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variant calling exome

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https://www.readbyqxmd.com/read/29334895/challenges-imposed-by-minor-reference-alleles-on-the-identification-and-reporting-of-clinical-variants-from-exome-data
#1
Mahmoud Koko, Mohammed O E Abdallah, Mutaz Amin, Muntaser Ibrahim
BACKGROUND: The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references. This hinders the correct identification of variants with minor and/or pathogenic reference alleles warranting additional approaches for variant calling. RESULTS: More than 26,000 Exome Aggregation Consortium (ExAC) variants have a minor reference allele including variants with known ClinVar disease alleles...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29323667/making-new-genetic-diagnoses-with-old-data-iterative-reanalysis-and-reporting-from-genome-wide-data-in-1-133-families-with-developmental-disorders
#2
Caroline F Wright, Jeremy F McRae, Stephen Clayton, Giuseppe Gallone, Stuart Aitken, Tomas W FitzGerald, Philip Jones, Elena Prigmore, Diana Rajan, Jenny Lord, Alejandro Sifrim, Rosemary Kelsell, Michael J Parker, Jeffrey C Barrett, Matthew E Hurles, David R FitzPatrick, Helen V Firth
PurposeGiven the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge.MethodsWe tested this hypothesis in the United Kingdom-wide Deciphering Developmental Disorders study, where in 2014 we reported a diagnostic yield of 27% through whole-exome sequencing of 1,133 children with severe developmental disorders and their parents. We reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes...
January 11, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29305224/snpitty-an-intuitive-web-application-for-interactive-b-allele-frequency-and-copy-number-visualization-of-next-generation-sequencing-data
#3
Job van Riet, Niels M G Krol, Peggy N Atmodimedjo, Erwin Brosens, Wilfred F J van IJcken, Maurice P H M Jansen, John W M Martens, Leendert H Looijenga, Guido Jenster, Hendrikus J Dubbink, Winand N M Dinjens, Harmen J G van de Werken
Exploration and visualization of next-generation sequencing data is crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions-of-interest coupled with dynamic heuristic filtering of genetic aberrations is however lacking. Therefore, we developed the web-application SNPitty that allows interactive visualization and interrogation of variant call format (VCF) files by utilizing B-allele frequencies of single nucleotide polymorphisms and single nucleotide variants, coverage metrics and copy-numbers analysis results...
January 2, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29206995/concordance-of-circulating-tumor-dna-and-matched-metastatic-tissue-biopsy-in-prostate-cancer
#4
Alexander W Wyatt, Matti Annala, Rahul Aggarwal, Kevin Beja, Felix Feng, Jack Youngren, Adam Foye, Paul Lloyd, Matti Nykter, Tomasz M Beer, Joshi J Alumkal, George V Thomas, Robert E Reiter, Matthew B Rettig, Christopher P Evans, Allen C Gao, Kim N Chi, Eric J Small, Martin E Gleave
Background: Real-time knowledge of the somatic genome can influence management of patients with metastatic castration-resistant prostate cancer (mCRPC). While routine metastatic tissue biopsy is challenging in mCRPC, plasma circulating tumor DNA (ctDNA) has emerged as a minimally invasive tool to sample the tumor genome. However, no systematic comparisons of matched "liquid" and "solid" biopsies have been performed that would enable ctDNA profiling to replace the need for direct tissue sampling...
December 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29206863/blood-collection-in-cell-stabilizing-tubes-does-not-impact-germline-dna-quality-for-pediatric-patients
#5
Bruce M Wollison, Edwin Thai, Aimee Mckinney, Abigail Ward, Andrea Clapp, Catherine Clinton, Anwesha Nag, Aaron R Thorner, Julie M Gastier-Foster, Brian D Crompton
OBJECTIVES: Liquid biopsy technologies allow non-invasive tumor profiling for patients with solid tumor malignancies by sequencing circulating tumor DNA. These studies may be useful in risk-stratification, monitoring for relapse, and understanding tumor evolution. The quality of DNA obtained for these studies is improved when blood samples are collected in tubes that stabilizing white blood cells (WBC). However, ongoing germline research in pediatric oncology generally requires obtaining blood samples in EDTA tubes, which do not contain a WBC-stabilizing preservative...
