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Jonathan Marchini

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https://www.readbyqxmd.com/read/27863252/the-allelic-landscape-of-human-blood-cell-trait-variation-and-links-to-common-complex-disease
#1
William J Astle, Heather Elding, Tao Jiang, Dave Allen, Dace Ruklisa, Alice L Mann, Daniel Mead, Heleen Bouman, Fernando Riveros-Mckay, Myrto A Kostadima, John J Lambourne, Suthesh Sivapalaratnam, Kate Downes, Kousik Kundu, Lorenzo Bomba, Kim Berentsen, John R Bradley, Louise C Daugherty, Olivier Delaneau, Kathleen Freson, Stephen F Garner, Luigi Grassi, Jose Guerrero, Matthias Haimel, Eva M Janssen-Megens, Anita Kaan, Mihir Kamat, Bowon Kim, Amit Mandoli, Jonathan Marchini, Joost H A Martens, Stuart Meacham, Karyn Megy, Jared O'Connell, Romina Petersen, Nilofar Sharifi, Simon M Sheard, James R Staley, Salih Tuna, Martijn van der Ent, Klaudia Walter, Shuang-Yin Wang, Eleanor Wheeler, Steven P Wilder, Valentina Iotchkova, Carmel Moore, Jennifer Sambrook, Hendrik G Stunnenberg, Emanuele Di Angelantonio, Stephen Kaptoge, Taco W Kuijpers, Enrique Carrillo-de-Santa-Pau, David Juan, Daniel Rico, Alfonso Valencia, Lu Chen, Bing Ge, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yang, Roderic Guigo, Stephan Beck, Dirk S Paul, Tomi Pastinen, David Bujold, Guillaume Bourque, Mattia Frontini, John Danesh, David J Roberts, Willem H Ouwehand, Adam S Butterworth, Nicole Soranzo
Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains...
November 17, 2016: Cell
https://www.readbyqxmd.com/read/27697780/the-oncoarray-consortium-a-network-for-understanding-the-genetic-architecture-of-common-cancers
#2
Christopher I Amos, Joe Dennis, Zhaoming Wang, Jinyoung Byun, Fredrick R Schumacher, Simon A Gayther, Graham Casey, David J Hunter, Thomas A Sellers, Stephen B Gruber, Alison M Dunning, Kyriaki Michailidou, Laura Fachal, Kimberly Doheny, Amanda B Spurdle, Yafang Li, Xiangjun Xiao, Jane Romm, Elizabeth Pugh, Gerhard A Coetzee, Dennis J Hazelett, Stig E Bojesen, Charlisse Caga-Anan, Christopher A Haiman, Ahsan Kamal, Craig Luccarini, Daniel Tessier, Daniel Vincent, Francois Bacot, David J Van Den Berg, Stefanie Nelson, Stephen Demetriades, David E Goldgar, Fergus J Couch, Judith L Forman, Graham G Giles, David V Conti, Heike Bickeböller, Angela Risch, Melanie Waldenberger, Irene Brüske-Hohlfeld, Belynda D Hicks, Hua Ling, Lesley McGuffog, Andrew Lee, Karoline Kuchenbaecker, Penny Soucy, Judith Manz, Julie M Cunningham, Katja Butterbach, Zsofia Kote-Jarai, Peter Kraft, Liesel FitzGerald, Sara Lindstrom, Marcia Adams, James D McKay, Catherine M Phelan, Sara Benlloch, Linda E Kelemen, Paul Brennan, Marjorie Riggan, Tracy A O'Mara, Hongbing Shen, Yong-Yong Shi, Deborah J Thompson, Marc T Goodman, Sune F Nielsen, Andrew Berchuck, Sylvie Laboissiere, Stephanie L Schmit, Tameka Shelford, Christopher K Edlund, Jack A Taylor, John Kirkpatrick Field, Sue K Park, Kenneth Offit, Mads Thomassen, Rita Schmutzler, Laura Ottini, Rayjean J Hung, Jonathan Marchini, Ali Amin Al Olama, Ulrike Peters, Rosalind A Eeles, Michael F Seldin, Elizabeth Gillanders, Daniela Seminara, Antonis C Antoniou, Paul D P Pharoah, Georgia Chenevix-Trench, Stephen J Chanock, Jacques Simard, Douglas F Easton
BACKGROUND: Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers and cancer related traits...
