Literature DB >> 26076425

Efficient set tests for the genetic analysis of correlated traits.

Francesco Paolo Casale1, Barbara Rakitsch1, Christoph Lippert2, Oliver Stegle1.   

Abstract

Set tests are a powerful approach for genome-wide association testing between groups of genetic variants and quantitative traits. We describe mtSet (http://github.com/PMBio/limix), a mixed-model approach that enables joint analysis across multiple correlated traits while accounting for population structure and relatedness. mtSet effectively combines the benefits of set tests with multi-trait modeling and is computationally efficient, enabling genetic analysis of large cohorts (up to 500,000 individuals) and multiple traits.

Mesh：

Year:  2015        PMID： 26076425     DOI： 10.1038/nmeth.3439

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  30 in total

1.  Powerful SNP-set analysis for case-control genome-wide association studies.

Authors:  Michael C Wu; Peter Kraft; Michael P Epstein; Deanne M Taylor; Stephen J Chanock; David J Hunter; Xihong Lin
Journal:  Am J Hum Genet       Date:  2010-06-11       Impact factor: 11.025

2.  Principal components analysis corrects for stratification in genome-wide association studies.

Authors:  Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich
Journal:  Nat Genet       Date:  2006-07-23       Impact factor: 38.330

3.  A multivariate test of association.

Authors:  Manuel A R Ferreira; Shaun M Purcell
Journal:  Bioinformatics       Date:  2008-11-19       Impact factor: 6.937

4.  FaST linear mixed models for genome-wide association studies.

Authors:  Christoph Lippert; Jennifer Listgarten; Ying Liu; Carl M Kadie; Robert I Davidson; David Heckerman
Journal:  Nat Methods       Date:  2011-09-04       Impact factor: 28.547

5.  Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases.

Authors:  Alexander Gusev; S Hong Lee; Gosia Trynka; Hilary Finucane; Bjarni J Vilhjálmsson; Han Xu; Chongzhi Zang; Stephan Ripke; Brendan Bulik-Sullivan; Eli Stahl; Anna K Kähler; Christina M Hultman; Shaun M Purcell; Steven A McCarroll; Mark Daly; Bogdan Pasaniuc; Patrick F Sullivan; Benjamin M Neale; Naomi R Wray; Soumya Raychaudhuri; Alkes L Price
Journal:  Am J Hum Genet       Date:  2014-11-06       Impact factor: 11.025

6.  Angptl3 regulates lipid metabolism in mice.

Authors:  Ryuta Koishi; Yosuke Ando; Mitsuru Ono; Mitsuru Shimamura; Hiroaki Yasumo; Toshihiko Fujiwara; Hiroyoshi Horikoshi; Hidehiko Furukawa
Journal:  Nat Genet       Date:  2002-01-14       Impact factor: 38.330

7.  Regulation of p100 (NFKB2) expression in human monocytes in response to inflammatory mediators and lymphokines.

Authors:  H de Wit; W H Dokter; S B Koopmans; C Lummen; M van der Leij; J W Smit; E Vellenga
Journal:  Leukemia       Date:  1998-03       Impact factor: 11.528

Review 8.  Pleiotropy in complex traits: challenges and strategies.

Authors:  Nadia Solovieff; Chris Cotsapas; Phil H Lee; Shaun M Purcell; Jordan W Smoller
Journal:  Nat Rev Genet       Date:  2013-06-11       Impact factor: 53.242

9.  Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals.

Authors:  Alkes L Price; Agnar Helgason; Gudmar Thorleifsson; Steven A McCarroll; Augustine Kong; Kari Stefansson
Journal:  PLoS Genet       Date:  2011-02-24       Impact factor: 5.917

10.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962
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  46 in total

1.  Genetic variants regulating expression levels and isoform diversity during embryogenesis.

Authors:  Enrico Cannavò; Nils Koelling; Dermot Harnett; David Garfield; Francesco P Casale; Lucia Ciglar; Hilary E Gustafson; Rebecca R Viales; Raquel Marco-Ferreres; Jacob F Degner; Bingqing Zhao; Oliver Stegle; Ewan Birney; Eileen E M Furlong
Journal:  Nature       Date:  2016-12-26       Impact factor: 49.962

2.  Promoter shape varies across populations and affects promoter evolution and expression noise.

Authors:  Ignacio E Schor; Jacob F Degner; Dermot Harnett; Enrico Cannavò; Francesco P Casale; Heejung Shim; David A Garfield; Ewan Birney; Matthew Stephens; Oliver Stegle; Eileen E M Furlong
Journal:  Nat Genet       Date:  2017-02-13       Impact factor: 38.330

