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Exome sequencing

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https://www.readbyqxmd.com/read/28535206/clinical-exome-sequencing-reports-current-informatics-practice-and-future-opportunities
#1
Rajeswari Swaminathan, Yungui Huang, Caroline Astbury, Sara Fitzgerald-Butt, Katherine Miller, Justin Cole, Christopher Bartlett, Simon Lin
The increased adoption of clinical whole exome sequencing (WES) has improved the diagnostic yield for patients with complex genetic conditions. However, the informatics practice for handling information contained in whole exome reports is still in its infancy, as evidenced by the lack of a common vocabulary within clinical sequencing reports generated across genetic laboratories. Genetic testing results are mostly transmitted using portable document format, which can make secondary analysis and data extraction challenging...
May 23, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28534967/whole%C3%A2-exome-sequencing-identifies-a-novel-mutation-r367g-in-scn5a-to-be-associated-with-familial-cardiac-conduction-disease
#2
Rong Yu, Xue-Feng Fan, Chan Chen, Zheng-Hua Liu
Cardiac conduction disease is a primary cause of sudden cardiac death. Sodium voltage‑gated channel‑α subunit 5 (SCN5A) mutations have been reported to underlie a variety of inherited arrhythmias. Numerous disease‑causing mutations of SCN5A have been identified in patients with ≥10 different conditions, including type 3 long‑QT syndrome and Brugada syndrome. The present study investigated a family with a history of arrhythmia, with the proband having a history of arrhythmia and syncope. Whole‑exome sequencing was applied in order to detect the disease‑causing mutation in this family, and Sanger sequencing was used to confirm the co‑segregation among the family members...
May 17, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28534666/human-aminoacyl-trna-synthetases-in-diseases-of-the-nervous-system
#3
Jana Ognjenović, Miljan Simonović
Aminoacyl-tRNA synthetases (AaRSs) are ubiquitously expressed enzymes that ensure accurate translation of the genetic information into functional proteins. These enzymes also execute a variety of non-canonical functions that are significant for regulation of diverse cellular processes and that reside outside the realm of protein synthesis. Associations between faults in AaRS-mediated processes and human diseases have been long recognized. Most recent research findings strongly argue that 10 cytosolic and 14 mitochondrial AaRSs are implicated in some form of pathology of the human nervous system...
May 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/28534081/power-of-pedigree-likelihood-analysis-in-extended-pedigrees-to-classify-rare-variants-of-uncertain-significance-in-cancer-risk-genes
#4
Elisabeth A Rosenthal, John Michael O Ranola, Brian H Shirts
Rare and private variants of uncertain significance (VUS) are routinely identified in clinical panel, exome, and genome sequencing. We investigated the power of single family co-segregation analysis to aid classification of VUS. We simulated thousands of pedigrees using demographics in China and the United States, segregating benign and pathogenic variants. Genotypes and phenotypes were simulated using penetrance models for Lynch syndrome and breast/ovarian cancer. We calculated LOD scores adjusted for proband ascertainment (LODadj), to determine power to yield quantitative evidence for, or against, pathogenicity of the VUS...
May 22, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28534044/hsp-and-deafness-neurocristopathy-caused-by-a-novel-mosaic-sox10-mutation
#5
Sandra Donkervoort, Diana Bharucha-Goebel, Pomi Yun, Ying Hu, Payam Mohassel, Ahmet Hoke, Wadih M Zein, Daniel Ezzo, Andrea M Atherton, Ann C Modrcin, Majed Dasouki, A Reghan Foley, Carsten G Bönnemann
OBJECTIVE: To identify the underlying genetic cause in 2 sisters affected with progressive lower extremity spasticity, neuropathy, and early-onset deafness. METHODS: Whole-exome sequencing was performed, and segregation testing of variants was investigated using targeted Sanger sequencing. An inherited paternal mosaic mutation was further evaluated through quantitative analysis of the ratio of mutant vs wild-type allele in genomic DNA from various tissues, including blood, dermal fibroblasts, and saliva...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28532469/a-pipeline-combining-multiple-strategies-for-prioritizing-heterozygous-variants-for-the-identification-of-candidate-genes-in-exome-datasets
#6
Teresa Requena, Alvaro Gallego-Martinez, Jose A Lopez-Escamez
BACKGROUND: The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and prioritizing of heterozygous variants using exome-sequencing datasets in familial Meniere disease: an in-house Pathogenic Variant (PAVAR) score, the Variant Annotation Analysis and Search Tool (VAAST-Phevor), Exomiser-v2, CADD, and FATHMM. We also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets...
