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variant calling exome

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https://www.readbyqxmd.com/read/29155419/catching-hidden-variation-systematic-correction-of-reference-minor-allele-annotation-in-clinical-variant-calling
#1
Yury A Barbitoff, Igor V Bezdvornykh, Dmitrii E Polev, Elena A Serebryakova, Andrey S Glotov, Oleg S Glotov, Alexander V Predeus
PurposeWe comprehensively assessed the influence of reference minor alleles (RMAs), one of the inherent problems of the human reference genome sequence.MethodsThe variant call format (VCF) files provided by the 1000 Genomes and Exome Aggregation Consortium (ExAC) consortia were used to identify RMA sites. All coding RMA sites were checked for concordance with UniProt and the presence of same codon variants. RMA-corrected predictions of functional effect were obtained with SIFT, PolyPhen-2, and PROVEAN standalone tools and compared with dbNSFP v2...
October 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29144510/characterizing-reduced-coverage-regions-through-comparison-of-exome-and-genome-sequencing-data-across-10-centers
#2
Rashesh V Sanghvi, Christian J Buhay, Bradford C Powell, Ellen A Tsai, Michael O Dorschner, Celine S Hong, Matthew S Lebo, Ariella Sasson, David S Hanna, Sean McGee, Kevin M Bowling, Gregory M Cooper, David E Gray, Robert J Lonigro, Andrew Dunford, Christine A Brennan, Carrie Cibulskis, Kimberly Walker, Mauricio O Carneiro, Joshua Sailsbery, Lucia A Hindorff, Dan R Robinson, Avni Santani, Mahdi Sarmady, Heidi L Rehm, Leslie G Biesecker, Deborah A Nickerson, Carolyn M Hutter, Levi Garraway, Donna M Muzny, Nikhil Wagle
PurposeAs massively parallel sequencing is increasingly being used for clinical decision making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and describe a set of standards for variant calling in clinical sequencing applications.MethodsTo enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCID) to identify reduced coverage loci within genes or regions of particular interest...
November 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29126409/genomic-determinants-of-long-term-cardiometabolic-complications-in-childhood-acute-lymphoblastic-leukemia-survivors
#3
Jade England, Simon Drouin, Patrick Beaulieu, Pascal St-Onge, Maja Krajinovic, Caroline Laverdière, Emile Levy, Valérie Marcil, Daniel Sinnett
BACKGROUND: While cure rates for childhood acute lymphoblastic leukemia (cALL) now exceed 80%, over 60% of survivors will face treatment-related long-term sequelae, including cardiometabolic complications such as obesity, insulin resistance, dyslipidemia and hypertension. Although genetic susceptibility contributes to the development of these problems, there are very few studies that have so far addressed this issue in a cALL survivorship context. METHODS: In this study, we aimed at evaluating the associations between common and rare genetic variants and long-term cardiometabolic complications in survivors of cALL...
November 10, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29122469/sensitivity-of-whole-exome-sequencing-in-detecting-infantile-and-late-onset-pompe-disease
#4
Mari Mori, Gloria Haskell, Zoheb Kazi, Xiaolin Zhu, Stephanie M DeArmey, Jennifer L Goldstein, Deeksha Bali, Catherine Rehder, Elizabeth T Cirulli, Priya S Kishnani
Pompe disease is a metabolic myopathy with a wide spectrum of clinical presentation. The gold-standard diagnostic test is acid alpha-glucosidase assay on skin fibroblasts, muscle or blood. Identification of two GAA pathogenic variants in-trans is confirmatory. Optimal effectiveness of enzyme replacement therapy hinges on early diagnosis, which is challenging in late-onset form of the disease due to non-specific presentation. Next-generation sequencing-based panels effectively facilitate diagnosis, but the sensitivity of whole-exome sequencing (WES) in detecting pathogenic GAA variants remains unknown...
October 17, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29120066/a-novel-nonsense-variant-in-reep6-is-involved-in-a-sporadic-rod-cone-dystrophy-case
#5
C Méjécase, S Mohand-Saïd, S El Shamieh, A Antonio, C Condroyer, S Blanchard, M Letexier, J-P Saraiva, J-A Sahel, I Audo, C Zeitz
Rod-cone dystrophy (RCD), also called retinitis pigmentosa, is the most common form of progressive inherited retinal disorders secondary to photoreceptor degeneration. It is a genetically heterogeneous disease characterized by night blindness, followed by visual field constriction and, in most severe cases, total blindness. The aim of our study was to identify the underlying gene defect leading to severe RCD in a 60-year-old woman. The patient's DNA was investigated by targeted next generation sequencing followed by whole exome sequencing...
