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https://www.readbyqxmd.com/read/28643794/enrichment-of-low-frequency-functional-variants-revealed-by-whole-genome-sequencing-of-multiple-isolated-european-populations
#1
Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti, Nicole Soranzo, Daniela Toniolo, James F Wilson, Richard Durbin, Chris Tyler-Smith, Eleftheria Zeggini
The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28560825/phredem-a-phred-score-informed-genotype-calling-approach-for-next-generation-sequencing-studies
#2
Peizhou Liao, Glen A Satten, Yi-Juan Hu
A fundamental challenge in analyzing next-generation sequencing (NGS) data is to determine an individual's genotype accurately, as the accuracy of the inferred genotype is essential to downstream analyses. Correctly estimating the base-calling error rate is critical to accurate genotype calls. Phred scores that accompany each call can be used to decide which calls are reliable. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates from phred scores or recalibrated base quality scores...
May 31, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28552196/whole-genome-sequencing-coupled-to-imputation-discovers-genetic-signals-for-anthropometric-traits
#3
Ioanna Tachmazidou, Dániel Süveges, Josine L Min, Graham R S Ritchie, Julia Steinberg, Klaudia Walter, Valentina Iotchkova, Jeremy Schwartzentruber, Jie Huang, Yasin Memari, Shane McCarthy, Andrew A Crawford, Cristina Bombieri, Massimiliano Cocca, Aliki-Eleni Farmaki, Tom R Gaunt, Pekka Jousilahti, Marjolein N Kooijman, Benjamin Lehne, Giovanni Malerba, Satu Männistö, Angela Matchan, Carolina Medina-Gomez, Sarah J Metrustry, Abhishek Nag, Ioanna Ntalla, Lavinia Paternoster, Nigel W Rayner, Cinzia Sala, William R Scott, Hashem A Shihab, Lorraine Southam, Beate St Pourcain, Michela Traglia, Katerina Trajanoska, Gialuigi Zaza, Weihua Zhang, María S Artigas, Narinder Bansal, Marianne Benn, Zhongsheng Chen, Petr Danecek, Wei-Yu Lin, Adam Locke, Jian'an Luan, Alisa K Manning, Antonella Mulas, Carlo Sidore, Anne Tybjaerg-Hansen, Anette Varbo, Magdalena Zoledziewska, Chris Finan, Konstantinos Hatzikotoulas, Audrey E Hendricks, John P Kemp, Alireza Moayyeri, Kalliope Panoutsopoulou, Michal Szpak, Scott G Wilson, Michael Boehnke, Francesco Cucca, Emanuele Di Angelantonio, Claudia Langenberg, Cecilia Lindgren, Mark I McCarthy, Andrew P Morris, Børge G Nordestgaard, Robert A Scott, Martin D Tobin, Nicholas J Wareham, Paul Burton, John C Chambers, George Davey Smith, George Dedoussis, Janine F Felix, Oscar H Franco, Giovanni Gambaro, Paolo Gasparini, Christopher J Hammond, Albert Hofman, Vincent W V Jaddoe, Marcus Kleber, Jaspal S Kooner, Markus Perola, Caroline Relton, Susan M Ring, Fernando Rivadeneira, Veikko Salomaa, Timothy D Spector, Oliver Stegle, Daniela Toniolo, André G Uitterlinden, Inês Barroso, Celia M T Greenwood, John R B Perry, Brian R Walker, Adam S Butterworth, Yali Xue, Richard Durbin, Kerrin S Small, Nicole Soranzo, Nicholas J Timpson, Eleftheria Zeggini
Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28546572/corrigendum-mutations-in-the-histone-methyltransferase-gene-kmt2b-cause-complex-early-onset-dystonia
#4
Esther Meyer, Keren J Carss, Julia Rankin, John M E Nichols, Detelina Grozeva, Agnel P Joseph, Niccolo E Mencacci, Apostolos Papandreou, Joanne Ng, Serena Barral, Adeline Ngoh, Hilla Ben-Pazi, Michel A Willemsen, David Arkadir, Angela Barnicoat, Hagai Bergman, Sanjay Bhate, Amber Boys, Niklas Darin, Nicola Foulds, Nicholas Gutowski, Alison Hills, Henry Houlden, Jane A Hurst, Zvi Israel, Margaret Kaminska, Patricia Limousin, Daniel Lumsden, Shane McKee, Shibalik Misra, Shekeeb S Mohammed, Vasiliki Nakou, Joost Nicolai, Magnus Nilsson, Hardev Pall, Kathryn J Peall, Gregory B Peters, Prab Prabhakar, Miriam S Reuter, Patrick Rump, Reeval Segel, Margje Sinnema, Martin Smith, Peter Turnpenny, Susan M White, Dagmar Wieczorek, Sarah Wiethoff, Brian T Wilson, Gidon Winter, Christopher Wragg, Simon Pope, Simon J H Heales, Deborah Morrogh, Alan Pittman, Lucinda J Carr, Belen Perez-Dueñas, Jean-Pierre Lin, Andre Reis, William A Gahl, Camilo Toro, Kailash P Bhatia, Nicholas W Wood, Erik-Jan Kamsteeg, Wui K Chong, Paul Gissen, Maya Topf, Russell C Dale, Jonathan R Chubb, F Lucy Raymond, Manju A Kurian
No abstract text is available yet for this article.