October 3, 2016: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/27561768/cystatin-c-and-cardiovascular-disease-a-mendelian-randomization-study
#3
Sander W van der Laan, Tove Fall, Aicha Soumaré, Alexander Teumer, Sanaz Sedaghat, Jens Baumert, Delilah Zabaneh, Jessica van Setten, Ivana Isgum, Tessel E Galesloot, Johannes Arpegård, Philippe Amouyel, Stella Trompet, Melanie Waldenberger, Marcus Dörr, Patrik K Magnusson, Vilmantas Giedraitis, Anders Larsson, Andrew P Morris, Janine F Felix, Alanna C Morrison, Nora Franceschini, Joshua C Bis, Maryam Kavousi, Christopher O'Donnell, Fotios Drenos, Vinicius Tragante, Patricia B Munroe, Rainer Malik, Martin Dichgans, Bradford B Worrall, Jeanette Erdmann, Christopher P Nelson, Nilesh J Samani, Heribert Schunkert, Jonathan Marchini, Riyaz S Patel, Aroon D Hingorani, Lars Lind, Nancy L Pedersen, Jacqueline de Graaf, Lambertus A L M Kiemeney, Sebastian E Baumeister, Oscar H Franco, Albert Hofman, André G Uitterlinden, Wolfgang Koenig, Christa Meisinger, Annette Peters, Barbara Thorand, J Wouter Jukema, Bjørn Odvar Eriksen, Ingrid Toft, Tom Wilsgaard, N Charlotte Onland-Moret, Yvonne T van der Schouw, Stéphanie Debette, Meena Kumari, Per Svensson, Pim van der Harst, Mika Kivimaki, Brendan J Keating, Naveed Sattar, Abbas Dehghan, Alex P Reiner, Erik Ingelsson, Hester M den Ruijter, Paul I W de Bakker, Gerard Pasterkamp, Johan Ärnlöv, Michael V Holmes, Folkert W Asselbergs
BACKGROUND: Epidemiological studies show that high circulating cystatin C is associated with risk of cardiovascular disease (CVD), independent of creatinine-based renal function measurements. It is unclear whether this relationship is causal, arises from residual confounding, and/or is a consequence of reverse causation. OBJECTIVES: The aim of this study was to use Mendelian randomization to investigate whether cystatin C is causally related to CVD in the general population...
August 30, 2016: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/27479908/tensor-decomposition-for-multiple-tissue-gene-expression-experiments
#4
Victoria Hore, Ana Viñuela, Alfonso Buil, Julian Knight, Mark I McCarthy, Kerrin Small, Jonathan Marchini
Genome-wide association studies of gene expression traits and other cellular phenotypes have successfully identified links between genetic variation and biological processes. The majority of discoveries have uncovered cis-expression quantitative trait locus (eQTL) effects via mass univariate testing of SNPs against gene expression in single tissues. Here we present a Bayesian method for multiple-tissue experiments focusing on uncovering gene networks linked to genetic variation. Our method decomposes the 3D array (or tensor) of gene expression measurements into a set of latent components...
September 2016: Nature Genetics
https://www.readbyqxmd.com/read/27270105/haplotype-estimation-for-biobank-scale-data-sets
#5
Jared O'Connell, Kevin Sharp, Nick Shrine, Louise Wain, Ian Hall, Martin Tobin, Jean-Francois Zagury, Olivier Delaneau, Jonathan Marchini
The UK Biobank (UKB) has recently released genotypes on 152,328 individuals together with extensive phenotypic and lifestyle information. We present a new phasing method, SHAPEIT3, that can handle such biobank-scale data sets and results in switch error rates as low as ∼0.3%. The method exhibits O(NlogN) scaling with sample size N, enabling fast and accurate phasing of even larger cohorts.
July 2016: Nature Genetics
https://www.readbyqxmd.com/read/27153703/phasing-for-medical-sequencing-using-rare-variants-and-large-haplotype-reference-panels
#6
Kevin Sharp, Warren Kretzschmar, Olivier Delaneau, Jonathan Marchini
MOTIVATION: There is growing recognition that estimating haplotypes from high coverage sequencing of single samples in clinical settings is an important problem. At the same time very large datasets consisting of tens and hundreds of thousands of high-coverage sequenced samples will soon be available. We describe a method that takes advantage of these huge human genetic variation resources and rare variant sharing patterns to estimate haplotypes on single sequenced samples. Sharing rare variants between two individuals is more likely to arise from a recent common ancestor and, hence, also more likely to indicate similar shared haplotypes over a substantial flanking region of sequence...
