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Whole exome sequencing

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https://www.readbyqxmd.com/read/29036499/vcf-explorer-filtering-and-analysing-whole-genome-vcf-files
#1
Mete Akgün, Hüseyin Demirci
Summary: The decreasing cost in high-throughput technologies led to a number of sequencing projects consisting of thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyse exome files are not adequate for larger VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Memory efficiency and avoiding computationally costly pre-processing step enable to carry out the analysis to be performed with ordinary computers...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036293/rare-germline-variants-in-known-melanoma-susceptibility-genes-in-familial-melanoma
#2
Alisa M Goldstein, Yanzi Xiao, Joshua Sampson, Bin Zhu, Melissa Rotunno, Hunter Bennett, Yixuan Wen, Kristine Jones, Aurelie Vogt, Laurie Burdette, Wen Luo, Bin Zhu, Meredith Yeager, Belynda Hicks, Jiali Han, Immaculata De Vivo, Stella Koutros, Gabriella Andreotti, Laura Beane-Freeman, Mark Purdue, Neal D Freedman, Stephen J Chanock, Margaret A Tucker, Xiaohong R Yang
Known high-risk cutaneous malignant melanoma (CMM) genes account for melanoma risk in < 40% of melanoma-prone families, suggesting the existence of additional high-risk genes or perhaps a polygenic mechanism involving multiple genetic modifiers. The goal of this study was to systematically characterize rare germline variants in 42 established melanoma genes among 144 CMM patients in 76 American CMM families without known mutations using data from whole-exome sequencing. We identified 68 rare (<0.1% in public and in-house control datasets) nonsynonymous variants in 25 genes...
October 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29035371/lncrna-mir100hg-derived-mir-100-and-mir-125b-mediate-cetuximab-resistance-via-wnt-%C3%AE-catenin-signaling
#3
Yuanyuan Lu, Xiaodi Zhao, Qi Liu, Cunxi Li, Ramona Graves-Deal, Zheng Cao, Bhuminder Singh, Jeffrey L Franklin, Jing Wang, Huaying Hu, Tianying Wei, Mingli Yang, Timothy J Yeatman, Ethan Lee, Kenyi Saito-Diaz, Scott Hinger, James G Patton, Christine H Chung, Stephan Emmrich, Jan-Henning Klusmann, Daiming Fan, Robert J Coffey
De novo and acquired resistance, which are largely attributed to genetic alterations, are barriers to effective anti-epidermal-growth-factor-receptor (EGFR) therapy. To generate cetuximab-resistant cells, we exposed cetuximab-sensitive colorectal cancer cells to cetuximab in three-dimensional culture. Using whole-exome sequencing and transcriptional profiling, we found that the long non-coding RNA MIR100HG and two embedded microRNAs, miR-100 and miR-125b, were overexpressed in the absence of known genetic events linked to cetuximab resistance...
October 16, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29033309/ethical-considerations-in-prenatal-testing-genomic-testing-and-medical-uncertainty
#4
REVIEW
Anastasia Richardson, Kelly E Ormond
Prenatal diagnostic testing has recently progressed from karyotype to routinely available chromosomal microarray, and the potential for fetal whole exome sequencing, both through invasive diagnostic testing and, in some cases, non-invasive prenatal testing. These tests bring beneficence through providing a higher diagnostic yield, often with lower risks of miscarriage than previously available testing, but also raise the question of harms related to an increase in uncertain and unknown results. Some parents-to-be report a desire to learn as much information as possible prenatally, and there may be beneficence in providing them with this information...
October 12, 2017: Seminars in Fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/29033165/molecular-epidemiological-study-of-familial-amyotrophic-lateral-sclerosis-in-japanese-population-by-whole-exome-sequencing-and-identification-of-novel-hnrnpa1-mutation
#5
Hiroya Naruse, Hiroyuki Ishiura, Jun Mitsui, Hidetoshi Date, Yuji Takahashi, Takashi Matsukawa, Masaki Tanaka, Akiko Ishii, Akira Tamaoka, Keiichi Hokkoku, Masahiro Sonoo, Mari Segawa, Yoshikazu Ugawa, Koichiro Doi, Jun Yoshimura, Shinichi Morishita, Jun Goto, Shoji Tsuji
To elucidate the genetic epidemiology of familial amyotrophic lateral sclerosis (FALS) in the Japanese population, we conducted whole-exome sequencing analysis of 30 FALS families in whom causative mutations have not been identified in previous studies. Consequently, whole-exome sequencing analysis revealed novel mutations in HNRNPA1, TBK1, and VCP. Taken together with our previous results of mutational analyses by direct nucleotide sequencing analysis, a microarray-based resequencing method, or repeat-primed PCR analysis, causative mutations were identified in 41 of the 68 families (60...
