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Mol Syst Biol. 2017 Dec 21;13(12):957. doi: 10.15252/msb.20177908.

A framework for exhaustively mapping functional missense variants.

Weile J1,2,3,4, Sun S1,2,3,4,5, Cote AG1,2,3, Knapp J1,2,3, Verby M1,2,3, Mellor JC2,6, Wu Y1,2,3,4, Pons C7, Wong C1,2, van Lieshout N1, Yang F1,2,3,4, Tasan M1,2,3,4, Tan G2,3, Yang S8, Fowler DM9, Nussbaum R8, Bloom JD10, Vidal M11,12, Hill DE11, Aloy P7,13, Roth FP14,2,3,4,15.

Author information

1
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
2
The Donnelly Centre, University of Toronto, Toronto, ON, Canada.
3
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
4
Department of Computer Science, University of Toronto, Toronto, ON, Canada.
5
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
6
SeqWell Inc, Boston, MA, USA.
7
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.
8
Invitae Corp., San Francisco, CA, USA.
9
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
10
Fred Hutchinson Research Center, Seattle, WA, USA.
11
Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.
12
Department of Genetics, Harvard Medical School, Boston, MA, USA.
13
Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
14
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada fritz.roth@utoronto.ca.
15
Canadian Institute for Advanced Research, Toronto, ON, Canada.

Abstract

Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin-like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.

KEYWORDS:

complementation; deep mutational scanning; genotype–phenotype; variants of uncertain significance

PMID:
29269382
PMCID:
PMC5740498
DOI:
10.15252/msb.20177908
[Indexed for MEDLINE]
Free PMC Article

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