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https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#1
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920410/a-novel-splice-site-mutation-in-the-aspm-gene-underlies-autosomal-recessive-primary-microcephaly
#2
Jamil A Hashmi, Khalid M Al-Harbi, Khushnooda Ramzan, Alia M Albalawi, Amir Mehmood, Mohammed I Samman, Sulman Basit
BACKGROUND: Autosomal recessive primary microcephaly (MCPH) is a clinically and genetically heterogeneous disorder. Patients with MCPH exhibit reduced occipito-frontal head circumference and non-progressive intellectual disability. To date, 17 genes have been known as an underlying cause of MCPH in humans. ASPM (abnormal spindle-like, microcephaly associated) is the most commonly mutated MCPH gene. OBJECTIVE: Identify the genetic defect underlying MCPH in a Saudi family...
November 2016: Annals of Saudi Medicine
https://www.readbyqxmd.com/read/27920155/sos2-and-acp1-loci-identified-through-large-scale-exome-chip-analysis-regulate-kidney-development-and-function
#3
Man Li, Yong Li, Olivia Weeks, Vladan Mijatovic, Alexander Teumer, Jennifer E Huffman, Gerard Tromp, Christian Fuchsberger, Mathias Gorski, Leo-Pekka Lyytikäinen, Teresa Nutile, Sanaz Sedaghat, Rossella Sorice, Adrienne Tin, Qiong Yang, Tarunveer S Ahluwalia, Dan E Arking, Nathan A Bihlmeyer, Carsten A Böger, Robert J Carroll, Daniel I Chasman, Marilyn C Cornelis, Abbas Dehghan, Jessica D Faul, Mary F Feitosa, Giovanni Gambaro, Paolo Gasparini, Franco Giulianini, Iris Heid, Jinyan Huang, Medea Imboden, Anne U Jackson, Janina Jeff, Min A Jhun, Ronit Katz, Annette Kifley, Tuomas O Kilpeläinen, Ashish Kumar, Markku Laakso, Ruifang Li-Gao, Kurt Lohman, Yingchang Lu, Reedik Mägi, Giovanni Malerba, Evelin Mihailov, Karen L Mohlke, Dennis O Mook-Kanamori, Antonietta Robino, Douglas Ruderfer, Erika Salvi, Ursula M Schick, Christina-Alexandra Schulz, Albert V Smith, Jennifer A Smith, Michela Traglia, Laura M Yerges-Armstrong, Wei Zhao, Mark O Goodarzi, Aldi T Kraja, Chunyu Liu, Jennifer Wessel, Eric Boerwinkle, Ingrid B Borecki, Jette Bork-Jensen, Erwin P Bottinger, Daniele Braga, Ivan Brandslund, Jennifer A Brody, Archie Campbell, David J Carey, Cramer Christensen, Josef Coresh, Errol Crook, Gary C Curhan, Daniele Cusi, Ian H de Boer, Aiko P J de Vries, Joshua C Denny, Olivier Devuyst, Albert W Dreisbach, Karlhans Endlich, Tõnu Esko, Oscar H Franco, Tibor Fulop, Glenn S Gerhard, Charlotte Glümer, Omri Gottesman, Niels Grarup, Vilmundur Gudnason, Tamara B Harris, Caroline Hayward, Lynne Hocking, Albert Hofman, Frank B Hu, Lise Lotte N Husemoen, Rebecca D Jackson, Torben Jørgensen, Marit E Jørgensen, Mika Kähönen, Sharon L R Kardia, Wolfgang König, Charles Kooperberg, Jennifer Kriebel, Lenore J Launer, Torsten Lauritzen, Terho Lehtimäki, Daniel Levy, Pamela Linksted, Allan Linneberg, Yongmei Liu, Ruth J F Loos, Antonio Lupo, Christine Meisinger, Olle Melander, Andres Metspalu, Paul Mitchell, Matthias Nauck, Peter Nürnberg, Marju Orho-Melander, Afshin Parsa, Oluf Pedersen, Annette Peters, Ulrike Peters, Ozren Polasek, David Porteous, Nicole M Probst-Hensch, Bruce M Psaty, Lu Qi, Olli T Raitakari, Alex P Reiner, Rainer Rettig, Paul M Ridker, Fernando Rivadeneira, Jacques E Rossouw, Frank Schmidt, David Siscovick, Nicole Soranzo, Konstantin Strauch, Daniela Toniolo, Stephen T Turner, André G Uitterlinden, Sheila Ulivi, Dinesh Velayutham, Uwe Völker, Henry Völzke, Melanie Waldenberger, Jie Jin Wang, David R Weir, Daniel Witte, Helena Kuivaniemi, Caroline S Fox, Nora Franceschini, Wolfram Goessling, Anna Köttgen, Audrey Y Chu
Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3...