September 6, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29033130/tumor-and-microenvironment-evolution-during-immunotherapy-with-nivolumab
#6
Nadeem Riaz, Jonathan J Havel, Vladimir Makarov, Alexis Desrichard, Walter J Urba, Jennifer S Sims, F Stephen Hodi, Salvador Martín-Algarra, Rajarsi Mandal, William H Sharfman, Shailender Bhatia, Wen-Jen Hwu, Thomas F Gajewski, Craig L Slingluff, Diego Chowell, Sviatoslav M Kendall, Han Chang, Rachna Shah, Fengshen Kuo, Luc G T Morris, John-William Sidhom, Jonathan P Schneck, Christine E Horak, Nils Weinhold, Timothy A Chan
The mechanisms by which immune checkpoint blockade modulates tumor evolution during therapy are unclear. We assessed genomic changes in tumors from 68 patients with advanced melanoma, who progressed on ipilimumab or were ipilimumab-naive, before and after nivolumab initiation (CA209-038 study). Tumors were analyzed by whole-exome, transcriptome, and/or T cell receptor (TCR) sequencing. In responding patients, mutation and neoantigen load were reduced from baseline, and analysis of intratumoral heterogeneity during therapy demonstrated differential clonal evolution within tumors and putative selection against neoantigenic mutations on-therapy...
October 11, 2017: Cell
https://www.readbyqxmd.com/read/29032884/the-genetics-underlying-idiopathic-ventricular-fibrillation-a-special-role-for-catecholaminergic-polymorphic-ventricular-tachycardia
#7
Jaakko T Leinonen, Lia Crotti, Aurora Djupsjöbacka, Silvia Castelletti, Nella Junna, Alice Ghidoni, Annukka M Tuiskula, Carla Spazzolini, Federica Dagradi, Matti Viitasalo, Kimmo Kontula, Maria-Christina Kotta, Elisabeth Widén, Heikki Swan, Peter J Schwartz
BACKGROUND: Ventricular fibrillation (VF) is a major cause of sudden cardiac death. In some cases clinical investigations fail to identify the underlying cause and the event is classified as idiopathic (IVF). Since mutations in arrhythmia-associated genes frequently determine arrhythmia susceptibility, screening for disease-predisposing variants could improve IVF diagnostics. METHODS AND RESULTS: The study included 76 Finnish and Italian patients with a mean age of 31...
October 5, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/29031008/identification-of-a-novel-homozygous-trappc9-gene-mutation-causing-non-syndromic-intellectual-disability-speech-disorder-and-secondary-microcephaly
#8
Ansar A Abbasi, Kathrin Blaesius, Hao Hu, Zahid Latif, Sylvie Picker-Minh, Muhammad N Khan, Sundas Farooq, Muzammil A Khan, Angela M Kaindl
TRAPPC9 gene mutations have been linked recently to autosomal recessive mental retardation 13 (MRT13; MIM#613192) with only eight families reported world-wide. We assessed patients from two consanguineous pedigrees of Pakistani descent with non-syndromic intellectual disability and postnatal microcephaly through whole exome sequencing (WES) and cosegregation analysis. Here we report six further patients from two pedigrees with homozygous TRAPPC9 gene mutations, the novel nonsense mutation c.2065G>T (p.E689*) and the previously identified nonsense mutation c...
October 14, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/29030856/mitochondrial-3-hydroxy-3-methylglutaryl-coa-synthase-deficiency-unique-presenting-laboratory-values-and-a-review-of-biochemical-and-clinical-features
#9
Erin Conboy, Filippo Vairo, Matthew Schultz, Katherine Agre, Ross Ridsdale, David Deyle, Devin Oglesbee, Dimitar Gavrilov, Eric W Klee, Brendan Lanpher
We report an 8-month-old infant with decreased consciousness after a febrile episode and reduced oral intake. He was profoundly acidotic but his lactate was normal. Serum triglycerides were markedly elevated and HDL cholesterol was very low. The urine organic acid analysis during the acute episode revealed a complex pattern of relative hypoketotic dicarboxylic aciduria, suggestive of a potential fatty acid oxidation disorder. MRI showed extensive brain abnormalities concerning for a primary energy deficiency...
