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LocusFocus: A web-based colocalization tool for the annotation and functional follow-up of GWAS

View ORCID ProfileNaim Panjwani, Fan Wang, Cheng Wang, Gengming He, View ORCID ProfileScott Mastromatteo, Allen Bao, Jiafen Gong, View ORCID ProfileJohanna M Rommens, Lei Sun, View ORCID ProfileLisa J Strug
doi: https://doi.org/10.1101/2020.01.02.891291
Naim Panjwani
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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  • ORCID record for Naim Panjwani
Fan Wang
Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
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Cheng Wang
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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Gengming He
Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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Scott Mastromatteo
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, CanadaThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
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Allen Bao
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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Jiafen Gong
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, CanadaThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
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Johanna M Rommens
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, CanadaDepartment of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Lei Sun
Department of Statistical Sciences, University of Toronto, Toronto, Ontario, CanadaDivision of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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Lisa J Strug
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, CanadaDepartment of Statistical Sciences, University of Toronto, Toronto, Ontario, CanadaThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, CanadaDivision of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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  • ORCID record for Lisa J Strug
  • For correspondence: lisa.strug@sickkids.ca
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Abstract

Genome-wide association studies (GWAS) have primarily identified trait-associated loci in the non-coding genome. Colocalization analyses of SNP-level associations from GWAS with expression quantitative trait loci (eQTL) evidence enable the generation of hypotheses about responsible mechanism, genes and tissues of origin to guide functional characterization. Here, we present a web-based colocalization browsing and testing tool named LocusFocus (https://locusfocus.research.sickkids.ca). LocusFocus formally tests colocalization using our established Simple Sum method to identify the most relevant genes and tissues for a particular GWAS locus in the presence of high linkage disequilibrium and/or allelic heterogeneity. Full documentation and source code for LocusFocus are publicly available.

Footnotes

  • https://locusfocus.research.sickkids.ca/

  • https://github.com/naim-panjwani/LocusFocus

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 02, 2020.
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LocusFocus: A web-based colocalization tool for the annotation and functional follow-up of GWAS
Naim Panjwani, Fan Wang, Cheng Wang, Gengming He, Scott Mastromatteo, Allen Bao, Jiafen Gong, Johanna M Rommens, Lei Sun, Lisa J Strug
bioRxiv 2020.01.02.891291; doi: https://doi.org/10.1101/2020.01.02.891291
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LocusFocus: A web-based colocalization tool for the annotation and functional follow-up of GWAS
Naim Panjwani, Fan Wang, Cheng Wang, Gengming He, Scott Mastromatteo, Allen Bao, Jiafen Gong, Johanna M Rommens, Lei Sun, Lisa J Strug
bioRxiv 2020.01.02.891291; doi: https://doi.org/10.1101/2020.01.02.891291

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