RICOPILI: Rapid Imputation for COnsortias PIpeLIne

被引：170

作者：

Lam, Max ^{[1
,2
,3
,4
,5
]}

Awasthi, Swapnil ^{[1
,6
]}

Watson, Hunna J. ^{[7
,8
,9
]}

Goldstein, Jackie ^{[1
,2
]}

Panagiotaropoulou, Georgia ^{[1
,6
]}

Trubetskoy, Vassily ^{[1
,6
]}

Karlsson, Robert ^{[10
]}

Frei, Oleksander ^{[11
]}

Fan, Chun-Chieh ^{[11
]}

De Witte, Ward ^{[12
]}

Mota, Nina R. ^{[12
,13
]}

Mullins, Niamh ^{[14
]}

Brugger, Kim ^{[15
]}

Lee, S. Hong ^{[16
]}

Wray, Naomi R. ^{[17
,18
]}

Skarabis, Nora ^{[6
]}

Huang, Hailiang ^{[1
,2
]}

Neale, Benjamin ^{[1
,2
]}

Daly, Mark J. ^{[1
,2
]}

Mattheisen, Manuel ^{[19
,20
,21
]}

Walters, Raymond ^{[1
,2
]}

Ripke, Stephan ^{[1
,2
,6
]}

机构：

[1] Broad Inst Harvard & MIT, Stanley Ctr Psychiat Res, Cambridge, MA 02142 USA

[2] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Cambridge, MA 02114 USA

[3] Northwell Hlth, Div Psychiat Res, Zucker Hillside Hosp, Glen Oaks, NY 11004 USA

[4] Inst Mental Hlth Singapore, Res Div, Singapore 539747, Singapore

[5] Genome Inst Singapore, Human Genet, Singapore 138672, Singapore

[6] Charite, Dept Psychiat & Psychotherapy, D-10117 Berlin, Germany

[7] Univ N Carolina, Dept Psychiat, Chapel Hill, NC 27515 USA

[8] Univ Western Australia, Sch Med, Div Paediat, Perth, WA 6009, Australia

[9] Curtin Univ, Sch Psychol, Perth, WA 6102, Australia

[10] Karolinska Inst, Dept Med Epidemiol & Biostat, S-17177 Stockholm, Sweden

[11] Univ Oslo, Ulleval Hosp, KG Jebsen Ctr Psychosis Res, Inst Clin Med,NORMENT, N-0424 Oslo, Norway

[12] Donders Inst Brain Cognit & Behav, Dept Human Genet, Nijmegen, Netherlands

[13] Radboud Univ Nijmegen, Donders Inst Brain, Dept Psychiat, Med Ctr, NL-6525 GA Nijmegen, Netherlands

[14] Icahn Sch Med Mt Sinai, Dept Genet & Genom Sci, Pamela Sklar Div Psychiat Genom, New York, NY 10029 USA

[15] Univ Bergen, Dept Informat, N-5020 Bergen, Norway

[16] Univ South Australia, Canc Res Inst, Australian Ctr Precis Hlth, Adelaide, SA 5000, Australia

[17] Univ Queensland, Inst Mol Biosci, Brisbane, Qld 4072, Australia

[18] Univ Queensland, Queensland Brain Inst, Brisbane, Qld 4072, Australia

[19] Univ Hosp Wurzburg, Ctr Mental Hlth, Dept Psychiat Psychosomat & Psychotherapy, Wurzburg, Germany

[20] Karolinska Inst, Ctr Psychiat Res, Dept Clin Neurosci, Stockholm, Sweden

[21] Aarhus Univ, Dept Biomed, Aarhus, Denmark

来源：

BIOINFORMATICS | 2020年 / 36卷 / 03期

基金：

美国国家卫生研究院; 英国医学研究理事会;

关键词：

GENOME-WIDE ASSOCIATION; GENOTYPE IMPUTATION;

D O I：

10.1093/bioinformatics/btz633

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A Summary: Genome-wide association study (GWAS) analyses, at sufficient sample sizes and power, have successfully revealed biological insights for several complex traits. RICOPILI, an open-sourced Perl-based pipeline was developed to address the challenges of rapidly processing large-scale multi-cohort GWAS studies including quality control (QC), imputation and downstream analyses. The pipeline is computationally efficient with portability to a wide range of high-performance computing environments. RICOPILI was created as the Psychiatric Genomics Consortium pipeline for GWAS and adopted by other users. The pipeline features (i) technical and genomic QC in case-control and trio cohorts, (ii) genome-wide phasing and imputation, (iv) association analysis, (v) meta-analysis, (vi) polygenic risk scoring and (vii) replication analysis. Notably, a major differentiator from other GWAS pipelines, RICOPILI leverages on automated parallelization and cluster job management approaches for rapid production of imputed genome-wide data. A comprehensive meta-analysis of simulated GWAS data has been incorporated demonstrating each step of the pipeline. This includes all the associated visualization plots, to allow ease of data interpretation and manuscript preparation. Simulated GWAS datasets are also packaged with the pipeline for user training tutorials and developer work.

引用

页码：930 / 933

页数：4

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