Genomic control for association studies.
Bernie Devlin,Kathryn Roeder +1 more
Reads0
Chats0
TLDR
The performance of the genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.Abstract:
A dense set of single nucleotide polymorphisms (SNP) covering the genome and an efficient method to assess SNP genotypes are expected to be available in the near future. An outstanding question is how to use these technologies efficiently to identify genes affecting liability to complex disorders. To achieve this goal, we propose a statistical method that has several optimal properties: It can be used with case control data and yet, like family-based designs, controls for population heterogeneity; it is insensitive to the usual violations of model assumptions, such as cases failing to be strictly independent; and, by using Bayesian outlier methods, it circumvents the need for Bonferroni correction for multiple tests, leading to better performance in many settings while still constraining risk for false positives. The performance of our genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.read more
Citations
More filters
Journal ArticleDOI
Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus
Zhan Su,Amy Strange,Claire Palles,Gavin Band,David C. Whiteman,Francesco Lescai,Cordelia Langford,Manoj Nanji,Sarah Edkins,Anouk Van Der Winkel,David K. Levine,Peter Sasieni,Céline Bellenguez,Kimberley Howarth,Colin Freeman,Nigel Trudgill,Art Tucker,Matti Pirinen,Maikel P. Peppelenbosch,Luc J. W. van der Laan,Ernst J. Kuipers,Joost P.H. Drenth,Wilbert H.M. Peters,John V. Reynolds,Dermot Kelleher,Ross McManus,Heike I. Grabsch,Hans Prenen,Raf Bisschops,Kausila Krishnadath,Peter D. Siersema,Jantine W. P. M. van Baal,Mark R. Middleton,Russell D. Petty,Richard S. Gillies,Nicola Burch,Pradeep Bhandari,S Paterson,Cathryn Edwards,Ian D. Penman,Kishor Vaidya,Yeng Ang,Iain A. Murray,Praful Patel,Weimin Ye,Paul Mullins,Anna H. Wu,Nigel C. Bird,Helen Dallal,Nicholas J. Shaheen,Liam J. Murray,Konrad Koss,Leslie Bernstein,Yvonne Romero,Laura J. Hardie,Rui Zhang,Helen Winter,Douglas A. Corley,Simon Panter,Harvey A. Risch,Brian J. Reid,Ian Sargeant,Marilie D. Gammon,H Smart,Anjan Dhar,Hugh McMurtry,Haythem Ali,Geoffrey Liu,Alan G. Casson,Wong Ho Chow,Matthew D. Rutter,Ashref Tawil,Danielle Morris,Chuka U. Nwokolo,Peter Isaacs,Colin Rodgers,Krish Ragunath,Christopher Macdonald,Chris Haigh,David Monk,Gareth E. Davies,Saj Wajed,David Johnston,Michael Gibbons,Sue Cullen,Nicholas I. Church,Ruth E Langley,M Griffin,Derek Alderson,Panos Deloukas,Sarah E. Hunt,Emma Gray,Serge Dronov,Simon C. Potter,Avazeh Tashakkori-Ghanbaria,Mark S. Anderson,Claire Brooks,Jenefer M. Blackwell,Jenefer M. Blackwell,Elvira Bramon,Elvira Bramon,Matthew A. Brown,Juan P. Casas,Juan P. Casas,Aiden Corvin,Audrey Duncanson,Hugh S. Markus,Christopher G. Mathew,Colin N. A. Palmer,Robert Plomin,Anna Rautanen,Stephen Sawcer,Richard C. Trembath,Ananth C. Viswanathan,Nicholas W. Wood,Gosia Trynka,Cisca Wijmenga,Jean-Baptiste Cazier,Paul Atherfold,Anna M. Nicholson,Nichola L. Gellatly,Deborah Glancy,Sheldon C. Cooper,David Cunningham,Tore Lind,Julie Hapeshi,David Ferry,Barrie Rathbone,Julia Brown,Sharon Love,Stephen Attwood,Stuart MacGregor,Peter H. Watson,Scott Sanders,Weronica E. Ek,Rebecca Harrison,Paul Moayyedi,John de Caestecker,Hugh Barr,Elia Stupka,Elia Stupka,Elia Stupka,Thomas L. Vaughan,Leena Peltonen,Chris C. A. Spencer,Ian Tomlinson,Peter Donnelly,Janusz Jankowski,Janusz Jankowski,Janusz Jankowski +149 more
TL;DR: Evidence is found that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's Esophagus.
