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https://www.readbyqxmd.com/read/28532386/extremely-low-coverage-whole-genome-sequencing-in-south-asians-captures-population-genomics-information
#1
Navin Rustagi, Anbo Zhou, W Scott Watkins, Erika Gedvilaite, Shuoguo Wang, Naveen Ramesh, Donna Muzny, Richard A Gibbs, Lynn B Jorde, Fuli Yu, Jinchuan Xing
BACKGROUND: The cost of Whole Genome Sequencing (WGS) has decreased tremendously in recent years due to advances in next-generation sequencing technologies. Nevertheless, the cost of carrying out large-scale cohort studies using WGS is still daunting. Past simulation studies with coverage at ~2x have shown promise for using low coverage WGS in studies focused on variant discovery, association study replications, and population genomics characterization. However, the performance of low coverage WGS in populations with a complex history and no reference panel remains to be determined...
May 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#2
Robert J Mashl, Adam D Scott, Kuan-Lin Huang, Matthew A Wyczalkowski, Christopher J Yoon, Beifang Niu, Erin DeNardo, Venkata D Yellapantula, Robert E Handsaker, Ken Chen, Daniel C Koboldt, Kai Ye, David Fenyö, Benjamin Raphael, Michael C Wendl, Li Ding
Identifying genomic variants is a fundamental first step towards the understanding of the role of inherited and acquired variations in disease. The accelerating growth in the corpus of sequencing data that underpins such analysis is making the data-download bottleneck more evident, placing substantial burdens on the research community to keep pace. As a result, the search for alternative approaches to the traditional 'download and analyze' paradigm on local computing resources has led to a rapidly growing demand for cloud-computing solutions for genomics analysis...
May 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28512242/a-systematic-analysis-of-oncogenic-gene-fusions-in-primary-colon-cancer
#3
Wigard P Kloosterman, Robert R J Coebergh van den Braak, Mark Pieterse, Markus J van Roosmalen, Anieta M Sieuwerts, Christina Stangl, Ronne Brunekreef, Zarina S Lalmahomed, Salo Ooft, Anne van Galen, Marcel Smid, Armel Lefebvre, Fried Zwartkruis, John W M Martens, John A Foekens, Katharina Biermann, Marco J Koudijs, Jan N M IJzermans, Emile E Voest
Genomic rearrangements that give rise to oncogenic gene fusions can offer actionable targets for cancer therapy. Here we present a systematic analysis of oncogenic gene fusions among a clinically well-characterized, prospectively collected set of 278 primary colon cancers spanning diverse tumor stages and clinical outcomes. Gene fusions and somatic genetic variations were identified in fresh frozen clinical specimens by Illumina RNA-sequencing, the STAR fusion gene detection pipeline, and GATK RNA-seq variant calling...
May 16, 2017: Cancer Research
https://www.readbyqxmd.com/read/28422394/homozygous-variant-in-c21orf2-in-a-case-of-jeune-syndrome-with-severe-thoracic-involvement-extending-the-phenotypic-spectrum
#4
Aideen M McInerney-Leo, Lawrie Wheeler, Mhairi S Marshall, Lisa K Anderson, Andreas Zankl, Matthew A Brown, Paul J Leo, Carol Wicking, Emma L Duncan
We previously reported exome sequencing in a short-rib thoracic dystrophy (SRTD) cohort, in whom recessive mutations were identified in SRTD-associated genes in 10 of 11 cases. A heterozygous stop mutation in the known SRTD gene WDR60 was identified in the remaining case; no novel candidate gene/s were suggested by homozygous/compound heterozygous analysis. This case was thus considered unsolved. Re-analysis following an analysis pipeline update identified a homozygous mutation in C21orf2 (c.218G > C; p...
April 19, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28363643/genetic-features-of-aflatoxin-associated-hepatocellular-carcinomas
#5
Weilong Zhang, Huan He, Mengya Zang, Qifeng Wu, Hong Zhao, Ling-Ling Lu, Peiqing Ma, Hongwei Zheng, Nengjin Wang, Ying Zhang, Siyuan He, Xiaoyan Chen, Zhiyuan Wu, Xiaoyue Wang, Jianqiang Cai, Zhihua Liu, Zongtang Sun, Yi-Xin Zeng, Chunfeng Qu, Yuchen Jiao
BACKGROUND & AIMS: Dietary exposure to aflatoxin is an important risk factor for hepatocellular carcinoma (HCC). However, little is known about the genomic features and mutations of aflatoxin-associated HCCs compared with HCCs not associated with aflatoxin exposure. We investigated the genetic features of aflatoxin-associated HCC that can be used to differentiate them from HCCs not associated with this carcinogen. METHODS: We obtained HCC tumor tissues and matched non-tumor liver tissues from 49 patients, collected from 1990 through 2016, at the Qidong Liver Cancer Hospital Institute in China-a high-risk region for aflatoxin exposure (38...