December 5, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27919237/a-novel-ano3-variant-identified-in-a-53-year-old-woman-presenting-with-hyperkinetic-dysarthria-blepharospasm-hyperkinesias-and-complex-motor%C3%A2-tics
#4
Patrick R Blackburn, Michael T Zimmermann, Jennifer M Gass, Kimberly G Harris, Margot A Cousin, Nicole J Boczek, Owen A Ross, Eric W Klee, Paul W Brazis, Jay A Van Gerpen, Paldeep S Atwal
BACKGROUND: Cervical dystonias have a variable presentation and underlying etiology, but collectively represent the most common form of focal dystonia. There are a number of known genetic forms of dystonia (DYT1-27); however the heterogeneity of disease presentation does not always make it easy to categorize the disease by phenotype-genotype comparison. CASE PRESENTATION: In this report, we describe a 53-year-old female who presented initially with hand tremor following a total hip arthroplasty...
December 5, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27918759/the-functional-effect-of-rare-variants-in-complement-genes-on-c3b-degradation-in-patients-with-age-related-macular-degeneration
#5
Maartje J Geerlings, Mariann Kremlitzka, Bjorn Bakker, Sara C Nilsson, Nicole T Saksens, Yara T Lechanteur, Marc Pauper, Jordi Corominas, Sascha Fauser, Carel B Hoyng, Anna M Blom, Eiko K de Jong, Anneke I den Hollander
Importance: In age-related macular degeneration (AMD), rare variants in the complement system have been described, but their functional consequences remain largely unexplored. Objectives: To identify new rare variants in complement genes and determine the functional effect of identified variants on complement levels and complement regulation in serum samples from carriers and noncarriers. Design, Setting, and Participants: This study evaluated affected (n = 114) and unaffected (n = 60) members of 22 families with AMD and a case-control cohort consisting of 1831 unrelated patients with AMD and 1367 control individuals from the European Genetic Database from March 29, 2006, to April 26, 2013, in Nijmegen, the Netherlands, and Cologne, Germany...
December 1, 2016: JAMA Ophthalmology
https://www.readbyqxmd.com/read/27917589/the-petale-study-late-adverse-effects-and-biomarkers-in-childhood-acute-lymphoblastic-leukemia-survivors
#6
Sophie Marcoux, Simon Drouin, Caroline Laverdière, Nathalie Alos, Gregor U Andelfinger, Laurence Bertout, Daniel Curnier, Matthias G Friedrich, Ekaterini A Kritikou, Geneviève Lefebvre, Emile Levy, Sarah Lippé, Valérie Marcil, Marie-Josée Raboisson, Frank Rauch, Philippe Robaey, Mariia Samoilenko, Chantal Séguin, Serge Sultan, Maja Krajinovic, Daniel Sinnett
BACKGROUND: Childhood cancer survivorship issues represent an established public health challenge. Most late adverse effects (LAEs) have been demonstrated to be time and treatment dependent. The PETALE study is a multidisciplinary research project aiming to comprehensively characterize LAEs and identify associated predictive biomarkers in childhood acute lymphoblastic leukemia (cALL) survivors. METHODS: cALL survivors treated at Sainte-Justine University Health Center with Dana-Farber Cancer Institution-ALL protocols 87-01 through 2005-01 were eligible...