Journal ArticleDOI
Tracing the ancestry of modern bread wheats
Caroline Pont,Thibault Leroy,Thibault Leroy,Michael Seidel,Alessandro Tondelli,Wandrille Duchemin,David Armisen,Daniel Lang,Daniela Bustos-Korts,Nadia Goué,François Balfourier,Márta Molnár-Láng,Jacob Lage,Benjamin Kilian,Hakan Özkan,Darren Waite,Sarah Dyer,Thomas Letellier,Michael Alaux,Joanne Russell,Beat Keller,Fred A. van Eeuwijk,Manuel Spannagl,Klaus F. X. Mayer,Robbie Waugh,Robbie Waugh,Robbie Waugh,Nils Stein,Luigi Cattivelli,Georg Haberer,Gilles Charmet,Jérôme Salse +31 more
TL;DR: Exome sequencing of a worldwide panel of 487 wheat genotypes, including landraces, cultivars and modern varieties, sheds light on wheat genomic diversity and the evolution of modern bread wheat.
Journal ArticleDOI
Genetic epidemiologic studies of preterm birth: guidelines for research.
Craig E. Pennell,Craig E. Pennell,Bo Jacobsson,Bo Jacobsson,Scott M. Williams,Rebecca M. Buus,Louis J. Muglia,Siobhan M. Dolan,Nils-Halvdan Morken,Hilmi Ozcelik,Stephen J. Lye,Caroline L Relton +11 more
TL;DR: This review aims to develop research guidelines for the conduct of genetic epidemiology studies of preterm birth with the expectation that this will ultimately facilitate the comparison of data sets between study cohorts, both nationally and internationally.
Journal ArticleDOI
Meta-analysis of genome-wide association data identifies a risk locus for major mood disorders on 3p21.1
Francis J. McMahon,Nirmala Akula,Thomas G. Schulze,Pierandrea Muglia,Pierandrea Muglia,Federica Tozzi,Sevilla D. Detera-Wadleigh,C. J. M. Steele,René Breuer,Jana Strohmaier,Jens R. Wendland,Manuel Mattheisen,Thomas W. Mühleisen,Wolfgang Maier,Markus M. Nöthen,Sven Cichon,Anne Farmer,John B. Vincent,Florian Holsboer,Martin Preisig,Marcella Rietschel +20 more
TL;DR: A meta-analysis of five case-control cohorts for major mood disorder, including over 13,600 individuals genotyped on high-density SNP arrays, identified SNPs at 3p21.1 associated with major mood disorders, providing an example of a shared genetic susceptibility locus for bipolar disorder and MDD.
Journal ArticleDOI
SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.
TL;DR: The developed SLICER (Selective Locally Linear Inference of Cellular Expression Relationships) can infer highly nonlinear trajectories, select genes without prior knowledge of the process, and automatically determine the location and number of branches and loops.
References
More filters
Journal ArticleDOI
Stastical Decision Theory and Bayesian Analysis.
Malay Ghosh,James O. Berger +1 more
Book
Statistical Decision Theory and Bayesian Analysis
TL;DR: An overview of statistical decision theory, which emphasizes the use and application of the philosophical ideas and mathematical structure of decision theory.
Journal ArticleDOI
The Future of Genetic Studies of Complex Human Diseases
TL;DR: The identification of the genetic basis of complex human diseases such as schizophrenia and diabetes has proven difficult as mentioned in this paper, and Risch and Merikangas proposed that they can best accomplish this goal by combining the power of the human genome project with association studies.
Journal ArticleDOI
An Introduction to Population Genetics Theory
James F. Crow,Motoo Kimura +1 more
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics Theory, Population Genetics theory, Population genetics theory as discussed by the authors, Population genetics, population genetics, and population genetics theories, Population Genetic Theory
Book
An introduction to population genetics theory
James F. Crow,Motoo Kimura +1 more
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics theory, and more.
