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https://www.readbyqxmd.com/read/28939748/in-depth-genetic-analysis-of-sclerosing-epithelioid-fibrosarcoma-reveals-recurrent-genomic-alterations-and-potential-treatment-targets
#1
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
#2
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
#3
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-exome-single-nucleotide-variants-using-targeted-sequencing-in-the-clinical-setting
#4
Darine Villela, Silvia Souza da 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
https://www.readbyqxmd.com/read/28792971/optimized-detection-of-insertions-deletions-indels-in-whole-exome-sequencing-data
#11
Bo-Young Kim, Jung Hoon Park, Hye-Yeong Jo, Soo Kyung Koo, Mi-Hyun Park
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging...
2017: PloS One
https://www.readbyqxmd.com/read/28759038/high-depth-high-accuracy-microsatellite-genotyping-enables-precision-lung-cancer-risk-classification
#12
K R Velmurugan, R T Varghese, N C Fonville, H R Garner
There remains a large discrepancy between the known genetic contributions to cancer and that which can be explained by genomic variants, both inherited and somatic. Recently, understudied repetitive DNA regions called microsatellites have been identified as genetic risk markers for a number of diseases including various cancers (breast, ovarian and brain). In this study, we demonstrate an integrated process for identifying and further evaluating microsatellite-based risk markers for lung cancer using data from the cancer genome atlas and the 1000 genomes project...
July 31, 2017: Oncogene
https://www.readbyqxmd.com/read/28751446/gene-copy-number-estimation-from-targeted-next-generation-sequencing-of-prostate-cancer-biopsies-analytic-validation-and-clinical-qualification
#13
George Seed, Wei Yuan, Joaquin Mateo, Suzanne Carreira, Claudia Bertan, Maryou Lambros, Gunther Boysen, Roberta Ferraldeschi, Susana Miranda, Ines Figueiredo, Ruth Riisnaes, Mateus Crespo, Daniel Nava Rodrigues, Eric Talevich, Dan R Robinson, Lakshmi P Kunju, Yi-Mi Wu, Robert Lonigro, Shahneen Sandhu, Arul Chinnayan, Johann S de Bono
Abstract <p>Purpose</p> <p>Precise detection of copy number aberrations (CNAs) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next generation sequencing (NGS) is inexpensive, high throughput and easily feasible, allowing single nucleotide variant calls, but CNA estimation from this remains challenging..</p> <p>Experimental Design</p> <p>We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration resistant prostate cancer biopsies, and used capture based whole exome sequencing (WES), array comparative genomic hybridization (aCGH), and fluorescent in situ hybridization (FISH) to explore the viability of this approach...
July 27, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28742119/doestrare-a-statistical-test-to-identify-local-enrichments-in-rare-genomic-variants-associated-with-disease
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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)...
August 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28659176/isown-accurate-somatic-mutation-identification-in-the-absence-of-normal-tissue-controls
#20
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
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