May 22, 2017: Human Genomics
https://www.readbyqxmd.com/read/28530713/bach2-immunodeficiency-illustrates-an-association-between-super-enhancers-and-haploinsufficiency
#7
Behdad Afzali, Juha Grönholm, Jana Vandrovcova, Charlotte O'Brien, Hong-Wei Sun, Ine Vanderleyden, Fred P Davis, Ahmad Khoder, Yu Zhang, Ahmed N Hegazy, Alejandro V Villarino, Ira W Palmer, Joshua Kaufman, Norman R Watts, Majid Kazemian, Olena Kamenyeva, Julia Keith, Anwar Sayed, Dalia Kasperaviciute, Michael Mueller, Jason D Hughes, Ivan J Fuss, Mohammed F Sadiyah, Kim Montgomery-Recht, Joshua McElwee, Nicholas P Restifo, Warren Strober, Michelle A Linterman, Paul T Wingfield, Holm H Uhlig, Rahul Roychoudhuri, Timothy J Aitman, Peter Kelleher, Michael J Lenardo, John J O'Shea, Nichola Cooper, Arian D J Laurence
The transcriptional programs that guide lymphocyte differentiation depend on the precise expression and timing of transcription factors (TFs). The TF BACH2 is essential for T and B lymphocytes and is associated with an archetypal super-enhancer (SE). Single-nucleotide variants in the BACH2 locus are associated with several autoimmune diseases, but BACH2 mutations that cause Mendelian monogenic primary immunodeficiency have not previously been identified. Here we describe a syndrome of BACH2-related immunodeficiency and autoimmunity (BRIDA) that results from BACH2 haploinsufficiency...
May 22, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28526340/unfolding-the-pathogenesis-of-scleroderma-through-genomics-and-epigenomics
#8
REVIEW
Pei-Suen Tsou, Amr H Sawalha
With unknown etiology, scleroderma (SSc) is a multifaceted disease characterized by immune activation, vascular complications, and excessive fibrosis in internal organs. Genetic studies, including candidate gene association studies, genome-wide association studies, and whole-exome sequencing have supported the notion that while genetic susceptibility to SSc appears to be modest, SSc patients are genetically predisposed to this disease. The strongest genetic association for SSc lies within the MHC region, with loci in HLA-DRB1, HLA-DQB1, HLA-DPB1, and HLA-DOA1 being the most replicated...
May 16, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28526010/next-generation-sequencing-for-d47n-mutation-in-cx50-analysis-associated-with-autosomal-dominant-congenital-cataract-in-a-six-generation-chinese-family
#9
Chao Shen, Jingbing Wang, Xiaotang Wu, Fuchao Wang, Yang Liu, Xiaoying Guo, Lina Zhang, Yanfei Cao, Xiuhua Cao, Hongxing Ma
BACKGROUND: Congenital cataract is the most frequent cause of blindness during infancy or early childhood. To date, more than 40 loci associated with congenital cataract have been identified, including at least 26 genes on different chromosomes associated with inherited cataract. This present study aimed to identify the genetic mutation in a six-generation Chinese family affected with congenital cataract. METHODS: A detailed six-generation Chinese cataract family history and clinical data of the family members were recorded...
May 19, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28524179/a-fkbp5-mutation-is-associated-with-paget-s-disease-of-bone-and-enhances-osteoclastogenesis
#10
Bingru Lu, Yulian Jiao, Yinchang Wang, Jing Dong, Muyun Wei, Bin Cui, Yafang Sun, Laicheng Wang, Bingchang Zhang, Zijiang Chen, Yueran Zhao
Paget's disease of bone (PDB) is a common metabolic bone disease that is characterized by aberrant focal bone remodeling, which is caused by excessive osteoclastic bone resorption followed by disorganized osteoblastic bone formation. Genetic factors are a critical determinant of PDB pathogenesis, and several susceptibility genes and loci have been reported, including SQSTM1, TNFSF11A, TNFRSF11B, VCP, OPTN, CSF1 and DCSTAMP. Herein, we report a case of Chinese familial PDB without mutations in known genes and identify a novel c...
May 19, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28524162/targeted-sequencing-based-analyses-of-candidate-gene-variants-in-ulcerative-colitis-associated-colorectal-neoplasia
#11
Sanjiban Chakrabarty, Vinay Koshy Varghese, Pranoy Sahu, Pradyumna Jayaram, Bhadravathi M Shivakumar, Cannanore Ganesh Pai, Kapaettu Satyamoorthy
BACKGROUND: Long-standing ulcerative colitis (UC) leading to colorectal cancer (CRC) is one of the most serious and life-threatening consequences acknowledged globally. Ulcerative colitis-associated colorectal carcinogenesis showed distinct molecular alterations when compared with sporadic colorectal carcinoma. METHODS: Targeted sequencing of 409 genes in tissue samples of 18 long-standing UC subjects at high risk of colorectal carcinoma (UCHR) was performed to identify somatic driver mutations, which may be involved in the molecular changes during the transformation of non-dysplastic mucosa to high-grade dysplasia...