July 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26901065/a-multiple-phenotype-imputation-method-for-genetic-studies
#7
Andrew Dahl, Valentina Iotchkova, Amelie Baud, Åsa Johansson, Ulf Gyllensten, Nicole Soranzo, Richard Mott, Andreas Kranis, Jonathan Marchini
Genetic association studies have yielded a wealth of biological discoveries. However, these studies have mostly analyzed one trait and one SNP at a time, thus failing to capture the underlying complexity of the data sets. Joint genotype-phenotype analyses of complex, high-dimensional data sets represent an important way to move beyond simple genome-wide association studies (GWAS) with great potential. The move to high-dimensional phenotypes will raise many new statistical problems. Here we address the central issue of missing phenotypes in studies with any level of relatedness between samples...
April 2016: Nature Genetics
https://www.readbyqxmd.com/read/26432245/a-global-reference-for-human-genetic-variation
#8
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis
The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84...
October 1, 2015: Nature
https://www.readbyqxmd.com/read/26423011/novel-insights-into-the-genetics-of-smoking-behaviour-lung-function-and-chronic-obstructive-pulmonary-disease-uk-bileve-a-genetic-association-study-in-uk-biobank
#9
Louise V Wain, Nick Shrine, Suzanne Miller, Victoria E Jackson, Ioanna Ntalla, María Soler Artigas, Charlotte K Billington, Abdul Kader Kheirallah, Richard Allen, James P Cook, Kelly Probert, Ma'en Obeidat, Yohan Bossé, Ke Hao, Dirkje S Postma, Peter D Paré, Adaikalavan Ramasamy, Reedik Mägi, Evelin Mihailov, Eva Reinmaa, Erik Melén, Jared O'Connell, Eleni Frangou, Olivier Delaneau, Colin Freeman, Desislava Petkova, Mark McCarthy, Ian Sayers, Panos Deloukas, Richard Hubbard, Ian Pavord, Anna L Hansell, Neil C Thomson, Eleftheria Zeggini, Andrew P Morris, Jonathan Marchini, David P Strachan, Martin D Tobin, Ian P Hall
BACKGROUND: Understanding the genetic basis of airflow obstruction and smoking behaviour is key to determining the pathophysiology of chronic obstructive pulmonary disease (COPD). We used UK Biobank data to study the genetic causes of smoking behaviour and lung health. METHODS: We sampled individuals of European ancestry from UK Biobank, from the middle and extremes of the forced expiratory volume in 1 s (FEV1) distribution among heavy smokers (mean 35 pack-years) and never smokers...
October 2015: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/26368830/improved-imputation-of-low-frequency-and-rare-variants-using-the-uk10k-haplotype-reference-panel
#10
Jie Huang, Bryan Howie, Shane McCarthy, Yasin Memari, Klaudia Walter, Josine L Min, Petr Danecek, Giovanni Malerba, Elisabetta Trabetti, Hou-Feng Zheng, Giovanni Gambaro, J Brent Richards, Richard Durbin, Nicholas J Timpson, Jonathan Marchini, Nicole Soranzo
Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated a data set of 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down to 0.1% minor allele frequency in the British population. Here we demonstrate the value of this resource for improving imputation accuracy at rare and low-frequency variants in both a UK and an Italian population...
September 14, 2015: Nature Communications
https://www.readbyqxmd.com/read/26242864/multicohort-analysis-of-the-maternal-age-effect-on-recombination
#11
Hilary C Martin, Ryan Christ, Julie G Hussin, Jared O'Connell, Scott Gordon, Hamdi Mbarek, Jouke-Jan Hottenga, Kerrie McAloney, Gonnecke Willemsen, Paolo Gasparini, Nicola Pirastu, Grant W Montgomery, Pau Navarro, Nicole Soranzo, Daniela Toniolo, Veronique Vitart, James F Wilson, Jonathan Marchini, Dorret I Boomsma, Nicholas G Martin, Peter Donnelly
Several studies have reported that the number of crossovers increases with maternal age in humans, but others have found the opposite. Resolving the true effect has implications for understanding the maternal age effect on aneuploidies. Here, we revisit this question in the largest sample to date using single nucleotide polymorphism (SNP)-chip data, comprising over 6,000 meioses from nine cohorts. We develop and fit a hierarchical model to allow for differences between cohorts and between mothers. We estimate that over 10 years, the expected number of maternal crossovers increases by 2...