May 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28493397/a-recurrent-de-novo-mutation-in-actg1-causes-isolated-ocular-coloboma
#5
Joe Rainger, Kathleen A Williamson, Dinesh C Soares, Julia Truch, Dominic Kurian, Gabriele Gillessen-Kaesbach, Anne Seawright, James Prendergast, Mihail Halachev, Ann Wheeler, Lynn McTeir, Andrew C Gill, Veronica van Heyningen, Megan G Davey, David R FitzPatrick
Ocular coloboma (OC) is a defect in optic fissure closure and is a common cause of severe congenital visual impairment. Bilateral OC is primarily genetically determined and shows marked locus heterogeneity. Whole-exome sequencing (WES) was used to analyze 12 trios (child affected with OC and both unaffected parents). This identified de novo mutations in 10 different genes in eight probands. Three of these genes encoded proteins associated with actin cytoskeleton dynamics: ACTG1, TWF1, and LCP1. Proband-only WES identified a second unrelated individual with isolated OC carrying the same ACTG1 allele, encoding p...
May 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/28472463/genome-wide-association-study-meta-analysis-for-quantitative-ultrasound-parameters-of-bone-identifies-five-novel-loci-for-broadband-ultrasound-attenuation
#6
Benjamin H Mullin, Jing Hua Zhao, Suzanne J Brown, John R B Perry, Jian'an Luan, Hou-Feng Zheng, Claudia Langenberg, Frank Dudbridge, Robert Scott, Nick J Wareham, Tim D Spector, J Brent Richards, John P Walsh, Scott G Wilson
Osteoporosis is a common and debilitating bone disease that is characterised by low bone mineral density, typically assessed using dual-energy X-ray absorptiometry. Quantitative ultrasound (QUS), commonly utilising the two parameters velocity of sound (VOS) and broadband ultrasound attenuation (BUA), is an alternative technology used to assess bone properties at peripheral skeletal sites. The genetic influence on the bone qualities assessed by QUS remains an under-studied area. We performed a comprehensive GWAS including low-frequency variants (MAF ≥0...
May 4, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28349888/screening-for-familial-hypercholesterolaemia-in-childhood-avon-longitudinal-study-of-parents-and-children-alspac
#7
Marta Futema, Jackie A Cooper, Marietta Charakida, Christopher Boustred, Naveed Sattar, John Deanfield, Debbie A Lawlor, Nicholas J Timpson, Steve E Humphries, Aroon D Hingorani
BACKGROUND AND AIMS: Familial hypercholesterolaemia (FH) is an autosomal-dominant disease with frequency of 1/500 to 1/250 that leads to premature coronary heart disease. New approaches to identify FH mutation-carriers early are needed to prevent premature cardiac deaths. In a cross-sectional study of the Avon Longitudinal Study of Parents and Children (ALSPAC), we evaluated the biochemical thresholds for FH screening in childhood, and modelled a two-stage biochemical and sequencing screening strategy for FH detection...