3.  Local Joint Testing Improves Power and Identifies Hidden Heritability in Association Studies.

Authors:  Brielin C Brown; Alkes L Price; Nikolaos A Patsopoulos; Noah Zaitlen
Journal:  Genetics       Date:  2016-05-06       Impact factor: 4.562

4.  A hierarchical clustering method for dimension reduction in joint analysis of multiple phenotypes.

Authors:  Xiaoyu Liang; Qiuying Sha; Yeonwoo Rho; Shuanglin Zhang
Journal:  Genet Epidemiol       Date:  2018-04-22       Impact factor: 2.135

5.  Joint analysis of multiple phenotypes in association studies using allele-based clustering approach for non-normal distributions.

Authors:  Xiaoyu Liang; Qiuying Sha; Shuanglin Zhang
Journal:  Ann Hum Genet       Date:  2018-06-22       Impact factor: 1.670

6.  Abdominal adiposity and cardiometabolic risk factors in children and adolescents: a Mendelian randomization analysis.

Authors:  Anna Viitasalo; Theresia M Schnurr; Niina Pitkänen; Mette Hollensted; Tenna R H Nielsen; Katja Pahkala; Mustafa Atalay; Mads V Lind; Sami Heikkinen; Christine Frithioff-Bøjsøe; Cilius E Fonvig; Niels Grarup; Mika Kähönen; Germán D Carrasquilla; Anni Larnkjaer; Oluf Pedersen; Kim F Michaelsen; Timo A Lakka; Jens-Christian Holm; Terho Lehtimäki; Olli Raitakari; Torben Hansen; Tuomas O Kilpeläinen
Journal:  Am J Clin Nutr       Date:  2019-11-01       Impact factor: 7.045

7.  A linear mixed-model approach to study multivariate gene-environment interactions.

Authors:  Rachel Moore; Francesco Paolo Casale; Marc Jan Bonder; Danilo Horta; Lude Franke; Inês Barroso; Oliver Stegle
Journal:  Nat Genet       Date:  2018-11-26       Impact factor: 38.330

8.  Haplotype-resolved diverse human genomes and integrated analysis of structural variation.

Authors:  Peter Ebert; Peter A Audano; Qihui Zhu; Bernardo Rodriguez-Martin; Charles Lee; Jan O Korbel; Tobias Marschall; Evan E Eichler; David Porubsky; Marc Jan Bonder; Arvis Sulovari; Jana Ebler; Weichen Zhou; Rebecca Serra Mari; Feyza Yilmaz; Xuefang Zhao; PingHsun Hsieh; Joyce Lee; Sushant Kumar; Jiadong Lin; Tobias Rausch; Yu Chen; Jingwen Ren; Martin Santamarina; Wolfram Höps; Hufsah Ashraf; Nelson T Chuang; Xiaofei Yang; Katherine M Munson; Alexandra P Lewis; Susan Fairley; Luke J Tallon; Wayne E Clarke; Anna O Basile; Marta Byrska-Bishop; André Corvelo; Uday S Evani; Tsung-Yu Lu; Mark J P Chaisson; Junjie Chen; Chong Li; Harrison Brand; Aaron M Wenger; Maryam Ghareghani; William T Harvey; Benjamin Raeder; Patrick Hasenfeld; Allison A Regier; Haley J Abel; Ira M Hall; Paul Flicek; Oliver Stegle; Mark B Gerstein; Jose M C Tubio; Zepeng Mu; Yang I Li; Xinghua Shi; Alex R Hastie; Kai Ye; Zechen Chong; Ashley D Sanders; Michael C Zody; Michael E Talkowski; Ryan E Mills; Scott E Devine
Journal:  Science       Date:  2021-02-25       Impact factor: 47.728

9.  Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation.

Authors:  Julie Jerber; Daniel D Seaton; Anna S E Cuomo; Natsuhiko Kumasaka; James Haldane; Juliette Steer; Minal Patel; Daniel Pearce; Malin Andersson; Marc Jan Bonder; Ed Mountjoy; Maya Ghoussaini; Madeline A Lancaster; John C Marioni; Florian T Merkle; Daniel J Gaffney; Oliver Stegle
Journal:  Nat Genet       Date:  2021-03-04       Impact factor: 38.330

10.  A multiple-phenotype imputation method for genetic studies.

Authors:  Andrew Dahl; Valentina Iotchkova; Amelie Baud; Åsa Johansson; Ulf Gyllensten; Nicole Soranzo; Richard Mott; Andreas Kranis; Jonathan Marchini
Journal:  Nat Genet       Date:  2016-02-22       Impact factor: 38.330
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