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A Multiplexed Assay for Exon Recognition Reveals That an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Disruptions to Splicing

63 Pages Posted: 3 Jun 2018 Sneak Peek Status: Under Review

See all articles by Rocky Cheung

Rocky Cheung

University of California, Los Angeles (UCLA) - Department of Chemistry and Biochemistry

Kimberly D. Insigne

University of California, Los Angeles (UCLA) - Bioinformatics Interdepartmental Graduate Program

David Yao​

Stanford University - Genetics Graduate Program

Christina P. Burghard

University of California, Los Angeles (UCLA) - Bioinformatics Interdepartmental Graduate Program

Eric M. Jones

University of California, Los Angeles (UCLA) - Department of Chemistry and Biochemistry

Daniel B. Goodman

University of California, San Francisco (UCSF) - ​Department of Microbiology and Immunology

Sriram Kosuri

University of California, Los Angeles (UCLA) - Department of Chemistry and Biochemistry; University of California, Los Angeles (UCLA) - UCLA-DOE Institute; University of California, Los Angeles (UCLA) - Molecular Biology Institute; University of California, Los Angeles (UCLA) - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research; University of California, Los Angeles (UCLA) - Jonsson Comprehensive Cancer Center

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Abstract

Any individual’s genome contains ~4-5 million genetic variants that differ from reference, and understanding how these variants give rise to trait diversity and disease susceptibility is a central goal of human genetics (Auton et al., 2015). A vast majority (96-99%) of an individual’s variants are common, though at the population level the overwhelming majority of variants are rare (Montgomery et al., 2011; Nelson et al., 2012; Tennessen et al., 2012; UK10K Consortium et al., 2015). Because of their scarcity in an individual’s genome, rare variants that play important roles in complex traits are likely to have large functional effects (Bomba et al., 2017; Gibson, 2012). Mutations that cause an exon to be skipped can have severe functional consequences on gene function, and many known disease-causing mutations reduce or eliminate exon recognition (Baralle and Buratti, 2017). Here we explore the extent to which rare genetic variation in humans results in near complete loss of exon recognition. We developed a Multiplexed Functional Assay of Splicing using Sort-seq (MFASS) that allows us to measure exon inclusion in thousands of human exons and surrounding intronic sequence simultaneously. We assayed 27,733 extant variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,339 human exons, and found that 3.8% (1,050) of the variants, almost all of which were extremely rare, led to large-effect defects in exon recognition. Importantly, we find that 83% of these splicedisrupting variants (SDVs) are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predict a priori. Our results indicate that loss of exon recognition is an important and underappreciated means by which rare variants exert large functional effects, and that MFASS enables their empirical assessment for large-effect splicing defects at scale.

Suggested Citation

Cheung, Rocky and Insigne, Kimberly D. and Yao​, David and Burghard, Christina P. and Jones, Eric M. and Goodman, Daniel B. and Kosuri, Sriram, A Multiplexed Assay for Exon Recognition Reveals That an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Disruptions to Splicing (2018). Available at SSRN: https://ssrn.com/abstract=3188378 or http://dx.doi.org/10.2139/ssrn.3188378
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Rocky Cheung

University of California, Los Angeles (UCLA) - Department of Chemistry and Biochemistry

Los Angeles, CA 90095
United States

Kimberly D. Insigne

University of California, Los Angeles (UCLA) - Bioinformatics Interdepartmental Graduate Program

172 Boyer Hall
611 Charles E. Young Drive
Los Angeles, CA 90095-1570
United States

David Yao​

Stanford University - Genetics Graduate Program

Stanford, CA 94305-5120
United States

Christina P. Burghard

University of California, Los Angeles (UCLA) - Bioinformatics Interdepartmental Graduate Program

172 Boyer Hall
611 Charles E. Young Drive
Los Angeles, CA 90095-1570
United States

Eric M. Jones

University of California, Los Angeles (UCLA) - Department of Chemistry and Biochemistry

Los Angeles, CA 90095
United States

Daniel B. Goodman

University of California, San Francisco (UCSF) - ​Department of Microbiology and Immunology

513 Parnassus Ave
San Francisco, CA 94143
United States

Sriram Kosuri (Contact Author)

University of California, Los Angeles (UCLA) - Department of Chemistry and Biochemistry ( email )

Los Angeles, CA 90095
United States

University of California, Los Angeles (UCLA) - UCLA-DOE Institute

Los Angeles, CA
United States

University of California, Los Angeles (UCLA) - Molecular Biology Institute

405 Hilgard Avenue
Box 951361
Los Angeles, CA 90095
United States

University of California, Los Angeles (UCLA) - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research

615 Charles E Young Dr. S.
Los Angeles, CA 90095
United States

University of California, Los Angeles (UCLA) - Jonsson Comprehensive Cancer Center

10833 Le Conte Avenue
Los Angeles, CA 90095-6939
United States