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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 publication

DOI

10.1038/s41586-020-2267-z

Type

Journal article

Journal

Nature

Publication Date

27/05/2020

Volume

581

Pages

459 - 464

Addresses

Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. eminikel@broadinstitute.org.

Keywords

Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Humans, Neurodegenerative Diseases, tau Proteins, Artifacts, Reproducibility of Results, Sample Size, Consanguinity, Gene Frequency, Heterozygote, Homozygote, Genes, Essential, Exons, Automation, Gene Knockdown Techniques, Molecular Targeted Therapy, Prion Proteins, Huntingtin Protein, Leucine-Rich Repeat Serine-Threonine Protein Kinase-2, Loss of Function Mutation, Gain of Function Mutation