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

Rockie Chong; Kimberly D Insigne; David Yao; Christina P Burghard; Jeffrey Wang; Yun-Hua E Hsiao; Eric M Jones; Daniel B Goodman; Xinshu Xiao; Sriram Kosuri

doi:10.1016/j.molcel.2018.10.037

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

Mol Cell. 2019 Jan 3;73(1):183-194.e8. doi: 10.1016/j.molcel.2018.10.037. Epub 2018 Nov 29.

Authors

Affiliations

¹ Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
² Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
³ Department of Genetics, Stanford University, Stanford, CA 94035, USA.
⁴ Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁵ Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.
⁶ Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
⁷ Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: [email protected].

Abstract

Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter and found that 3.8% (1,050) of variants, most of which are extremely rare, led to large-effect splice-disrupting variants (SDVs). Importantly, we find that 83% of 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 extant, rare genetic variants can have large functional effects on splicing at appreciable rates, even outside the context of disease, and MFASS enables their empirical assessment at scale.

Keywords: exon recognition; massively parallel reporter assay; population variation; rare variation; splicing; variant classification.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Cell Separation
Computational Biology
Exons*
Flow Cytometry
Gene Expression Profiling / methods*
HEK293 Cells
HeLa Cells
Hep G2 Cells
High-Throughput Nucleotide Sequencing / methods*
Humans
Introns
K562 Cells
Mutation*
Oligonucleotide Array Sequence Analysis
RNA Splicing*
Reproducibility of Results
Sequence Analysis, DNA / methods*

Abstract

Publication types

MeSH terms

Grants and funding