May 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28176794/x-linked-primary-ciliary-dyskinesia-due-to-mutations-in-the-cytoplasmic-axonemal-dynein-assembly-factor-pih1d3
#8
Chiara Olcese, Mitali P Patel, Amelia Shoemark, Santeri Kiviluoto, Marie Legendre, Hywel J Williams, Cara K Vaughan, Jane Hayward, Alice Goldenberg, Richard D Emes, Mustafa M Munye, Laura Dyer, Thomas Cahill, Jeremy Bevillard, Corinne Gehrig, Michel Guipponi, Sandra Chantot, Philippe Duquesnoy, Lucie Thomas, Ludovic Jeanson, Bruno Copin, Aline Tamalet, Christel Thauvin-Robinet, Jean-François Papon, Antoine Garin, Isabelle Pin, Gabriella Vera, Paul Aurora, Mahmoud R Fassad, Lucy Jenkins, Christopher Boustred, Thomas Cullup, Mellisa Dixon, Alexandros Onoufriadis, Andrew Bush, Eddie M K Chung, Stylianos E Antonarakis, Michael R Loebinger, Robert Wilson, Miguel Armengot, Estelle Escudier, Claire Hogg, Serge Amselem, Zhaoxia Sun, Lucia Bartoloni, Jean-Louis Blouin, Hannah M Mitchison
By moving essential body fluids and molecules, motile cilia and flagella govern respiratory mucociliary clearance, laterality determination and the transport of gametes and cerebrospinal fluid. Primary ciliary dyskinesia (PCD) is an autosomal recessive disorder frequently caused by non-assembly of dynein arm motors into cilia and flagella axonemes. Before their import into cilia and flagella, multi-subunit axonemal dynein arms are thought to be stabilized and pre-assembled in the cytoplasm through a DNAAF2-DNAAF4-HSP90 complex akin to the HSP90 co-chaperone R2TP complex...
February 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28165464/genome-wide-association-analysis-implicates-dysregulation-of-immunity-genes-in-chronic-lymphocytic-leukaemia
#9
Philip J Law, Sonja I Berndt, Helen E Speedy, Nicola J Camp, Georgina P Sava, Christine F Skibola, Amy Holroyd, Vijai Joseph, Nicola J Sunter, Alexandra Nieters, Silvia Bea, Alain Monnereau, David Martin-Garcia, Lynn R Goldin, Guillem Clot, Lauren R Teras, Inés Quintela, Brenda M Birmann, Sandrine Jayne, Wendy Cozen, Aneela Majid, Karin E Smedby, Qing Lan, Claire Dearden, Angela R Brooks-Wilson, Andrew G Hall, Mark P Purdue, Tryfonia Mainou-Fowler, Claire M Vajdic, Graham H Jackson, Pierluigi Cocco, Helen Marr, Yawei Zhang, Tongzhang Zheng, Graham G Giles, Charles Lawrence, Timothy G Call, Mark Liebow, Mads Melbye, Bengt Glimelius, Larry Mansouri, Martha Glenn, Karen Curtin, W Ryan Diver, Brian K Link, Lucia Conde, Paige M Bracci, Elizabeth A Holly, Rebecca D Jackson, Lesley F Tinker, Yolanda Benavente, Paolo Boffetta, Paul Brennan, Marc Maynadie, James McKay, Demetrius Albanes, Stephanie Weinstein, Zhaoming Wang, Neil E Caporaso, Lindsay M Morton, Richard K Severson, Elio Riboli, Paolo Vineis, Roel C H Vermeulen, Melissa C Southey, Roger L Milne, Jacqueline Clavel, Sabine Topka, John J Spinelli, Peter Kraft, Maria Grazia Ennas, Geoffrey Summerfield, Giovanni M Ferri, Robert J Harris, Lucia Miligi, Andrew R Pettitt, Kari E North, David J Allsup, Joseph F Fraumeni, James R Bailey, Kenneth Offit, Guy Pratt, Henrik Hjalgrim, Chris Pepper, Stephen J Chanock, Chris Fegan, Richard Rosenquist, Silvia de Sanjose, Angel Carracedo, Martin J S Dyer, Daniel Catovsky, Elias Campo, James R Cerhan, James M Allan, Nathanial Rothman, Richard Houlston, Susan Slager
Several chronic lymphocytic leukaemia (CLL) susceptibility loci have been reported; however, much of the heritable risk remains unidentified. Here we perform a meta-analysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes and UK10K data, totalling 6,200 cases and 17,598 controls after replication. We identify nine risk loci at 1p36.11 (rs34676223, P=5.04 × 10(-13)), 1q42.13 (rs41271473, P=1.06 × 10(-10)), 4q24 (rs71597109, P=1.37 × 10(-10)), 4q35.1 (rs57214277, P=3...