March 28, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28361668/gatk-hard-filtering-tunable-parameters-to-improve-variant-calling-for-next-generation-sequencing-targeted-gene-panel-data
#6
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/28358893/halvade-rna-parallel-variant-calling-from-transcriptomic-data-using-mapreduce
#7
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized to run efficiently on large data sets. However, as variant calling in genomic data has become common practice, several methods have been proposed to reduce runtime for DNA-seq analysis through the use of parallel computing. Determining the effectively expressed variants from transcriptomics (RNA-seq) data has only recently become possible, and as such does not yet benefit from efficiently parallelized workflows...
2017: PloS One
https://www.readbyqxmd.com/read/28357044/characterization-of-brca1-2-mutations-in-patients-with-family-history-of-breast-cancer-in-armenia
#8
Sofi Atshemyan, Andranik Chavushyan, Nerses Berberian, Arthur Sahakyan, Roksana Zakharyan, Arsen Arakelyan
Background. Breast cancer is one of the most common cancers in women worldwide. The germline mutations of the BRCA1 and BRCA2 genes are the most significant and well characterized genetic risk factors for hereditary breast cancer. Intensive research in the last decades has demonstrated that the incidence of mutations varies widely among different populations. In this study we attempted to perform a pilot study for identification and characterization of mutations in BRCA1 and BRCA2 genes among Armenian patients with family history of breast cancer and their healthy relatives...
2017: F1000Research
https://www.readbyqxmd.com/read/28334241/rmats-dvr-rmats-discovery-of-differential-variants-in-rna
#9
Jinkai Wang, Yang Pan, Shihao Shen, Lan Lin, Yi Xing
Motivation: RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a specific perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular states. Such differential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA processing, as well as changes in RNA editing in response to cellular perturbations or stimuli...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28290094/evaluating-the-calling-performance-of-a-rare-disease-ngs-panel-for-single-nucleotide-and-copy-number-variants
#10
P Cacheiro, A Ordóñez-Ugalde, B Quintáns, S Piñeiro-Hermida, J Amigo, M García-Murias, S I Pascual-Pascual, F Grandas, J Arpa, A Carracedo, M J Sobrido
INTRODUCTION: Variant detection protocols for clinical next-generation sequencing (NGS) need application-specific optimization. Our aim was to analyze the performance of single nucleotide variant (SNV) and copy number (CNV) detection programs on an NGS panel for a rare disease. METHODS: Thirty genes were sequenced in 83 patients with hereditary spastic paraplegia. The variant calls obtained with LifeScope, GATK UnifiedGenotyper and GATK HaplotypeCaller were compared with Sanger sequencing...
June 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28249565/statistical-method-to-compare-massive-parallel-sequencing-pipelines
#11
M H Elsensohn, N Leblay, S Dimassi, A Campan-Fournier, A Labalme, F Roucher-Boulez, D Sanlaville, G Lesca, C Bardel, P Roy
BACKGROUND: Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients...
March 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28239666/making-the-most-of-rna-seq-pre-processing-sequencing-data-with-opossum-for-reliable-snp-variant-detection
#12
Laura Oikkonen, Stefano Lise
Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller...
January 17, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28223510/pemapper-and-pecaller-provide-a-simplified-approach-to-whole-genome-sequencing
#13
H Richard Johnston, Pankaj Chopra, Thomas S Wingo, Viren Patel, Michael P Epstein, Jennifer G Mulle, Stephen T Warren, Michael E Zwick, David J Cutler
The analysis of human whole-genome sequencing data presents significant computational challenges. The sheer size of datasets places an enormous burden on computational, disk array, and network resources. Here, we present an integrated computational package, PEMapper/PECaller, that was designed specifically to minimize the burden on networks and disk arrays, create output files that are minimal in size, and run in a highly computationally efficient way, with the single goal of enabling whole-genome sequencing at scale...