December 4, 2016: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/27915094/clinical-features-associated-with-ctnnb1-de-novo-loss-of-function-mutations-in-ten-individuals
#7
Mira Kharbanda, Daniela T Pilz, Susan Tomkins, Kate Chandler, Anand Saggar, Alan Fryer, Victoria McKay, Pedro Louro, Jill Clayton Smith, John Burn, Usha Kini, Anna De Burca, David R FitzPatrick, Esther Kinning, D D D Study
Loss of function mutations in CTNNB1 have been reported in individuals with intellectual disability [MIM #615075] associated with peripheral spasticity, microcephaly and central hypotonia, suggesting a recognisable phenotype associated with haploinsufficiency for this gene. Trio based whole exome sequencing via the Deciphering Developmental Disorders (DDD) study has identified eleven further individuals with de novo loss of function mutations in CTNNB1. Here we report detailed phenotypic information on ten of these...
November 30, 2016: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/27913932/almost-2-of-spanish-breast-cancer-families-are-associated-to-germline-pathogenic-mutations-in-the-atm-gene
#8
A Tavera-Tapia, L Pérez-Cabornero, J A Macías, M I Ceballos, G Roncador, M de la Hoya, A Barroso, V Felipe-Ponce, R Serrano-Blanch, C Hinojo, M D Miramar-Gallart, M Urioste, T Caldés, S Santillan-Garzón, J Benitez, A Osorio
PURPOSE: There is still a considerable percentage of hereditary breast and ovarian cancer (HBOC) cases not explained by BRCA1 and BRCA2 genes. In this report, next-generation sequencing (NGS) techniques were applied to identify novel variants and/or genes involved in HBOC susceptibility. METHODS: Using whole exome sequencing, we identified a novel germline mutation in the moderate-risk gene ATM (c.5441delT; p.Leu1814Trpfs*14) in a family negative for mutations in BRCA1/2 (BRCAX)...
December 2, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/27913610/whole-exome-sequencing-of-thymic-neuroendocrine-tumor-with-ectopic-acth-syndrome
#9
Yanli Li, Ying Peng, Xiuli Jiang, Yulong Cheng, Weiwei Zhou, Tingwei Su, Jing Xie, Xu Zhong, Dalong Song, Luming Wu, Liwen Fan, Min Li, Jie Hong, Weiqing Wang, Guang Ning, Yanan Cao
OBJECTIVE: Thymic neuroendocrine tumor is the second-most prevalent cause of ectopic adrenocorticotropic hormone (ACTH) syndrome (EAS), which is a rare disease characterized by ectopic ACTH oversecretion from nonpituitary tumors. However, the genetic abnormalities of thymic neuroendocrine tumors with EAS remain largely unknown. We aim to elucidate the genetic abnormalities and identify the somatic mutations of potential tumor-related genes of thymic neuroendocrine tumors with EAS by whole exome sequencing...
February 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/27913435/idh2-mutations-define-a-unique-subtype-of-breast-cancer-with-altered-nuclear-polarity
#10
Sarah Chiang, Britta Weigelt, Huei-Chi Wen, Fresia Pareja, Ashwini Raghavendra, Luciano G Martelotto, Kathleen A Burke, Thais Basili, Anqi Li, Felipe C Geyer, Salvatore Piscuoglio, Charlotte K Y Ng, Achim A Jungbluth, Jörg Balss, Stefan Pusch, Gabrielle M Baker, Kimberly S Cole, Andreas von Deimling, Julie M Batten, Jonathan D Marotti, Hwei-Choo Soh, Benjamin L McCalip, Jonathan Serrano, Raymond S Lim, Kalliopi P Siziopikou, Song Lu, Xiaolong Liu, Tarek Hammour, Edi Brogi, Matija Snuderl, A John Iafrate, Jorge S Reis-Filho, Stuart J Schnitt
Solid papillary carcinoma with reverse polarity (SPCRP) is a rare breast cancer subtype with an obscure etiology. In this study, we sought to describe its unique histopathologic features and to identify the genetic alterations that underpin SPCRP using massively parallel whole-exome and targeted sequencing. The morphologic and immunohistochemical features of SPCRP support the invasive nature of this subtype. Ten of 13 (77%) SPCRPs harbored hotspot mutations at R172 of the isocitrate dehydrogenase IDH2, of which 8 of 10 displayed concurrent pathogenic mutations affecting PIK3CA or PIK3R1 One of the IDH2 wild-type SPCRPs harbored a TET2 Q548* truncating mutation coupled with a PIK3CA H1047R hotspot mutation...
