Evaluating drug targets through human loss-of-function genetic variation

Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Eric Vallabh Minikel*, Konrad J. Karczewski, Hilary C. Martin, Beryl B. Cummings, Nicola Whiffin, Daniel Rhodes, Jessica Alföldi, Richard C. Trembath, David A. van Heel, Mark J. Daly, Jessica Alföldi, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Ryan L. Collins, Kristen M. Connolly, Miguel CovarrubiasBeryl B. Cummings, Mark J. Daly, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Laurent Francioli, Stacey Gabriel, Laura D. Gauthier, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Konrad J. Karczewski, Kristen M. Laricchia, Christopher Llanwarne, Eric V. Minikel, Ruchi Munshi, Benjamin M. Neale, Sam Novod, Anne H. O’Donnell-Luria, Nikelle Petrillo, Timothy Poterba, David Roazen, Valentin Ruano-Rubio, Andrea Saltzman, Kaitlin E. Samocha, Molly Schleicher, Cotton Seed, Matthew Solomonson, Jose Soto, Grace Tiao, Kathleen Tibbetts

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

93 Citations (Scopus)
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Abstract

Naturally occurring human genetic variants that are predicted to inactivate protein-coding genes provide an in vivo model of human gene inactivation that complements knockout studies in cells and model organisms. Here we report three key findings regarding the assessment of candidate drug targets using human loss-of-function variants. First, even essential genes, in which loss-of-function variants are not tolerated, can be highly successful as targets of inhibitory drugs. Second, in most genes, loss-of-function variants are sufficiently rare that genotype-based ascertainment of homozygous or compound heterozygous ‘knockout’ humans will await sample sizes that are approximately 1,000 times those presently available, unless recruitment focuses on consanguineous individuals. Third, automated variant annotation and filtering are powerful, but manual curation remains crucial for removing artefacts, and is a prerequisite for recall-by-genotype efforts. Our results provide a roadmap for human knockout studies and should guide the interpretation of loss-of-function variants in drug development.

Original languageEnglish
Pages (from-to)459-464
Number of pages6
JournalNature
Volume581
Issue number7809
Early online date27 May 2020
DOIs
Publication statusPublished - 28 May 2020

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