October 14, 2017: JIMD Reports
https://www.readbyqxmd.com/read/29030706/rare-adar-and-rnaseh2b-variants-and-a-type-i-interferon-signature-in-glioma-and-prostate-carcinoma-risk-and-tumorigenesis
#10
Ulrike Beyer, Frank Brand, Helge Martens, Julia Weder, Arne Christians, Natalie Elyan, Bettina Hentschel, Manfred Westphal, Gabriele Schackert, Torsten Pietsch, Bujung Hong, Joachim K Krauss, Amir Samii, Peter Raab, Anibh Das, Claudia A Dumitru, I Erol Sandalcioglu, Oliver W Hakenberg, Andreas Erbersdobler, Ulrich Lehmann, Guido Reifenberger, Michael Weller, Martin A M Reijns, Matthias Preller, Bettina Wiese, Christian Hartmann, Ruthild G Weber
In search of novel germline alterations predisposing to tumors, in particular to gliomas, we studied a family with two brothers affected by anaplastic gliomas, and their father and paternal great-uncle diagnosed with prostate carcinoma. In this family, whole-exome sequencing yielded rare, simultaneously heterozygous variants in the Aicardi-Goutières syndrome (AGS) genes ADAR and RNASEH2B co-segregating with the tumor phenotype. AGS is a genetically induced inflammatory disease particularly of the brain, which has not been associated with a consistently increased cancer risk to date...
October 13, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/29030401/a-comparison-of-whole-genome-sequencing-to-multigene-panel-testing-in-hypertrophic-cardiomyopathy-patients
#11
Allison L Cirino, Neal K Lakdawala, Barbara McDonough, Lauren Conner, Dale Adler, Mark Weinfeld, Patrick O'Gara, Heidi L Rehm, Kalotina Machini, Matthew Lebo, Carrie Blout, Robert C Green, Calum A MacRae, Christine E Seidman, Carolyn Y Ho
BACKGROUND: As DNA sequencing costs decline, genetic testing options have expanded. Whole exome sequencing and whole genome sequencing (WGS) are entering clinical use, posing questions about their incremental value compared with disease-specific multigene panels that have been the cornerstone of genetic testing. METHODS AND RESULTS: Forty-one patients with hypertrophic cardiomyopathy who had undergone targeted hypertrophic cardiomyopathy genetic testing (either multigene panel or familial variant test) were recruited into the MedSeq Project, a clinical trial of WGS...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29029963/genetic-risk-factors-in-finnish-patients-with-parkinson-s-disease
#12
Susanna Ylönen, Ari Siitonen, Michael A Nalls, Pauli Ylikotila, Jaana Autere, Johanna Eerola-Rautio, Raphael Gibbs, Mikko Hiltunen, Pentti J Tienari, Hilkka Soininen, Andrew B Singleton, Kari Majamaa
INTRODUCTION: Variation contributing to the risk of Parkinson's disease (PD) has been identified in several genes and at several loci including GBA, SMPD1, LRRK2, POLG1, CHCHD10 and MAPT, but the frequencies of risk variants seem to vary according to ethnic background. Our aim was to analyze how variation in these genes contributes to PD in the Finnish population. METHODS: The subjects consisted of 527 Finnish patients with early-onset PD, 325 patients with late-onset PD and 403 population controls...
September 29, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29029386/exome-sequencing-analysis-of-murine-medulloblastoma-models-identifies-wdr11-as-a-potential-tumor-suppressor-in-group-3-tumors
#13
Lei Wei, Brian L Murphy, Gang Wu, Matthew Parker, John Easton, Richard J Gilbertson, Jinghui Zhang, Martine F Roussel
Mouse models of human cancers are widely used in cancer research, yet questions frequently arise regarding their faithfulness in recapitulating their human counterparts. To compare the somatic mutations of murine models with human medulloblastoma (MB), we performed whole-exome sequencing on 12 tumors representing three distinct medulloblastoma subgroups: Wnt, Sonic Hedgehog (Shh) and Group 3 (G3). In total, 64 somatic mutations were identified and validated, including 40 predicted to cause amino acid changes...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29029192/paracoccidioidomycosis-associated-with-a-heterozygous-stat4-mutation-and-impaired-ifn-%C3%AE-immunity
#14
Lena F Schimke, James Hibbard, Ruben Martinez-Barricarte, Taj Ali Khan, Ricardo de Souza Cavalcante, Edgar Borges de Oliveira Junior, Tabata Takahashi França, Asif Iqbal, Guilherme Yamamoto, Christina Arslanian, Claudia Feriotti, Tania Alves da Costa, Jacinta Bustamante, Stéphanie Boisson-Dupuis, Jean-Laurent Casanova, José Alexandre Marzagao Barbuto, Mayana Zatz, Rinaldo Poncio Mendes, Vera Lucia Garcia Calich, Hans D Ochs, Troy R Torgerson, Otávio Cabral-Marques, Antonio Condino-Neto
Background: Mutations in genes affecting interferon (IFN)-γ immunity have contributed to understand the essential role of IFN-γ in the protection against intracellular pathogens. However, inborn errors in STAT4, which controls IL-12 responses, have not yet been reported. Objective: To determine the underlying genetic defect in a family with a history of paracoccidioidomycosis (PCM) disease. Methods: Genetic analysis was performed by whole-exome sequencing and sanger sequencing...