February 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28151491/clinical-and-molecular-consequences-of-disease-associated-de-novo-mutations-in-satb2
#10
Hemant Bengani, Mark Handley, Mohsan Alvi, Rita Ibitoye, Melissa Lees, Sally Ann Lynch, Wayne Lam, Madeleine Fannemel, Ann Nordgren, H Malmgren, M Kvarnung, Sarju Mehta, Shane McKee, Margo Whiteford, Fiona Stewart, Fiona Connell, Jill Clayton-Smith, Sahar Mansour, Shehla Mohammed, Alan Fryer, Jenny Morton, Detelina Grozeva, Tara Asam, David Moore, Alejandro Sifrim, Jeremy McRae, Matthew E Hurles, Helen V Firth, F Lucy Raymond, Usha Kini, Christoffer Nellåker, Ddd Study, David R FitzPatrick
PURPOSE: To characterize features associated with de novo mutations affecting SATB2 function in individuals ascertained on the basis of intellectual disability. METHODS: Twenty previously unreported individuals with 19 different SATB2 mutations (11 loss-of-function and 8 missense variants) were studied. Fibroblasts were used to measure mutant protein production. Subcellular localization and mobility of wild-type and mutant SATB2 were assessed using fluorescently tagged protein...
February 2, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28145424/whole-genome-view-of-the-consequences-of-a-population-bottleneck-using-2926-genome-sequences-from-finland-and-united-kingdom
#11
Himanshu Chheda, Priit Palta, Matti Pirinen, Shane McCarthy, Klaudia Walter, Seppo Koskinen, Veikko Salomaa, Mark Daly, Richard Durbin, Aarno Palotie, Tero Aittokallio, Samuli Ripatti
Isolated populations with enrichment of variants due to recent population bottlenecks provide a powerful resource for identifying disease-associated genetic variants and genes. As a model of an isolate population, we sequenced the genomes of 1463 Finnish individuals as part of the Sequencing Initiative Suomi (SISu) Project. We compared the genomic profiles of the 1463 Finns to a sample of 1463 British individuals that were sequenced in parallel as part of the UK10K Project. Whereas there were no major differences in the allele frequency of common variants, a significant depletion of variants in the rare frequency spectrum was observed in Finns when comparing the two populations...
April 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28117402/whole-exome-sequencing-of-228-patients-with-sporadic-parkinson-s-disease
#12
Cynthia Sandor, Frantisek Honti, Wilfried Haerty, Konrad Szewczyk-Krolikowski, Paul Tomlinson, Sam Evetts, Stephanie Millin, Thomas Keane, Shane A McCarthy, Richard Durbin, Kevin Talbot, Michele Hu, Caleb Webber, Chris P Ponting, Richard Wade-Martins
Parkinson's disease (PD) is the most common neurodegenerative movement disorder, affecting 1% of the population over 65 years characterized clinically by both motor and non-motor symptoms accompanied by the preferential loss of dopamine neurons in the substantia nigra pars compacta. Here, we sequenced the exomes of 244 Parkinson's patients selected from the Oxford Parkinson's Disease Centre Discovery Cohort and, after quality control, 228 exomes were available for analyses. The PD patient exomes were compared to 884 control exomes selected from the UK10K datasets...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28004816/a-combined-reference-panel-from-the-1000%C3%A2-genomes-and-uk10k-projects-improved-rare-variant-imputation-in-european-and-chinese-samples
#13
Wen-Chi Chou, Hou-Feng Zheng, Chia-Ho Cheng, Han Yan, Li Wang, Fang Han, J Brent Richards, David Karasik, Douglas P Kiel, Yi-Hsiang Hsu
Imputation using the 1000 Genomes haplotype reference panel has been widely adapted to estimate genotypes in genome wide association studies. To evaluate imputation quality with a relatively larger reference panel and a reference panel composed of different ethnic populations, we conducted imputations in the Framingham Heart Study and the North Chinese Study using a combined reference panel from the 1000 Genomes (N = 1,092) and UK10K (N = 3,781) projects. For rare variants with 0.01% < MAF ≤ 0...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27992417/mutations-in-the-histone-methyltransferase-gene-kmt2b-cause-complex-early-onset-dystonia