October 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27912749/whole-exome-sequencing-identifies-a-novel-missense-fbn2-mutation-co-segregating-in-a-four-generation-chinese-family-with-congenital-contractural-arachnodactyly
#11
Xingping Guo, Chunying Song, Yaping Shi, Hongxia Li, Weijing Meng, Qinzhao Yuan, Jinjie Xue, Jun Xie, Yunxia Liang, Yanan Yuan, Baofeng Yu, Huaixiu Wang, Yun Chen, Lixin Qi, Xinmin Li
BACKGROUND: Congenital contractural arachnodactyly (CCA) is an autosomal dominant rare genetic disease, estimated to be less than 1 in 10,000 worldwide. People with this condition often have permanently bent joints (contractures), like bent fingers and toes (camptodactyly). CASE PRESENTATION: In this study, we investigated the genetic aetiology of CCA in a four-generation Chinese family. The blood samples were collected from 22 living members of the family in the Yangquan County, Shanxi Province, China...
December 3, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27912315/genetics-of-infectious-and-inflammatory-diseases-overlapping-discoveries-from-association-and-exome-sequencing-studies
#12
David Langlais, Nassima Fodil, Philippe Gros
Genome technologies have defined a complex genetic architecture in major infectious, inflammatory, and autoimmune disorders. High density marker arrays and Immunochips have powered genome-wide association studies (GWAS) that have mapped nearly 450 genetic risk loci in 22 major inflammatory diseases, including a core of common genes that play a central role in pathological inflammation. Whole-exome and whole-genome sequencing have identified more than 265 genes in which mutations cause primary immunodeficiencies and rare forms of severe inflammatory bowel disease...
December 1, 2016: Annual Review of Immunology
https://www.readbyqxmd.com/read/27912044/mutations-in-prosc-disrupt-cellular-pyridoxal-phosphate-homeostasis-and-cause-vitamin-b6-dependent-epilepsy
#13
Niklas Darin, Emma Reid, Laurence Prunetti, Lena Samuelsson, Ralf A Husain, Matthew Wilson, Basma El Yacoubi, Emma Footitt, W K Chong, Louise C Wilson, Helen Prunty, Simon Pope, Simon Heales, Karine Lascelles, Mike Champion, Evangeline Wassmer, Pierangelo Veggiotti, Valérie de Crécy-Lagard, Philippa B Mills, Peter T Clayton
Pyridoxal 5'-phosphate (PLP), the active form of vitamin B6, functions as a cofactor in humans for more than 140 enzymes, many of which are involved in neurotransmitter synthesis and degradation. A deficiency of PLP can present, therefore, as seizures and other symptoms that are treatable with PLP and/or pyridoxine. Deficiency of PLP in the brain can be caused by inborn errors affecting B6 vitamer metabolism or by inactivation of PLP, which can occur when compounds accumulate as a result of inborn errors of other pathways or when small molecules are ingested...
December 1, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27911816/rapid-emergence-and-mechanisms-of-resistance-by-u87-glioblastoma-cells-to-doxorubicin-in-an-in-vitro-tumor-microfluidic-ecology
#14
Jeonghun Han, Yukyung Jun, So Hyun Kim, Hong-Hoa Hoang, Yeonjoo Jung, Suyeon Kim, Jaesang Kim, Robert H Austin, Sanghyuk Lee, Sungsu Park
In vitro prediction of the probable rapid emergence of resistance to a drug in tumors could act to winnow out potential candidates for further costly development. We have developed a microfluidic device consisting of ∼500 hexagonal microcompartments that provides a complex ecology with wide ranges of drug and nutrient gradients and local populations. This ecology of a fragmented metapopulation induced the drug resistance in stage IV U87 glioblastoma cells to doxorubicin in 7 d. Exome and transcriptome sequencing of the resistant cells identified mutations and differentially expressed genes...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911290/rare-genetic-variant-in-sorl1-may-increase-penetrance-of-alzheimer-s-disease-in-a-family-with-several-generations-of-apoe-%C3%A9-4-homozygosity
#15
Eva Louwersheimer, Petra E Cohn-Hokke, Yolande A L Pijnenburg, Marjan M Weiss, Erik A Sistermans, Annemieke J Rozemuller, Marc Hulsman, John C van Swieten, Cock M van Duijn, Frederik Barkhof, Teddy Koene, Philip Scheltens, Wiesje M Van der Flier, Henne Holstege
BACKGROUND: The major genetic risk factor for late onset Alzheimer's disease (AD) is the APOE-ɛ4 allele. However, APOE-ɛ4 homozygosity is not fully penetrant, suggesting co-occurrence of additional genetic variants. OBJECTIVE: To identify genetic factors that, next to APOE-ɛ4 homozygosity, contribute to the development of AD. METHODS: We identified a family with nine AD patients spanning four generations, with an inheritance pattern suggestive of autosomal dominant AD, with no variants in PSEN1, PSEN2, or APP...