November 9, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29089957/development-and-evaluation-of-a-barley-50k-iselect-snp-array
#6
Micha M Bayer, Paulo Rapazote-Flores, Martin Ganal, Pete E Hedley, Malcolm Macaulay, Jörg Plieske, Luke Ramsay, Joanne Russell, Paul D Shaw, William Thomas, Robbie Waugh
High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29020110/comprehensive-benchmarking-of-snv-callers-for-highly-admixed-tumor-data
#7
Regina Bohnert, Sonia Vivas, Gunther Jansen
Precision medicine attempts to individualize cancer therapy by matching tumor-specific genetic changes with effective targeted therapies. A crucial first step in this process is the reliable identification of cancer-relevant variants, which is considerably complicated by the impurity and heterogeneity of clinical tumor samples. We compared the impact of admixture of non-cancerous cells and low somatic allele frequencies on the sensitivity and precision of 19 state-of-the-art SNV callers. We studied both whole exome and targeted gene panel data and up to 13 distinct parameter configurations for each tool...
2017: PloS One
https://www.readbyqxmd.com/read/28985730/clinical-utility-of-the-low-density-infinium-qc-genotyping-array-in-a-genomics-based-diagnostics-laboratory
#8
Petr Ponomarenko, Alex Ryutov, Dennis T Maglinte, Ancha Baranova, Tatiana V Tatarinova, Xiaowu Gai
BACKGROUND: With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, and provides cost-efficient means for determining gender, ethnic ancestry, and sample kinships, that are important for data interpretation of NGS-based genetic tests. METHODS: We evaluated accuracy and reproducibility of Infinium QC genotyping calls by comparing them with genotyping data of the same samples from other genotyping platforms, whole genome/exome sequencing...
October 6, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28981122/base-resolution-stratification-of-cancer-mutations-using-functional-variomics
#9
Song Yi, Ning-Ning Liu, Limei Hu, Hui Wang, Nidhi Sahni
A complete understanding of human cancer variants requires new methods to systematically and efficiently assess the functional effects of genomic mutations at a large scale. Here, we describe a set of tools to rapidly clone and stratify thousands of cancer mutations at base resolution. This protocol provides a massively parallel pipeline to achieve high stringency and throughput. The approach includes high-throughput generation of mutant clones by Gateway, confirmation of variant identity by barcoding and next-generation sequencing, and stratification of cancer variants by multiplexed interaction profiling...
November 2017: Nature Protocols
https://www.readbyqxmd.com/read/28954988/construction-of-a-combinatorial-pipeline-using-two-somatic-variant%C3%A2-calling%C3%A2-methods%C3%A2-for-whole-exome-sequence-data-of-gastric-cancer
#10
Tomohiro Kohmoto, Kiyoshi Masuda, Takuya Naruto, Shoichiro Tange, Katsutoshi Shoda, Junichi Hamada, Masako Saito, Daisuke Ichikawa, Atsushi Tajima, Eigo Otsuji, Issei Imoto
High-throughput next-generation sequencing is a powerful tool to identify the genotypic landscapes of somatic variants and therapeutic targets in various cancers including gastric cancer, forming the basis for personalized medicine in the clinical setting. Although the advent of many computational algorithms leads to higher accuracy in somatic variant calling, no standard method exists due to the limitations of each method. Here, we constructed a new pipeline. We combined two different somatic variant callers with different algorithms, Strelka and VarScan 2, and evaluated performance using whole exome sequencing data obtained from 19 Japanese cases with gastric cancer (GC); then, we characterized these tumors based on identified driver molecular alterations...
2017: Journal of Medical Investigation: JMI
https://www.readbyqxmd.com/read/28939748/in-depth-genetic-analysis-of-sclerosing-epithelioid-fibrosarcoma-reveals-recurrent-genomic-alterations-and-potential-treatment-targets
#11
Elsa Arbajian, Florian Puls, Cristina R Antonescu, M Fernanda Amary, Raf Sciot, Maria Debiec-Rychter, Vaiyapuri Sumathi, Marcus Järås, Linda Magnusson, Jenny Nilsson, Jakob Hofvander, Fredrik Mertens
PURPOSE: Sclerosing epithelioid fibrosarcoma (SEF) is a highly aggressive soft tissue sarcoma closely related to low-grade fibromyxoid sarcoma (LGFMS). Some tumors display morphological characteristics of both SEF and LGFMS, so called hybrid SEF/LGFMS. Despite the overlap of gene fusion variants between these two tumor types, SEF is much more aggressive. The present study aimed to further characterize SEF and hybrid SEF/LGFMS genetically in order to better understand the role of the characteristic fusion genes and possible additional genetic alterations in tumorigenesis...
September 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28938720/deep-whole-genome-sequencing-of-90-han-chinese-genomes
#12
Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mengcheng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28886076/lower-frequency-of-tlr9-variant-associated-with-protection-from-breast-cancer-among-african-americans
#13
Madison R Chandler, Kimberly S Keene, Johanna M Tuomela, Andres Forero-Torres, Renee Desmond, Katri S Vuopala, Kevin W Harris, Nancy D Merner, Katri S Selander
INTRODUCTION: Toll-like receptor 9 (TLR9) is an innate immune system DNA-receptor that regulates tumor invasion and immunity in vitro. Low tumor TLR9 expression has been associated with poor survival in Caucasian patients with triple negative breast cancer (TNBC). African American (AA) patients with TNBC have worse prognosis than Caucasians but whether this is due to differences in tumor biology remains controversial. We studied the prognostic significance of tumor Toll like receptor-9 (TLR9) protein expression among African American (AA) triple negative breast cancer (TNBC) patients...
