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INFERNO - INFERring the molecular mechanisms of NOncoding genetic variants

View ORCID ProfileAlexandre Amlie-Wolf, Mitchell Tang, Elisabeth E. Mlynarski, Pavel P. Kuksa, Otto Valladares, Zivadin Katanic, Debby Tsuang, Christopher D. Brown, Gerard D. Schellenberg, Li-San Wang
doi: https://doi.org/10.1101/211599
Alexandre Amlie-Wolf
1Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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  • ORCID record for Alexandre Amlie-Wolf
Mitchell Tang
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Elisabeth E. Mlynarski
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Pavel P. Kuksa
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Otto Valladares
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Zivadin Katanic
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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Debby Tsuang
3VA Puget Sound Health Care System, Seattle, WA. Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Christopher D. Brown
1Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
4Department of Genetics. Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.
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Gerard D. Schellenberg
1Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
4Department of Genetics. Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.
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Li-San Wang
1Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
2Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
4Department of Genetics. Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.
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Abstract

The majority of variants identified by genome-wide association studies (GWAS) reside in the noncoding genome, where they affect regulatory elements including transcriptional enhancers. We propose INFERNO (INFERring the molecular mechanisms of NOncoding genetic variants), a novel method which integrates hundreds of diverse functional genomics data sources with GWAS summary statistics to identify putatively causal noncoding variants underlying association signals. INFERNO comprehensively infers the relevant tissue contexts, target genes, and downstream biological processes affected by causal variants. We apply INFERNO to schizophrenia GWAS data, recapitulating known schizophrenia-associated genes including CACNA1C and discovering novel signals related to transmembrane cellular processes.

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Posted October 30, 2017.
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INFERNO - INFERring the molecular mechanisms of NOncoding genetic variants
Alexandre Amlie-Wolf, Mitchell Tang, Elisabeth E. Mlynarski, Pavel P. Kuksa, Otto Valladares, Zivadin Katanic, Debby Tsuang, Christopher D. Brown, Gerard D. Schellenberg, Li-San Wang
bioRxiv 211599; doi: https://doi.org/10.1101/211599
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INFERNO - INFERring the molecular mechanisms of NOncoding genetic variants
Alexandre Amlie-Wolf, Mitchell Tang, Elisabeth E. Mlynarski, Pavel P. Kuksa, Otto Valladares, Zivadin Katanic, Debby Tsuang, Christopher D. Brown, Gerard D. Schellenberg, Li-San Wang
bioRxiv 211599; doi: https://doi.org/10.1101/211599

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