March 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28185561/optimized-pipeline-of-mutect-and-gatk-tools-to-improve-the-detection-of-somatic-single-nucleotide-polymorphisms-in-whole-exome-sequencing-data
#14
Ítalo Faria do Valle, Enrico Giampieri, Giorgia Simonetti, Antonella Padella, Marco Manfrini, Anna Ferrari, Cristina Papayannidis, Isabella Zironi, Marianna Garonzi, Simona Bernardi, Massimo Delledonne, Giovanni Martinelli, Daniel Remondini, Gastone Castellani
BACKGROUND: Detecting somatic mutations in whole exome sequencing data of cancer samples has become a popular approach for profiling cancer development, progression and chemotherapy resistance. Several studies have proposed software packages, filters and parametrizations. However, many research groups reported low concordance among different methods. We aimed to develop a pipeline which detects a wide range of single nucleotide mutations with high validation rates. We combined two standard tools - Genome Analysis Toolkit (GATK) and MuTect - to create the GATK-LODN method...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28068558/targeted-next-generation-sequencing-of-the-entire-vitamin-d-receptor-gene-reveals-polymorphisms-correlated-with-vitamin-d-deficiency-among-older-filipino-women-with-and-without-fragility-fracture
#15
Mark Pretzel Zumaraga, Paul Julius Medina, Juan Miguel Recto, Lauro Abrahan, Edelyn Azurin, Celeste C Tanchoco, Cecilia A Jimeno, Cynthia Palmes-Saloma
This study aimed to discover genetic variants in the entire 101 kB vitamin D receptor (VDR) gene for vitamin D deficiency in a group of postmenopausal Filipino women using targeted next generation sequencing (TNGS) approach in a case-control study design. A total of 50 women with and without osteoporotic fracture seen at the Philippine Orthopedic Center were included. Blood samples were collected for determination of serum vitamin D, calcium, phosphorus, glucose, blood urea nitrogen, creatinine, aspartate aminotransferase, alanine aminotransferase and as primary source for targeted VDR gene sequencing using the Ion Torrent Personal Genome Machine...
December 21, 2016: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28056804/indelseek-detection-of-complex-insertions-and-deletions-from-next-generation-sequencing-data
#16
Chun Hang Au, Anskar Y H Leung, Ava Kwong, Tsun Leung Chan, Edmond S K Ma
BACKGROUND: Complex insertions and deletions (indels) from next-generation sequencing (NGS) data were prone to escape detection by currently available variant callers as shown by large-scale human genomics studies. Somatic and germline complex indels in key disease driver genes could be missed in NGS-based genomics studies. RESULTS: INDELseek is an open-source complex indel caller designed for NGS data of random fragments and PCR amplicons. The key differentiating factor of INDELseek is that each NGS read alignment was examined as a whole instead of "pileup" of each reference position across multiple alignments...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28049408/detailed-simulation-of-cancer-exome-sequencing-data-reveals-differences-and-common-limitations-of-variant-callers
#17
Ariane L Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
BACKGROUND: Next-generation sequencing of matched tumor and normal biopsy pairs has become a technology of paramount importance for precision cancer treatment. Sequencing costs have dropped tremendously, allowing the sequencing of the whole exome of tumors for just a fraction of the total treatment costs. However, clinicians and scientists cannot take full advantage of the generated data because the accuracy of analysis pipelines is limited. This particularly concerns the reliable identification of subclonal mutations in a cancer tissue sample with very low frequencies, which may be clinically relevant...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28045987/high-throughput-resequencing-of-maize-landraces-at-genomic-regions-associated-with-flowering-time
#18
Tiffany M Jamann, Shilpa Sood, Randall J Wisser, James B Holland
Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequencing is a cost-effective strategy to obtain sequence information for loci of interest across many individuals, providing a less expensive approach to evaluating sequence variation at the population scale. Here we evaluate amplicon-based enrichment coupled with semiconductor sequencing on a validation set consisting of three maize inbred lines, two hybrids and 19 landrace accessions...
2017: PloS One
https://www.readbyqxmd.com/read/28035032/using-genotype-array-data-to-compare-multi-and-single-sample-variant-calls-and-improve-variant-call-sets-from-deep-coverage-whole-genome-sequencing-data
#19
Suyash S Shringarpure, Rasika A Mathias, Ryan D Hernandez, Timothy D O'Connor, Zachary A Szpiech, Raul Torres, Francisco M De La Vega, Carlos D Bustamante, Kathleen C Barnes, Margaret A Taub
MOTIVATION: Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X)...
December 29, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28008336/micado-looking-for-mutations-in-targeted-pacbio-cancer-data-an-alignment-free-method
#20
Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, Jonas Bergh, Macha Nikolski
Targeted sequencing is commonly used in clinical application of NGS technology since it enables generation of sufficient sequencing depth in the targeted genes of interest and thus ensures the best possible downstream analysis. This notwithstanding, the accurate discovery and annotation of disease causing mutations remains a challenging problem even in such favorable context. The difficulty is particularly salient in the case of third generation sequencing technology, such as PacBio. We present MICADo, a de Bruijn graph based method, implemented in python, that makes possible to distinguish between patient specific mutations and other alterations for targeted sequencing of a cohort of patients...
2016: Frontiers in Genetics
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