Antonio Mori, Vladan Mijatovic, Stefania Tommasi
BACKGROUND: NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on preset parameters that may not fit in a satisfactory manner for different genes. GATK, which is widely used in the academic world, is rich in parameters for variant calling. However the self-adjusting parameter calibration of GATK requires data from a large number of exomes...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28347285/whole-exome-sequencing-and-digital-pcr-identified-a-novel-compound-heterozygous-mutation-in-the-nphp1-gene-in-a-case-of-joubert-syndrome-and-related-disorders
#20
Shingo Koyama, Hidenori Sato, Manabu Wada, Toru Kawanami, Mitsuru Emi, Takeo Kato
BACKGROUND: Joubert syndrome and related disorders (JSRD) is a clinically and genetically heterogeneous condition with autosomal recessive or X-linked inheritance, which share a distinctive neuroradiological hallmark, the so-called molar tooth sign. JSRD is classified into six clinical subtypes based on associated variable multiorgan involvement. To date, 21 causative genes have been identified in JSRD, which makes genetic diagnosis difficult. CASE PRESENTATION: We report here a case of a 28-year-old Japanese woman diagnosed with JS with oculorenal defects with a novel compound heterozygous mutation (p...
March 27, 2017: BMC Medical Genetics
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