August 5, 2015: Nature Communications
https://www.readbyqxmd.com/read/25913401/molecular-signatures-of-major-depression
#12
Na Cai, Simon Chang, Yihan Li, Qibin Li, Jingchu Hu, Jieqin Liang, Li Song, Warren Kretzschmar, Xiangchao Gan, Jerome Nicod, Margarita Rivera, Hong Deng, Bo Du, Keqing Li, Wenhu Sang, Jingfang Gao, Shugui Gao, Baowei Ha, Hung-Yao Ho, Chunmei Hu, Jian Hu, Zhenfei Hu, Guoping Huang, Guoqing Jiang, Tao Jiang, Wei Jin, Gongying Li, Kan Li, Yi Li, Yingrui Li, Youhui Li, Yu-Ting Lin, Lanfen Liu, Tiebang Liu, Ying Liu, Yuan Liu, Yao Lu, Luxian Lv, Huaqing Meng, Puyi Qian, Hong Sang, Jianhua Shen, Jianguo Shi, Jing Sun, Ming Tao, Gang Wang, Guangbiao Wang, Jian Wang, Linmao Wang, Xueyi Wang, Xumei Wang, Huanming Yang, Lijun Yang, Ye Yin, Jinbei Zhang, Kerang Zhang, Ning Sun, Wei Zhang, Xiuqing Zhang, Zhen Zhang, Hui Zhong, Gerome Breen, Jun Wang, Jonathan Marchini, Yiping Chen, Qi Xu, Xun Xu, Richard Mott, Guo-Jen Huang, Kenneth Kendler, Jonathan Flint
Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with the discovery of molecular signatures of stress, some of which include alterations to an individual's somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between a stress-related disease, major depression, and the amount of mtDNA (p = 9.00 × 10(-42), odds ratio 1.33 [95% confidence interval [CI] = 1.29-1.37]) and telomere length (p = 2.84 × 10(-14), odds ratio 0...
May 4, 2015: Current Biology: CB
https://www.readbyqxmd.com/read/25653097/integrating-sequence-and-array-data-to-create-an-improved-1000-genomes-project-haplotype-reference-panel
#13
Olivier Delaneau, Jonathan Marchini
A major use of the 1000 Genomes Project (1000 GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy...
June 13, 2014: Nature Communications
https://www.readbyqxmd.com/read/24743097/a-general-approach-for-haplotype-phasing-across-the-full-spectrum-of-relatedness
#14
Jared O'Connell, Deepti Gurdasani, Olivier Delaneau, Nicola Pirastu, Sheila Ulivi, Massimiliano Cocca, Michela Traglia, Jie Huang, Jennifer E Huffman, Igor Rudan, Ruth McQuillan, Ross M Fraser, Harry Campbell, Ozren Polasek, Gershim Asiki, Kenneth Ekoru, Caroline Hayward, Alan F Wright, Veronique Vitart, Pau Navarro, Jean-Francois Zagury, James F Wilson, Daniela Toniolo, Paolo Gasparini, Nicole Soranzo, Manjinder S Sandhu, Jonathan Marchini
Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations, we have investigated the performance of different phasing methods designed for nominally 'unrelated' individuals. We find that SHAPEIT2 produces much lower switch error rates in all cohorts compared to other methods, including those designed specifically for isolated populations...
April 2014: PLoS Genetics
https://www.readbyqxmd.com/read/24388745/s-nitrosothiol-signaling-regulates-liver-development-and-improves-outcome-following-toxic-liver-injury
#15
Andrew G Cox, Diane C Saunders, Peter B Kelsey, Allie A Conway, Yevgenia Tesmenitsky, Julio F Marchini, Kristin K Brown, Jonathan S Stamler, Dorothy B Colagiovanni, Gary J Rosenthal, Kevin J Croce, Trista E North, Wolfram Goessling
Toxic liver injury is a leading cause of liver failure and death because of the organ's inability to regenerate amidst massive cell death, and few therapeutic options exist. The mechanisms coordinating damage protection and repair are poorly understood. Here, we show that S-nitrosothiols regulate liver growth during development and after injury in vivo; in zebrafish, nitric-oxide (NO) enhanced liver formation independently of cGMP-mediated vasoactive effects. After acetaminophen (APAP) exposure, inhibition of the enzymatic regulator S-nitrosoglutathione reductase (GSNOR) minimized toxic liver damage, increased cell proliferation, and improved survival through sustained activation of the cytoprotective Nrf2 pathway...