October 5, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29029121/clinical-heterogeneity-and-phenotypic-expansion-of-napi-iia-associated-disease
#15
Korcan Demir, Melek Yildiz, Hilla Bahat, Michael Goldman, Nisreen Hassan, Shay Tzur, Ayala Ofir, Daniella Magen
Context: NaPi-IIa, encoded by SLC34A1 is a key phosphate transporter in the mammalian proximal tubule, and plays a cardinal role in renal phosphate handling. NaPi-IIa impairment has been linked to various overlapping clinical syndromes, including hypophosphatemic nephrolithiasis with osteoporosis, renal Fanconi's syndrome with chronic kidney disease, and most recently, with idiopathic infantile hypercalcemia and nephrocalcinosis. Objectives: We studied the molecular basis of idiopathic infantile hypercalcemia with partial proximal tubulopathy in two apparently unrelated patients of Israeli and Turkish descent...
September 29, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29028887/identification-of-cancer-driver-genes-in-focal-genomic-aberrations-from-whole-exome-sequencing-data
#16
Ho Jang, Hyunju Lee
Summary: Whole-exome sequencing (WES) data have been used for identifying copy number aberrations in cancer cells. Nonetheless, the use of WES is still challenging for identification of focal aberrant regions in multiple samples that may contain cancer driver genes. In this study, we developed a wavelet-based method for identifying focal genomic aberrant regions in the WES data from cancer cells (WIFA-X). When we applied WIFA-X to glioblastoma multiforme and lung adenocarcinoma datasets, WIFA-X outperformed other approaches on identifying cancer driver genes...
September 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028823/novel-mutations-in-darier-disease-and-association-to-self-reported-disease-severity
#17
Ivone U S Leong, Alexander Stuckey, Tara Ahanian, Martin Cederlöf, Jakob D Wikstrom
Darier disease is a rare and severe autosomal dominant skin disease characterised by malodorous keratotic papules in seborrheic areas of the skin. Darier disease affects up to 1 in 30 000 people and is caused by mutations in the ATP2A2 gene, which encodes to the sarco/endoplasmic reticulum calcium-ATPase isoform 2 that pumps calcium into the endoplasmic reticulum. Although many ATP2A2 variants have been described, it is not known if genotype correlates with phenotype, which could be important for prognosis and treatment...
2017: PloS One
https://www.readbyqxmd.com/read/29027470/next-generation-sequencing-applications-for-cardiovascular-disease
#18
Samira Kalayinia, Hamidreza Goodarzynejad, Majid Maleki, Nejat Mahdieh
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs)...
October 13, 2017: Annals of Medicine
https://www.readbyqxmd.com/read/29024829/distal-renal-tubular-acidosis-in-a-libyan-patient-evidence-for-digenic-inheritance
#19
Majdi Nagara, Gregori Papagregoriou, Rim Ben Abdallah, Zied Landoulsi, Yosra Bouyacoub, Sahar Elouej, Rym Kefi, Tommaso Pippucci, Voskarides Konstantinos, Anu Bashamboo, Kenneth McElreavey, Mongia Hachicha, Giovanni Romeo, Marco Seri, Constantinos Deltas, Sonia Abdelhak
AIM OF THE STUDY: Recent advances in understanding the underlying molecular mechanism for distal renal tubular acidosis (dRTA), led to an increased attention towards the primary and the familial forms of the disease. Mutations in ATP6V1B1 and ATP6V0A4 are usually responsible for the recessive form of the disease. Mutations in gene AE1 encoding the Cl-/HCO3- exchanger, usually present as dominant dRTA, but a recessive pattern has been recently described. Our objective is to identify the mutational spectrum responsible of dRTA in a consanguineous Libyan family...
October 9, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29024827/left-ventricular-non-compaction-with-ebstein-anomaly-attributed-to-a-tpm1-mutation
#20
Aleksandra Nijak, Maaike Alaerts, Cuno Kuiperi, Anniek Corveleyn, Bert Suys, Bernard Paelinck, Johan Saenen, Emeline Van Craenenbroeck, Lut Van Laer, Bart Loeys, Aline Verstraeten
Left ventricular non-compaction (cardiomyopathy) (LVN(C)) is a rare hereditary cardiac condition, resulting from abnormal embryonic myocardial development. While it mostly occurs as an isolated condition, association with other cardiovascular manifestations such as Ebstein anomaly (EA) has been reported. This congenital heart defect is characterized by downward displacement of the tricuspid valve and leads to diminished ventricular size and function. In an autosomal dominant LVN(C) family consisting of five affected individuals, of which two also presented with EA and two others with mitral valve insufficiency, we pursued the genetic disease cause using whole exome sequencing (WES)...
October 9, 2017: European Journal of Medical Genetics
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