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

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; Genetic Investigation of ANthropometric Traits (GIANT) Consortium; Michael Boehnke; Soumya Raychaudhuri; Rudolf S. N. Fehrmann; Joel N. Hirschhorn; Lude Franke

doi:10.1038/ncomms6890

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

Tune H. Pers (Lead / Corresponding author)
, 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
, Genetic Investigation of ANthropometric Traits (GIANT) Consortium
, Michael Boehnke
, Soumya Raychaudhuri
, Rudolf S. N. Fehrmann
, Joel N. Hirschhorn (Lead / Corresponding author)
, Lude Franke (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

596 Citations (Scopus)

Abstract

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.

Original language	English
Article number	5890
Pages (from-to)	1-9
Number of pages	9
Journal	Nature Communications
Volume	6
DOIs	https://doi.org/10.1038/ncomms6890
Publication status	Published - 19 Jan 2015

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10.1038/ncomms6890

Additional file 2 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis
Global Lipids Genetics Consortium, Kanoni, S. (Creator), Graham, S. E. (Creator), Wang, Y. (Creator), Surakka, I. (Creator), Ramdas, S. (Creator), Zhu, X. (Creator), Clarke, S. L. (Creator), Bhatti, K. F. (Creator), Vedantam, S. (Creator), Winkler, T. W. (Creator), Locke, A. E. (Creator), Marouli, E. (Creator), Zajac, G. J. M. (Creator), Wu, K.-H. H. (Creator), Ntalla, I. (Creator), Hui, Q. (Creator), Klarin, D. (Creator), Hilliard, A. T. (Creator), Wang, Z. (Creator), Xue, C. (Creator), Thorleifsson, G. (Creator), Helgadottir, A. (Creator), Gudbjartsson, D. F. (Creator), Holm, H. (Creator), Olafsson, I. (Creator), Hwang, M. Y. (Creator), Han, S. (Creator), Akiyama, M. (Creator), Sakaue, S. (Creator), Terao, C. (Creator), Kanai, M. (Creator), Zhou, W. (Creator), Brumpton, B. M. (Creator), Rasheed, H. (Creator), Havulinna, A. S. (Creator), Veturi, Y. (Creator), Mitchell, R. E. (Creator), Smith, J. A. (Creator), Wang, J.-S. (Creator), Mitchell, P. (Creator), Bennett, D. A. (Creator), Palmer, C. N. A. (Creator), Strachan, D. P. (Creator), Smith, B. H. (Creator), Kim, B.-J. (Creator), Lynch, J. A. (Creator), Wilson, P. W. F. (Creator) & Morris, A. (Creator), figshare, 13 Apr 2023
DOI: 10.6084/m9.figshare.22600970
Dataset
Additional file 30 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis
Global Lipids Genetics Consortium, Kanoni, S. (Creator), Graham, S. E. (Creator), Wang, Y. (Creator), Surakka, I. (Creator), Ramdas, S. (Creator), Zhu, X. (Creator), Clarke, S. L. (Creator), Bhatti, K. F. (Creator), Vedantam, S. (Creator), Winkler, T. W. (Creator), Locke, A. E. (Creator), Marouli, E. (Creator), Zajac, G. J. M. (Creator), Wu, K.-H. H. (Creator), Ntalla, I. (Creator), Hui, Q. (Creator), Klarin, D. (Creator), Hilliard, A. T. (Creator), Wang, Z. (Creator), Xue, C. (Creator), Thorleifsson, G. (Creator), Helgadottir, A. (Creator), Gudbjartsson, D. F. (Creator), Holm, H. (Creator), Olafsson, I. (Creator), Hwang, M. Y. (Creator), Han, S. (Creator), Akiyama, M. (Creator), Sakaue, S. (Creator), Terao, C. (Creator), Kanai, M. (Creator), Zhou, W. (Creator), Brumpton, B. M. (Creator), Rasheed, H. (Creator), Havulinna, A. S. (Creator), Veturi, Y. (Creator), Pacheco, J. A. (Creator), Rosenthal, E. A. (Creator), Mitchell, R. E. (Creator), Smith, J. A. (Creator), Wang, J.-S. (Creator), Mitchell, P. (Creator), Bennett, D. A. (Creator), Palmer, C. N. A. (Creator), Strachan, D. P. (Creator), Smith, B. H. (Creator), Kim, B.-J. (Creator), Lynch, J. A. (Creator), Wilson, P. W. F. (Creator) & Morris, A. P. (Creator), figshare, 13 Apr 2023
DOI: 10.6084/m9.figshare.22601270
Dataset
Additional file 10 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis
Global Lipids Genetics Consortium, Kanoni, S. (Creator), Graham, S. E. (Creator), Wang, Y. (Creator), Surakka, I. (Creator), Ramdas, S. (Creator), Zhu, X. (Creator), Clarke, S. L. (Creator), Bhatti, K. F. (Creator), Vedantam, S. (Creator), Winkler, T. W. (Creator), Locke, A. E. (Creator), Marouli, E. (Creator), Zajac, G. J. M. (Creator), Wu, K.-H. H. (Creator), Ntalla, I. (Creator), Hui, Q. (Creator), Klarin, D. (Creator), Hilliard, A. T. (Creator), Wang, Z. (Creator), Xue, C. (Creator), Thorleifsson, G. (Creator), Helgadottir, A. (Creator), Gudbjartsson, D. F. (Creator), Holm, H. (Creator), Olafsson, I. (Creator), Hwang, M. Y. (Creator), Han, S. (Creator), Akiyama, M. (Creator), Sakaue, S. (Creator), Terao, C. (Creator), Kanai, M. (Creator), Zhou, W. (Creator), Brumpton, B. M. (Creator), Rasheed, H. (Creator), Havulinna, A. S. (Creator), Veturi, Y. (Creator), Pacheco, J. A. (Creator), Smith, J. A. (Creator), Rosenthal, E. A. (Creator), Mitchell, R. E. (Creator), Wang, J.-S. (Creator), Mitchell, P. (Creator), Bennett, D. A. (Creator), Palmer, C. N. A. (Creator), Strachan, D. P. (Creator), Smith, B. H. (Creator), Lynch, J. A. (Creator), Kim, B.-J. (Creator), Wilson, P. W. F. (Creator) & Morris, A. (Creator), figshare, 13 Apr 2023
DOI: 10.6084/m9.figshare.22601057
Dataset