#14
Esther Meyer, Keren J Carss, Julia Rankin, John M E Nichols, Detelina Grozeva, Agnel P Joseph, Niccolo E Mencacci, Apostolos Papandreou, Joanne Ng, Serena Barral, Adeline Ngoh, Hilla Ben-Pazi, Michel A Willemsen, David Arkadir, Angela Barnicoat, Hagai Bergman, Sanjay Bhate, Amber Boys, Niklas Darin, Nicola Foulds, Nicholas Gutowski, Alison Hills, Henry Houlden, Jane A Hurst, Zvi Israel, Margaret Kaminska, Patricia Limousin, Daniel Lumsden, Shane McKee, Shibalik Misra, Shekeeb S Mohammed, Vasiliki Nakou, Joost Nicolai, Magnus Nilsson, Hardev Pall, Kathryn J Peall, Gregory B Peters, Prab Prabhakar, Miriam S Reuter, Patrick Rump, Reeval Segel, Margje Sinnema, Martin Smith, Peter Turnpenny, Susan M White, Dagmar Wieczorek, Sarah Wiethoff, Brian T Wilson, Gidon Winter, Christopher Wragg, Simon Pope, Simon J H Heales, Deborah Morrogh, Alan Pittman, Lucinda J Carr, Belen Perez-Dueñas, Jean-Pierre Lin, Andre Reis, William A Gahl, Camilo Toro, Kailash P Bhatia, Nicholas W Wood, Erik-Jan Kamsteeg, Wui K Chong, Paul Gissen, Maya Topf, Russell C Dale, Jonathan R Chubb, F Lucy Raymond, Manju A Kurian
Histone lysine methylation, mediated by mixed-lineage leukemia (MLL) proteins, is now known to be critical in the regulation of gene expression, genomic stability, cell cycle and nuclear architecture. Despite MLL proteins being postulated as essential for normal development, little is known about the specific functions of the different MLL lysine methyltransferases. Here we report heterozygous variants in the gene KMT2B (also known as MLL4) in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance and characteristic brain magnetic resonance imaging findings...
February 2017: Nature Genetics
https://www.readbyqxmd.com/read/27903883/function-driven-discovery-of-disease-genes-in-zebrafish-using-an-integrated-genomics-big-data-resource
#15
Hongseok Shim, Ji Hyun Kim, Chan Yeong Kim, Sohyun Hwang, Hyojin Kim, Sunmo Yang, Ji Eun Lee, Insuk Lee
Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www...
November 16, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27799474/mirdnmr-a-gene-centered-database-of-background-de-novo-mutation-rates-in-human
#16
Yi Jiang, Zhongshan Li, Zhenwei Liu, Denghui Chen, Wanying Wu, Yaoqiang Du, Liying Ji, Zi-Bing Jin, Wei Li, Jinyu Wu
De novo germline mutations (DNMs) are the rarest genetic variants proven to cause a considerable number of sporadic genetic diseases, such as autism spectrum disorders, epileptic encephalopathy, schizophrenia, congenital heart disease, type 1 diabetes, and hearing loss. However, it is difficult to accurately assess the cause of DNMs and identify disease-causing genes from the considerable number of DNMs in probands. A common method to this problem is to identify genes that harbor significantly more DNMs than expected by chance, with accurate background DNM rate (DNMR) required...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27738015/detection-of-human-adaptation-during-the-past-2000-years
#17
Yair Field, Evan A Boyle, Natalie Telis, Ziyue Gao, Kyle J Gaulton, David Golan, Loic Yengo, Ghislain Rocheleau, Philippe Froguel, Mark I McCarthy, Jonathan K Pritchard
Detection of recent natural selection is a challenging problem in population genetics. Here we introduce the singleton density score (SDS), a method to infer very recent changes in allele frequencies from contemporary genome sequences. Applied to data from the UK10K Project, SDS reflects allele frequency changes in the ancestors of modern Britons during the past ~2000 to 3000 years. We see strong signals of selection at lactase and the major histocompatibility complex, and in favor of blond hair and blue eyes...