November 28, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27910721/care-delivery-considerations-for-widespread-and-equitable-implementation-of-inherited-cancer-predisposition-testing
#16
Deborah Cragun, Anita Y Kinney, Tuya Pal
DNA sequencing advances through next-generation sequencing (NGS) and several practice changing events, have led to shifting paradigms for inherited cancer predisposition testing. These changes necessitated a means by which to maximize health benefits without unnecessarily inflating healthcare costs and exacerbating health disparities. Areas covered: NGS-based tests encompass multi-gene panel tests, whole exome sequencing, and whole genome sequencing, all of which test for multiple genes simultaneously, compared to prior sequencing practices through which testing was performed sequentially for one or two genes...
December 2, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27910131/whole-exome-association-of-rare-deletions-in-multiplex-oral-cleft-families
#17
Jack Fu, Terri H Beaty, Alan F Scott, Jacqueline Hetmanski, Margaret M Parker, Joan E Bailey Wilson, Mary L Marazita, Elisabeth Mangold, Hasan Albacha-Hejazi, Jeffrey C Murray, Alexandre Bureau, Jacob Carey, Stephen Cristiano, Ingo Ruczinski, Robert B Scharpf
By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood...
December 1, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27910067/next-generation-sequencing
#18
Matthieu Le Gallo, Fred Lozy, Daphne W Bell
Endometrial cancers are the most frequently diagnosed gynecological malignancy and were expected to be the seventh leading cause of cancer death among American women in 2015. The majority of endometrial cancers are of serous or endometrioid histology. Most human tumors, including endometrial tumors, are driven by the acquisition of pathogenic mutations in cancer genes. Thus, the identification of somatic mutations within tumor genomes is an entry point toward cancer gene discovery. However, efforts to pinpoint somatic mutations in human cancers have, until recently, relied on high-throughput sequencing of single genes or gene families using Sanger sequencing...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27909223/exome-sequencing-identified-rps15a-as-a-novel-causative-gene-for-diamond-blackfan-anemia
#19
Fumika Ikeda, Kenichi Yoshida, Tsutomu Toki, Tamayo Uechi, Shiori Ishida, Yukari Nakajima, Yoji Sasahara, Yusuke Okuno, Rika Kanezaki, Kiminori Terui, Takuya Kamio, Akie Kobayashi, Takashi Fujita, Aiko Sato-Otsubo, Yuichi Shiraishi, Hiroko Tanaka, Kenichi Chiba, Hideki Muramatsu, Hitoshi Kanno, Shouichi Ohga, Akira Ohara, Seiji Kojima, Naoya Kenmochi, Satoru Miyano, Seishi Ogawa, Etsuro Ito
No abstract text is available yet for this article.
December 1, 2016: Haematologica
https://www.readbyqxmd.com/read/27908673/darwin-comes-to-clinic
#20
Arthur L Beaudet
What might be the benefits of whole-genome rather than whole-exome sequencing (WES) for identifying the genetic causes of human disabilities? A recent paper by Doan et al. focuses attention on mutations in human accelerated regions (HARs), a subset of genomic regulatory elements showing accelerated evolution between chimpanzees and humans.
November 28, 2016: Trends in Genetics: TIG
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