Cite this

Pers, T. H., Karjalainen, J. M., Chan, Y., Westra, H.-J., Wood, A. R., Yang, J., Lui, J. C., Vedantam, S., Gustafsson, S., Esko, T., Frayling, T., Speliotes, E. K., Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Boehnke, M., Raychaudhuri, S., Fehrmann, R. S. N., Hirschhorn, J. N., & Franke, L. (2015). Biological interpretation of genome-wide association studies using predicted gene functions. Nature Communications, 6, 1-9. Article 5890. https://doi.org/10.1038/ncomms6890

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title = "Biological interpretation of genome-wide association studies using predicted gene functions",

abstract = "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.",

author = "Pers, \{Tune H.\} and Karjalainen, \{Juha M.\} and Yingleong Chan and Harm-Jan Westra and Wood, \{Andrew R.\} and Jian Yang and Lui, \{Julian C.\} and Sailaja Vedantam and Stefan Gustafsson and Tonu Esko and Tim Frayling and Speliotes, \{Elizabeth K.\} and \{Genetic Investigation of ANthropometric Traits (GIANT) Consortium\} and Michael Boehnke and Soumya Raychaudhuri and Fehrmann, \{Rudolf S. N.\} and Hirschhorn, \{Joel N.\} and Lude Franke and Palmer, \{Colin Neil Alexander\}",

year = "2015",

month = jan,

day = "19",

doi = "10.1038/ncomms6890",

language = "English",

volume = "6",

pages = "1--9",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

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Pers, TH, Karjalainen, JM, Chan, Y, Westra, H-J, Wood, AR, Yang, J, Lui, JC, Vedantam, S, Gustafsson, S, Esko, T, Frayling, T, Speliotes, EK, Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Boehnke, M, Raychaudhuri, S, Fehrmann, RSN, Hirschhorn, JN & Franke, L 2015, 'Biological interpretation of genome-wide association studies using predicted gene functions', Nature Communications, vol. 6, 5890, pp. 1-9. https://doi.org/10.1038/ncomms6890

TY - JOUR

T1 - Biological interpretation of genome-wide association studies using predicted gene functions

AU - Pers, Tune H.

AU - Karjalainen, Juha M.

AU - Chan, Yingleong

AU - Westra, Harm-Jan

AU - Wood, Andrew R.

AU - Yang, Jian

AU - Lui, Julian C.

AU - Vedantam, Sailaja

AU - Gustafsson, Stefan

AU - Esko, Tonu

AU - Frayling, Tim

AU - Speliotes, Elizabeth K.

AU - Genetic Investigation of ANthropometric Traits (GIANT) Consortium

AU - Boehnke, Michael

AU - Raychaudhuri, Soumya

AU - Fehrmann, Rudolf S. N.

AU - Hirschhorn, Joel N.

AU - Franke, Lude

AU - Palmer, Colin Neil Alexander

PY - 2015/1/19

Y1 - 2015/1/19

N2 - 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.

AB - 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.

U2 - 10.1038/ncomms6890

DO - 10.1038/ncomms6890

M3 - Article

C2 - 25597830

SN - 2041-1723

VL - 6

SP - 1

EP - 9

JO - Nature Communications

JF - Nature Communications

M1 - 5890

ER -

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

Abstract

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Datasets

Additional file 2 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Additional file 30 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Additional file 10 of Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Cite this