May 18, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28522871/mug-mel2-a-novel-highly-pigmented-and-well-characterized-nras-mutated-human-melanoma-cell-line
#12
Beate Rinner, Greta Gandolfi, Katharina Meditz, Marie-Therese Frisch, Karin Wagner, Alessia Ciarrocchi, Federica Torricelli, Raili Koivuniemi, Johanna Niklander, Bernadette Liegl-Atzwanger, Birgit Lohberger, Ellen Heitzer, Nassim Ghaffari-Tabrizi-Wizsy, Dagmar Zweytick, Iris Zalaudek
NRAS mutation in melanoma has been associated with aggressive tumor biology and poor prognosis. Although targeted therapy has been tested for NRAS mutated melanoma, response rates still appear much weaker, than in BRAF mutated melanoma. While plenty of cell lines exist, however, only few melanogenic cell lines retain their in vivo characteristics. In this work we present an intensively pigmented and well-characterized cell line derived from a highly aggressive NRAS mutated cutaneous melanoma, named MUG-Mel2...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522810/integrative-analysis-of-genomic-sequencing-data-reveals-higher-prevalence-of-lrp1b-mutations-in-lung-adenocarcinoma-patients-with-copd
#13
Dakai Xiao, Fuqiang Li, Hui Pan, Han Liang, Kui Wu, Jianxing He
Both chronic Obstruction Pulmonary Disease (COPD) and lung cancer are leading causes of death globally. Although COPD and lung cancer coexist frequently, it is unknown whether lung cancer patients with COPD harbor distinct genomic characteristics compared to those without COPD. In this study, we retrospectively analyzed genomic sequencing data from 272 patients with lung adenocarcinoma (LUAD) and compared the genetic alterations in LUAD patients with and without COPD. Integrative analysis of whole-genome and exome sequencing data revealed that COPD and non-COPD groups showed high concordance in mutational burden and spectra...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522612/genomevip-a-cloud-platform-for-genomic-variant-discovery-and-interpretation
#14
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/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#15
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28521875/exome-sequencing-reveals-a-de-novo-pold1-mutation-causing-phenotypic-variability-in-mandibular-hypoplasia-deafness-progeroid-features-and-lipodystrophy-syndrome-mdpl
#16
Sahar Elouej, Ana Beleza-Meireles, Richard Caswell, Kevin Colclough, Sian Ellard, Jean Pierre Desvignes, Christophe Béroud, Nicolas Lévy, Shehla Mohammed, Annachiara De Sandre-Giovannoli
BACKGROUND: Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL) is an autosomal dominant systemic disorder characterized by prominent loss of subcutaneous fat, a characteristic facial appearance and metabolic abnormalities. This syndrome is caused by heterozygous de novo mutations in the POLD1 gene. To date, 19 patients with MDPL have been reported in the literature and among them 14 patients have been characterized at the molecular level. Twelve unrelated patients carried a recurrent in-frame deletion of a single codon (p...
June 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28521526/the-impact-of-genetics-on-future-drug-discovery-in-schizophrenia
#17
Mitsuyuki Matsumoto, Noah M Walton, Hiroshi Yamada, Yuji Kondo, Gerard J Marek, Katsunori Tajinda
Failures of investigational new drugs (INDs) for schizophrenia have left huge unmet medical needs for patients. Given the recent lackluster results, it is imperative that new drug discovery approaches (and resultant drug candidates) target pathophysiological alterations that are shared in specific, stratified patient populations that are selected based on pre-identified biological signatures. One path to implementing this paradigm is achievable by leveraging recent advances in genetic information and technologies...
May 18, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28521042/induced-pluripotent-stem-cell-modelling-of-hlhs-underlines-the-contribution-of-dysfunctional-notch-signalling-to-impaired-cardiogenesis
#18
Chunbo Yang, Yaobo Xu, Min Yu, David Lee, Sameer Alharti, Nicola Hellen, Noor Ahmad Shaik, Babajan Banaganapalli, Hussein Ali Mohamoud Sheikh, Elango Ramu, Stefan Przyborski, Gennadiy Tenin, Simon Williams, John O'Sullivan, Osman O Al-Radi, Jameel Atta, Sian E Harding, Bernard Keavney, Majlinda Lako, Lyle Armstrong
Hypoplastic left heart syndrome (HLHS) is among the most severe forms of congenital heart disease. Although the consensus view is that reduced flow through the left heart during development is a key factor in the development of the condition, the molecular mechanisms leading to hypoplasia of left heart structures are unknown. We have generated induced pluripotent stem cells (iPSC) from five HLHS patients and two unaffected controls, differentiated these to cardiomyocytes and identified reproducible in vitro cellular and functional correlates of the HLHS phenotype...
May 17, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28521008/gemstone-orchestrated-prioritization-of-human-germline-mutations-in-the-cloud
#19
Siwei Chen, Juan F Beltrán, Clara Esteban-Jurado, Sebastià Franch-Expósito, Sergi Castellví-Bel, Steven Lipkin, Xiaomu Wei, Haiyuan Yu
Integrative analysis of whole-genome/exome-sequencing data has been challenging, especially for the non-programming research community, as it requires simultaneously managing a large number of computational tools. Even computational biologists find it unexpectedly difficult to reproduce results from others or optimize their strategies in an end-to-end workflow. We introduce Germline Mutation Scoring Tool fOr Next-generation sEquencing data (GeMSTONE), a cloud-based variant prioritization tool with high-level customization and a comprehensive collection of bioinformatics tools and data libraries (http://gemstone...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520890/vcf-filter-interactive-prioritization-of-disease-linked-genetic-variants-from-sequencing-data
#20
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting...
May 17, 2017: Nucleic Acids Research
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