TY - JOUR
T1 - Transcript expression-aware annotation improves rare variant interpretation
AU - Genome Aggregation Database Production Team
AU - Genome Aggregation Database Consortium
AU - Cummings, Beryl B.
AU - Karczewski, Konrad J.
AU - Kosmicki, Jack A.
AU - Seaby, Eleanor G.
AU - Watts, Nicholas A.
AU - Singer-Berk, Moriel
AU - Mudge, Jonathan M.
AU - Karjalainen, Juha
AU - Satterstrom, F. Kyle
AU - O’Donnell-Luria, Anne H.
AU - Poterba, Timothy
AU - Seed, Cotton
AU - Solomonson, Matthew
AU - Alföldi, Jessica
AU - Alföldi, Jessica
AU - Armean, Irina M.
AU - Banks, Eric
AU - Bergelson, Louis
AU - Cibulskis, Kristian
AU - Collins, Ryan L.
AU - Connolly, Kristen M.
AU - Covarrubias, Miguel
AU - Cummings, Beryl B.
AU - Daly, Mark J.
AU - Donnelly, Stacey
AU - Farjoun, Yossi
AU - Ferriera, Steven
AU - Francioli, Laurent
AU - Gabriel, Stacey
AU - Gauthier, Laura D.
AU - Gentry, Jeff
AU - Gupta, Namrata
AU - Jeandet, Thibault
AU - Kaplan, Diane
AU - Karczewski, Konrad J.
AU - Laricchia, Kristen M.
AU - Llanwarne, Christopher
AU - Minikel, Eric V.
AU - Munshi, Ruchi
AU - Neale, Benjamin M.
AU - Novod, Sam
AU - O’Donnell-Luria, Anne H.
AU - Petrillo, Nikelle
AU - Poterba, Timothy
AU - Roazen, David
AU - Ruano-Rubio, Valentin
AU - Saltzman, Andrea
AU - Samocha, Kaitlin E.
AU - Schleicher, Molly
AU - Duggirala, Ravindranath
N1 - Funding Information:
Acknowledgements We thank all of the research participants for contributing their data. This work was supported by NIDDK U54 DK105566, NIGMS R01 GM104371, and the Broad Institute. KJK was supported by NIGMS F32 GM115208. A.O.L was supported by NICHD K12 HD052896. The GENCODE project is supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number U41HG007234. The results published here are in part based on data: (1) generated by The Cancer Genome Atlas (TCGA) managed by the NCI and NHGRI (accession: phs000178.v10.p8); information about TCGA can be found at http://cancergenome.nih.gov; (2) generated by the Genotype-Tissue Expression Project (GTEx) managed by the NIH Common Fund and NHGRI (accession: phs000424.v7.p2); (3) generated by the Exome Sequencing Project, managed by NHLBI; and (4) generated by the Alzheimer’s Disease Sequencing Project (ADSP), managed by the NIA and NHGRI (accession: phs000572. v7.p4). We thank E. Pierce-Hoffman for previous analysis and thoughts on characterizing loss-of-function variants in haploinsufficient genes. We thank the iPSYCH/SSI/Broad Institute psychiatric genetics study for the use of exome count data. We have complied with all relevant ethical regulations. This study was overseen by the Broad Institute’s Office of Research Subject Protection and the Partners Human Research Committee, and was given a determination of Not Human Subjects Research. Informed consent was obtained from all participants. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
PY - 2020/5/28
Y1 - 2020/5/28
N2 - The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the ‘proportion expressed across transcripts’, which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies.
AB - The acceleration of DNA sequencing in samples from patients and population studies has resulted in extensive catalogues of human genetic variation, but the interpretation of rare genetic variants remains problematic. A notable example of this challenge is the existence of disruptive variants in dosage-sensitive disease genes, even in apparently healthy individuals. Here, by manual curation of putative loss-of-function (pLoF) variants in haploinsufficient disease genes in the Genome Aggregation Database (gnomAD)1, we show that one explanation for this paradox involves alternative splicing of mRNA, which allows exons of a gene to be expressed at varying levels across different cell types. Currently, no existing annotation tool systematically incorporates information about exon expression into the interpretation of variants. We develop a transcript-level annotation metric known as the ‘proportion expressed across transcripts’, which quantifies isoform expression for variants. We calculate this metric using 11,706 tissue samples from the Genotype Tissue Expression (GTEx) project2 and show that it can differentiate between weakly and highly evolutionarily conserved exons, a proxy for functional importance. We demonstrate that expression-based annotation selectively filters 22.8% of falsely annotated pLoF variants found in haploinsufficient disease genes in gnomAD, while removing less than 4% of high-confidence pathogenic variants in the same genes. Finally, we apply our expression filter to the analysis of de novo variants in patients with autism spectrum disorder and intellectual disability or developmental disorders to show that pLoF variants in weakly expressed regions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly expressed exons are most strongly enriched among cases. Our annotation is fast, flexible and generalizable, making it possible for any variant file to be annotated with any isoform expression dataset, and will be valuable for the genetic diagnosis of rare diseases, the analysis of rare variant burden in complex disorders, and the curation and prioritization of variants in recall-by-genotype studies.
UR - http://www.scopus.com/inward/record.url?scp=85085576216&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85085576216&partnerID=8YFLogxK
U2 - 10.1038/s41586-020-2329-2
DO - 10.1038/s41586-020-2329-2
M3 - Article
C2 - 32461655
AN - SCOPUS:85085576216
VL - 581
SP - 452
EP - 458
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7809
ER -