2017: PloS One
https://www.readbyqxmd.com/read/29206278/clinical-sequencing-from-raw-data-to-diagnosis-with-lifetime-value
#6
REVIEW
S M Caspar, N Dubacher, A M Kopps, J Meienberg, C Henggeler, G Matyas
High-throughput sequencing (HTS) has revolutionized genetics by enabling the detection of sequence variants at hitherto unprecedented large scale. Despite these advances, however, there are still remaining challenges in the complete coverage of targeted regions (genes, exome or genome) as well as in HTS data analysis and interpretation. Moreover, it is easy to get overwhelmed by the plethora of available methods and tools for HTS. Here, we review the step-by-step process from the generation of sequence data to molecular diagnosis of Mendelian diseases...
December 5, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29188438/mapping-causal-mutations-by-exome-sequencing-in-a-wheat-tilling-population-a-tall-mutant-case-study
#7
Youngjun Mo, Tyson Howell, Hans Vasquez-Gross, Luis Alejandro de Haro, Jorge Dubcovsky, Stephen Pearce
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants...
November 29, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29185122/genomic-variations-in-the-counterpart-normal-controls-of-lung-squamous-cell-carcinomas
#8
Liwei Qu, Bo Zhou, Guizhen Wang, Guangbiao Zhou
Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas...
November 28, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/29174709/exome-sequencing-of-synchronously-resected-primary-colorectal-tumours-and-colorectal-liver-metastases-to-inform-oncosurgical-management
#9
P A Sutton, P V Jithesh, R P Jones, J P Evans, D Vimalachandran, H Z Malik, B K Park, C E Goldring, D H Palmer, N R Kitteringham
BACKGROUND: Next generation sequencing technology has facilitated mapping of the colorectal cancer genotype and furthered our understanding of metastogenesis. The aim of this study was to investigate for conserved and different mutations in the exomes of synchronously resected primary colorectal tumour and liver metastases. This information could potentially be utilised to guide the treatment of advanced disease with the help of biological information from the primary tumour. METHODS: We performed exome sequencing of synchronously resected primary colorectal cancer and colorectal liver metastases as well as normal colonic mucosa and liver parenchyma, from four patients who had received neo-adjuvant chemotherapy, at a depth of 50X using the Ion Proton platform...
November 13, 2017: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29162850/whole-exome-sequencing-reveals-new-candidate-genes-in-host-genomic-susceptibility-to-respiratory-syncytial-virus-disease
#10
Antonio Salas, Jacobo Pardo-Seco, Miriam Cebey-López, Alberto Gómez-Carballa, Pablo Obando-Pacheco, Irene Rivero-Calle, María-José Currás-Tuala, Jorge Amigo, José Gómez-Rial, Federico Martinón-Torres
Respiratory syncytial virus (RSV) is an important cause of serious lower respiratory tract disease in infants. Several studies have shown evidence pointing to the genome of the host as an important factor determining susceptibility to respiratory disease caused by RSV. We sequenced the complete exomes of 54 patients infected by RSV that needed hospitalization due to development of severe bronchiolitis. The Iberian sample (IBS) from The 1000 Genomes Project (1000G) was used as control group; all the association results were pseudo-replicated using other 1000G-European controls and Spanish controls...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29162841/detection-of-somatic-mutations-in-exome-sequencing-of-tumor-only-samples
#11
Yu-Chin Hsu, Yu-Ting Hsiao, Tzu-Yuan Kao, Jan-Gowth Chang, Grace S Shieh
Due to lack of normal samples in clinical diagnosis and to reduce costs, detection of small-scale mutations from tumor-only samples is required but remains relatively unexplored. We developed an algorithm (GATKcan) augmenting GATK with two statistics and machine learning to detect mutations in cancer. The averaged performance of GATKcan in ten experiments outperformed GATK in detecting mutations of randomly sampled 231 from 241 TCGA endometrial tumors (EC). In external validations, GATKcan outperformed GATK in TCGA breast cancer (BC), ovarian cancer (OC) and melanoma tumors, in terms of Matthews correlation coefficient (MCC) and precision, where MCC takes both sensitivity and specificity into account...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29155419/catching-hidden-variation-systematic-correction-of-reference-minor-allele-annotation-in-clinical-variant-calling
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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