January 16, 2014: Cell Reports
https://www.readbyqxmd.com/read/24186853/distinct-loci-in-the-chrna5-chrna3-chrnb4-gene-cluster-are-associated-with-onset-of-regular-smoking
#16
Sarah H Stephens, Sarah M Hartz, Nicole R Hoft, Nancy L Saccone, Robin C Corley, John K Hewitt, Christian J Hopfer, Naomi Breslau, Hilary Coon, Xiangning Chen, Francesca Ducci, Nicole Dueker, Nora Franceschini, Josef Frank, Younghun Han, Nadia N Hansel, Chenhui Jiang, Tellervo Korhonen, Penelope A Lind, Jason Liu, Leo-Pekka Lyytikäinen, Martha Michel, John R Shaffer, Susan E Short, Juzhong Sun, Alexander Teumer, John R Thompson, Nicole Vogelzangs, Jacqueline M Vink, Angela Wenzlaff, William Wheeler, Bao-Zhu Yang, Steven H Aggen, Anthony J Balmforth, Sebastian E Baumeister, Terri H Beaty, Daniel J Benjamin, Andrew W Bergen, Ulla Broms, David Cesarini, Nilanjan Chatterjee, Jingchun Chen, Yu-Ching Cheng, Sven Cichon, David Couper, Francesco Cucca, Danielle Dick, Tatiana Foroud, Helena Furberg, Ina Giegling, Nathan A Gillespie, Fangyi Gu, Alistair S Hall, Jenni Hällfors, Shizhong Han, Annette M Hartmann, Kauko Heikkilä, Ian B Hickie, Jouke Jan Hottenga, Pekka Jousilahti, Marika Kaakinen, Mika Kähönen, Philipp D Koellinger, Stephen Kittner, Bettina Konte, Maria-Teresa Landi, Tiina Laatikainen, Mark Leppert, Steven M Levy, Rasika A Mathias, Daniel W McNeil, Sarah E Medland, Grant W Montgomery, Tanda Murray, Matthias Nauck, Kari E North, Peter D Paré, Michele Pergadia, Ingo Ruczinski, Veikko Salomaa, Jorma Viikari, Gonneke Willemsen, Kathleen C Barnes, Eric Boerwinkle, Dorret I Boomsma, Neil Caporaso, Howard J Edenberg, Clyde Francks, Joel Gelernter, Hans Jörgen Grabe, Hyman Hops, Marjo-Riitta Jarvelin, Magnus Johannesson, Kenneth S Kendler, Terho Lehtimäki, Patrik K E Magnusson, Mary L Marazita, Jonathan Marchini, Braxton D Mitchell, Markus M Nöthen, Brenda W Penninx, Olli Raitakari, Marcella Rietschel, Dan Rujescu, Nilesh J Samani, Ann G Schwartz, Sanjay Shete, Margaret Spitz, Gary E Swan, Henry Völzke, Juha Veijola, Qingyi Wei, Chris Amos, Dale S Cannon, Richard Grucza, Dorothy Hatsukami, Andrew Heath, Eric O Johnson, Jaakko Kaprio, Pamela Madden, Nicholas G Martin, Victoria L Stevens, Robert B Weiss, Peter Kraft, Laura J Bierut, Marissa A Ehringer
Neuronal nicotinic acetylcholine receptor (nAChR) genes (CHRNA5/CHRNA3/CHRNB4) have been reproducibly associated with nicotine dependence, smoking behaviors, and lung cancer risk. Of the few reports that have focused on early smoking behaviors, association results have been mixed. This meta-analysis examines early smoking phenotypes and SNPs in the gene cluster to determine: (1) whether the most robust association signal in this region (rs16969968) for other smoking behaviors is also associated with early behaviors, and/or (2) if additional statistically independent signals are important in early smoking...