Related Papers (5)
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Inference of population structure using multilocus genotype data
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
Paul Burton,David Clayton,Lon R. Cardon,Nicholas John Craddock,Panos Deloukas,Audrey Duncanson,Dominic P. Kwiatkowski,Mark I. McCarthy,Willem H. Ouwehand,Nilesh J. Samani,John A. Todd,Peter Donnelly,Jeffrey C. Barrett,Dan Davison,Doug Easton,David M. Evans,H. T. Leung,Jonathan Marchini,Andrew P. Morris,Chris C. A. Spencer,Martin D. Tobin,Antony P. Attwood,James P. Boorman,Barbara Cant,Ursula Everson,Judith M. Hussey,Jennifer Jolley,Alexandra S. Knight,Kerstin Koch,Elizabeth Meech,Sarah Nutland,Christopher Prowse,Helen Stevens,Niall C. Taylor,Graham R. Walters,Neil Walker,Nicholas A. Watkins,Thilo Winzer,Richard Jones,Wendy L. McArdle,Susan M. Ring,David P. Strachan,Marcus Pembrey,Gerome Breen,David St Clair,Sian Caesar,Katherine Gordon-Smith,Lisa Jones,Christine Fraser,Elaine K. Green,Detelina Grozeva,Marian L. Hamshere,Peter Holmans,Ian Jones,George Kirov,Valentina Moskvina,Ivan Nikolov,Michael Conlon O'Donovan,Michael John Owen,David A. Collier,Amanda Elkin,Anne Farmer,Richard Williamson,Peter McGuffin,Allan H. Young,I. Nicol Ferrier,Stephen G. Ball,Anthony J. Balmforth,Jennifer H. Barrett,D. Timothy Bishop,Mark M. Iles,Azhar Maqbool,Nadira Yuldasheva,Alistair S. Hall,Peter S. Braund,Richard J. Dixon,Massimo Mangino,Suzanne Stevens,John R. Thompson,Francesca Bredin,Mark Tremelling,Miles Parkes,Hazel E. Drummond,Charlie W. Lees,Elaine R. Nimmo,Jack Satsangi,Sheila A. Fisher,Alastair Forbes,Cathryn M. Lewis,Clive M. Onnie,Natalie J. Prescott,Jeremy D. Sanderson,Christopher G. Mathew,Jamie Barbour,M. Khalid Mohiuddin,Catherine E. Todhunter,John C. Mansfield,Tariq Ahmad,Fraser Cummings,Derek P. Jewell,John Webster,Morris J. Brown,G. Mark Lathrop,John M. C. Connell,Anna F. Dominiczak,Carolina A. Braga Marcano,Beverley Burke,Richard Dobson,Johannie Gungadoo,Kate L. Lee,Patricia B. Munroe,Stephen Newhouse,Abiodun Onipinla,Chris Wallace,Mingzhan Xue,Mark J. Caulfield,Martin Farrall,Anne Barton,Ian N. Bruce,Hannah Donovan,Steve Eyre,Paul D. Gilbert,Samantha L. Hider,Anne Hinks,Sally John,Catherine Potter,Alan J. Silman,Deborah P M Symmons,Wendy Thomson,Jane Worthington,David B. Dunger,Barry Widmer,Timothy M. Frayling,Rachel M. Freathy,Hana Lango,John R. B. Perry,Beverley M. Shields,Michael N. Weedon,Andrew T. Hattersley,Graham A. Hitman,Mark Walker,Kate S. Elliott,Christopher J. Groves,Cecilia M. Lindgren,Nigel W. Rayner,Nicholas J. Timpson,Eleftheria Zeggini,Melanie J. Newport,Giorgio Sirugo,Emily J. Lyons,Fredrik O. Vannberg,Adrian V. S. Hill,Linda A. Bradbury,C Farrar,J J Pointon,Paul Wordsworth,Matthew A. Brown,Jayne A. Franklyn,Joanne M. Heward,Matthew J. Simmonds,Stephen C. L. Gough,Sheila Seal,Michael R. Stratton,Nazneen Rahman,Maria Ban,An Goris,Stephen Sawcer,Alastair Compston,David J. Conway,Muminatou Jallow,Kirk A. Rockett,Suzannah Bumpstead,Amy Chaney,Kate Downes,Mohammed J. R. Ghori,Rhian Gwilliam,Sarah E. Hunt,Michael Inouye,Andrew Keniry,Emma King,Ralph McGinnis,Simon C. Potter,Rathi Ravindrarajah,Pamela Whittaker,Claire Widden,David Withers,Niall Cardin,Teresa Ferreira,Joanne Pereira-Gale,Ingileif B. Hallgrímsdóttir,Bryan Howie,Zhan Su,Yik Ying Teo,Damjan Vukcevic,David Bentley,A Compston +195 more