November 11, 2016: Science
https://www.readbyqxmd.com/read/27694927/a-genome-wide-association-study-identifies-risk-loci-for-childhood-acute-lymphoblastic-leukemia-at-10q26-13-and-12q23-1
#18
J Vijayakrishnan, R Kumar, M Y R Henrion, A V Moorman, P S Rachakonda, I Hosen, M I da Silva Filho, A Holroyd, S E Dobbins, R Koehler, H Thomsen, J A Irving, J M Allan, T Lightfoot, E Roman, S E Kinsey, E Sheridan, P D Thompson, P Hoffmann, M M Nöthen, S Heilmann-Heimbach, K H Jöckel, M Greaves, C J Harrison, C R Bartram, M Schrappe, M Stanulla, K Hemminki, R S Houlston
Genome-wide association studies (GWASs) have shown that common genetic variation contributes to the heritable risk of childhood acute lymphoblastic leukemia (ALL). To identify new susceptibility loci for the largest subtype of ALL, B-cell precursor ALL (BCP-ALL), we conducted a meta-analysis of two GWASs with imputation using 1000 Genomes and UK10K Project data as reference (totaling 1658 cases and 7224 controls). After genotyping an additional 2525 cases and 3575 controls, we identify new susceptibility loci for BCP-ALL mapping to 10q26...
March 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27668658/discovery-and-refinement-of-genetic-loci-associated-with-cardiometabolic-risk-using-dense-imputation-maps
#19
Valentina Iotchkova, Jie Huang, John A Morris, Deepti Jain, Caterina Barbieri, Klaudia Walter, Josine L Min, Lu Chen, William Astle, Massimilian Cocca, Patrick Deelen, Heather Elding, Aliki-Eleni Farmaki, Christopher S Franklin, Mattias Franberg, Tom R Gaunt, Albert Hofman, Tao Jiang, Marcus E Kleber, Genevieve Lachance, Jian'an Luan, Giovanni Malerba, Angela Matchan, Daniel Mead, Yasin Memari, Ioanna Ntalla, Kalliope Panoutsopoulou, Raha Pazoki, John R B Perry, Fernando Rivadeneira, Maria Sabater-Lleal, Bengt Sennblad, So-Youn Shin, Lorraine Southam, Michela Traglia, Freerk van Dijk, Elisabeth M van Leeuwen, Gianluigi Zaza, Weihua Zhang, Najaf Amin, Adam Butterworth, John C Chambers, George Dedoussis, Abbas Dehghan, Oscar H Franco, Lude Franke, Mattia Frontini, Giovanni Gambaro, Paolo Gasparini, Anders Hamsten, Aaron Issacs, Jaspal S Kooner, Charles Kooperberg, Claudia Langenberg, Winfried Marz, Robert A Scott, Morris A Swertz, Daniela Toniolo, Andre G Uitterlinden, Cornelia M van Duijn, Hugh Watkins, Eleftheria Zeggini, Mathew T Maurano, Nicholas J Timpson, Alexander P Reiner, Paul L Auer, Nicole Soranzo
Large-scale whole-genome sequence data sets offer novel opportunities to identify genetic variation underlying human traits. Here we apply genotype imputation based on whole-genome sequence data from the UK10K and 1000 Genomes Project into 35,981 study participants of European ancestry, followed by association analysis with 20 quantitative cardiometabolic and hematological traits. We describe 17 new associations, including 6 rare (minor allele frequency (MAF) < 1%) or low-frequency (1% < MAF < 5%) variants with platelet count (PLT), red blood cell indices (MCH and MCV) and HDL cholesterol...
November 2016: Nature Genetics
https://www.readbyqxmd.com/read/27587665/gtrac-fast-retrieval-from-compressed-collections-of-genomic-variants
#20
Kedar Tatwawadi, Mikel Hernaez, Idoia Ochoa, Tsachy Weissman
MOTIVATION: The dramatic decrease in the cost of sequencing has resulted in the generation of huge amounts of genomic data, as evidenced by projects such as the UK10K and the Million Veteran Project, with the number of sequenced genomes ranging in the order of 10 K to 1 M. Due to the large redundancies among genomic sequences of individuals from the same species, most of the medical research deals with the variants in the sequences as compared with a reference sequence, rather than with the complete genomic sequences...
September 1, 2016: Bioinformatics
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