December 2013: Genetic Epidemiology
https://www.readbyqxmd.com/read/24094745/haplotype-estimation-using-sequencing-reads
#17
Olivier Delaneau, Bryan Howie, Anthony J Cox, Jean-François Zagury, Jonathan Marchini
High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called...
October 3, 2013: American Journal of Human Genetics
https://www.readbyqxmd.com/read/23478400/the-origin-evolution-and-functional-impact-of-short-insertion-deletion-variants-identified-in-179-human-genomes
#18
Stephen B Montgomery, David L Goode, Erika Kvikstad, Cornelis A Albers, Zhengdong D Zhang, Xinmeng Jasmine Mu, Guruprasad Ananda, Bryan Howie, Konrad J Karczewski, Kevin S Smith, Vanessa Anaya, Rhea Richardson, Joe Davis, Daniel G MacArthur, Arend Sidow, Laurent Duret, Mark Gerstein, Kateryna D Makova, Jonathan Marchini, Gil McVean, Gerton Lunter
Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 individuals representing three diverse human populations. We show that rates of indel mutagenesis are highly heterogeneous, with 43%-48% of indels occurring in 4.03% of the genome, whereas in the remaining 96% their prevalence is 16 times lower than SNPs...
May 2013: Genome Research
https://www.readbyqxmd.com/read/23284291/genome-wide-joint-meta-analysis-of-snp-and-snp-by-smoking-interaction-identifies-novel-loci-for-pulmonary-function
#19
Dana B Hancock, María Soler Artigas, Sina A Gharib, Amanda Henry, Ani Manichaikul, Adaikalavan Ramasamy, Daan W Loth, Medea Imboden, Beate Koch, Wendy L McArdle, Albert V Smith, Joanna Smolonska, Akshay Sood, Wenbo Tang, Jemma B Wilk, Guangju Zhai, Jing Hua Zhao, Hugues Aschard, Kristin M Burkart, Ivan Curjuric, Mark Eijgelsheim, Paul Elliott, Xiangjun Gu, Tamara B Harris, Christer Janson, Georg Homuth, Pirro G Hysi, Jason Z Liu, Laura R Loehr, Kurt Lohman, Ruth J F Loos, Alisa K Manning, Kristin D Marciante, Ma'en Obeidat, Dirkje S Postma, Melinda C Aldrich, Guy G Brusselle, Ting-hsu Chen, Gudny Eiriksdottir, Nora Franceschini, Joachim Heinrich, Jerome I Rotter, Cisca Wijmenga, O Dale Williams, Amy R Bentley, Albert Hofman, Cathy C Laurie, Thomas Lumley, Alanna C Morrison, Bonnie R Joubert, Fernando Rivadeneira, David J Couper, Stephen B Kritchevsky, Yongmei Liu, Matthias Wjst, Louise V Wain, Judith M Vonk, André G Uitterlinden, Thierry Rochat, Stephen S Rich, Bruce M Psaty, George T O'Connor, Kari E North, Daniel B Mirel, Bernd Meibohm, Lenore J Launer, Kay-Tee Khaw, Anna-Liisa Hartikainen, Christopher J Hammond, Sven Gläser, Jonathan Marchini, Peter Kraft, Nicholas J Wareham, Henry Völzke, Bruno H C Stricker, Timothy D Spector, Nicole M Probst-Hensch, Deborah Jarvis, Marjo-Riitta Jarvelin, Susan R Heckbert, Vilmundur Gudnason, H Marike Boezen, R Graham Barr, Patricia A Cassano, David P Strachan, Myriam Fornage, Ian P Hall, Josée Dupuis, Martin D Tobin, Stephanie J London
Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second (FEV(1)), and its ratio to forced vital capacity (FEV(1)/FVC). Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA) of single nucleotide polymorphism (SNP) and SNP-by-smoking (ever-smoking or pack-years) associations on FEV(1) and FEV(1)/FVC across 19 studies (total N = 50,047). We identified three novel loci not previously associated with pulmonary function...
2012: PLoS Genetics
https://www.readbyqxmd.com/read/23136122/multiway-admixture-deconvolution-using-phased-or-unphased-ancestral-panels
#20
Claire Churchhouse, Jonathan Marchini
We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels...
January 2013: Genetic Epidemiology
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