Biological interpretation of genome-wide association studies using predicted gene functions

被引：0

作者：

Tune H. Pers

Juha M. Karjalainen

Yingleong Chan

Harm-Jan Westra

Andrew R. Wood

Jian Yang

Julian C. Lui

Sailaja Vedantam

Stefan Gustafsson

Tonu Esko

Tim Frayling

Elizabeth K. Speliotes

Michael Boehnke

Soumya Raychaudhuri

Rudolf S. N. Fehrmann

Joel N. Hirschhorn

Lude Franke

机构：

[1] Boston Children’s Hospital,Division of Endocrinology and Center for Basic and Translational Obesity Research

[2] Medical and Population Genetics Program,Department of Genetics

[3] Broad Institute of MIT and Harvard,Department of Genetics

[4] University of Groningen,Division of Genetics

[5] University Medical Centre Groningen,Department of Medical Sciences

[6] Harvard Medical School,Department of Internal Medicine, Division of Gastroenterology, and Department of Computational Medicine and Bioinformatics

[7] Brigham and Women’s Hospital,Department of Biostatistics and Center for Statistical Genetics

[8] Genetics of Complex Traits,Division of Rheumatology

[9] University of Exeter Medical School,undefined

[10] University of Exeter,undefined

[11] Queensland Brain Institute,undefined

[12] The University of Queensland,undefined

[13] The University of Queensland Diamantina Institute,undefined

[14] The Translation Research Institute,undefined

[15] Section on Growth and Development,undefined

[16] Program in Developmental Endocrinology and Genetics,undefined

[17] Eunice Kennedy Shriver National Institute of Child Health and Human Development,undefined

[18] National Institutes of Health,undefined

[19] Molecular Epidemiology and Science for Life Laboratory,undefined

[20] Uppsala University,undefined

[21] Estonian Genome Center,undefined

[22] University of Tartu,undefined

[23] University of Michigan,undefined

[24] University of Michigan,undefined

[25] Partners HealthCare Center for Personalized Genetic Medicine,undefined

[26] Immunology and Allergy,undefined

[27] Brigham and Women’s Hospital,undefined

[28] Faculty of Medical and Human Sciences,undefined

[29] University of Manchester,undefined

来源：

Nature Communications | / 6卷

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摘要：

The main challenge for gaining biological insights from genetic associations is identifying which genes and pathways explain the associations. Here we present DEPICT, an integrative tool that employs predicted gene functions to systematically prioritize the most likely causal genes at associated loci, highlight enriched pathways and identify tissues/cell types where genes from associated loci are highly expressed. DEPICT is not limited to genes with established functions and prioritizes relevant gene sets for many phenotypes.

引用

共 50 条

[1] Biological interpretation of genome-wide association studies using predicted gene functions
Pers, Tune H.
Karjalainen, Juha M.
Chan, Yingleong
Westra, Harm-Jan
Wood, Andrew R.
Yang, Jian
Lui, Julian C.
Vedantam, Sailaja
Gustafsson, Stefan
Esko, Tonu
Frayling, Tim
Speliotes, Elizabeth K.
Boehnke, Michael
Raychaudhuri, Soumya
Fehrmann, Rudolf S. N.
Hirschhorn, Joel N.
Franke, Lude
NATURE COMMUNICATIONS, 2015, 6
[2] Reporting and interpretation in genome-wide association studies
Wakefield, Jon
INTERNATIONAL JOURNAL OF EPIDEMIOLOGY, 2008, 37 (03) : 641 - 653
[3] Genome-wide association studies: power, limits and interpretation
Clerget-Darpoux, F.
ANNALS OF HUMAN GENETICS, 2009, 73 : 662 - 662
[4] Incorporating biological knowledge in the search for gene × gene interaction in genome-wide association studies
Alisa K Manning
Julius Suh Ngwa
Audrey E Hendricks
Ching-Ti Liu
Andrew D Johnson
Josée Dupuis
L Adrienne Cupples
BMC Proceedings, 3 (Suppl 7)
[5] Analysing biological pathways in genome-wide association studies
Kai Wang
Mingyao Li
Hakon Hakonarson
Nature Reviews Genetics, 2010, 11 : 843 - 854
[6] Analysing biological pathways in genome-wide association studies
Wang, Kai
Li, Mingyao
Hakonarson, Hakon
NATURE REVIEWS GENETICS, 2010, 11 (12) : 843 - 854
[7] The search for gene-gene interactions in genome-wide association studies: challenges in abundance of methods, practical considerations, and biological interpretation
Ritchie, Marylyn D.
Van Steen, Kristel
ANNALS OF TRANSLATIONAL MEDICINE, 2018, 6 (08)
[8] Using biological networks to search for interacting loci in genome-wide association studies
Emily, Mathieu
Mailund, Thomas
Hein, Jotun
Schauser, Leif
Schierup, Mikkel Heide
EUROPEAN JOURNAL OF HUMAN GENETICS, 2009, 17 (10) : 1231 - 1240
[9] Using biological networks to search for interacting loci in genome-wide association studies
Mathieu Emily
Thomas Mailund
Jotun Hein
Leif Schauser
Mikkel Heide Schierup
European Journal of Human Genetics, 2009, 17 : 1231 - 1240
[10] Gene Set analysis in Genome-wide Association Studies
Tintle, Nathan L.
GENETIC EPIDEMIOLOGY, 2009, 33 (08) : 805 - 806

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