2017: PloS One
https://www.readbyqxmd.com/read/28882788/efficient-detection-of-chromosome-imbalances-and-single-nucleotide-variants-using-targeted-sequencing-in-the-clinical-setting
#14
Darine Villela, Silvia Souza Costa, Angela M Vianna-Morgante, Ana C V Krepischi, Carla Rosenberg
We evaluated an approach to detect copy number variants (CNVs) and single nucleotide changes (SNVs), using a clinically focused exome panel complemented with a backbone and SNP probes that allows for genome-wide copy number changes and copy-neutral absence of heterozygosity (AOH) calls; this approach potentially substitutes the use of chromosomal microarray testing and sequencing into a single test. A panel of 16 DNA samples with known alterations ranging from megabase-scale CNVs to single base modifications were used as positive controls for sequencing data analysis...
September 4, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28870871/clinical-genomic-sequencing-as-a-routine-technology-for-case-finding-and-diagnosis-in-unselected-patient-populations-should-not-proceed-without-formal-comparative-evaluation-of-health-outcomes-and-system-impacts
#15
Brenda J Wilson, Fiona Alice Miller, François Rousseau
Next generation genomic sequencing (NGS) technologies - whole genome and whole exome sequencing - are now cheap enough to be within the grasp of many healthcare organizations. To many, NGS is symbolic of cutting edge healthcare, offering the promise of 'precision' and 'personalized' medicine. Historically, research and clinical application has been a two way street in clinical genetics: research often driven directly by the desire to understand and try to solve immediate clinical problems affecting real, identifiable patients and families, accompanied by a low threshold of willingness to apply research-driven interventions without resort to formal empirical evaluations...
September 1, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28867142/exonic-mosaic-mutations-contribute-risk-for-autism-spectrum-disorder
#16
Deidre R Krupp, Rebecca A Barnard, Yannis Duffourd, Sara A Evans, Ryan M Mulqueen, Raphael Bernier, Jean-Baptiste Rivière, Eric Fombonne, Brian J O'Roak
Genetic risk factors for autism spectrum disorder (ASD) have yet to be fully elucidated. Postzygotic mosaic mutations (PMMs) have been implicated in several neurodevelopmental disorders and overgrowth syndromes. By leveraging whole-exome sequencing data on a large family-based ASD cohort, the Simons Simplex Collection, we systematically evaluated the potential role of PMMs in autism risk. Initial re-evaluation of published single-nucleotide variant (SNV) de novo mutations showed evidence consistent with putative PMMs for 11% of mutations...
September 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28862766/genomic-profiles-of-lung-cancer-associated-with-idiopathic-pulmonary-fibrosis
#17
Ji An Hwang, Deokhoon Kim, Sung-Min Chun, SooHyun Bae, Joon Seon Song, Mi Young Kim, Hyun Jung Koo, Jin Woo Song, Woo Sung Kim, Jae Cheol Lee, Hyeong Ryul Kim, Chang-Min Choi, Se Jin Jang
Little is known on the pathogenesis or molecular profiles of idiopathic pulmonary fibrosis-associated lung cancer (IPF-LC). This study was performed to investigate the genomic profiles of IPF-LC and to explore the possibility of defining potential therapeutic targets in IPF-LC. We assessed genomic profiles of IPF-LC using targeted exome sequencing (OncoPanel version 2) in 35 matched tumor/normal pairs surgically resected between 2004 and 2014. Germline and somatic variant calling was performed using GATK HaplotypeCaller and MuTect with GATK SomaticIndelocator, respectively...
September 1, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28852425/evaluation-of-three-read-depth-based-cnv-detection-tools-using-whole-exome-sequencing-data
#18
Ruen Yao, Cheng Zhang, Tingting Yu, Niu Li, Xuyun Hu, Xiumin Wang, Jian Wang, Yiping Shen
BACKGROUND: Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. The aim of this study was to evaluate three commonly used, WES read-depth based CNV detection programs using high-resolution chromosomal microarray analysis (CMA) as a standard...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28821228/sg-adviser-mtdna-a-web-server-for-mitochondrial-dna-annotation-with-data-from-200-samples-of-a-healthy-aging-cohort
#19
Manuel Rueda, Ali Torkamani
BACKGROUND: Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians...
August 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28808973/discovery-of-variants-underlying-host-susceptibility-to-virus-infection-using-whole-exome-sequencing
#20
Gabriel A Leiva-Torres, Nestor Nebesio, Silvia M Vidal
The clinical course of any viral infection greatly differs in individuals. This variation results from various viral, host, and environmental factors. The identification of host genetic factors influencing inter-individual variation in susceptibility to several pathogenic viruses has tremendously increased our understanding of the mechanisms and pathways required for immunity. Next-generation sequencing of whole exomes represents a powerful tool in biomedical research. In this chapter, we briefly introduce whole-exome sequencing in the context of genetic approaches to identify host susceptibility genes to viral infections...
2017: Methods in Molecular Biology
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