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2017 ; 101
(3
): 315-325
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Variant Interpretation: Functional Assays to the Rescue
#MMPMID28886340
Starita LM
; Ahituv N
; Dunham MJ
; Kitzman JO
; Roth FP
; Seelig G
; Shendure J
; Fowler DM
Am J Hum Genet
2017[Sep]; 101
(3
): 315-325
PMID28886340
show ga
Classical genetic approaches for interpreting variants, such as case-control or
co-segregation studies, require finding many individuals with each variant.
Because the overwhelming majority of variants are present in only a few living
humans, this strategy has clear limits. Fully realizing the clinical potential of
genetics requires that we accurately infer pathogenicity even for rare or private
variation. Many computational approaches to predicting variant effects have been
developed, but they can identify only a small fraction of pathogenic variants
with the high confidence that is required in the clinic. Experimentally measuring
a variant's functional consequences can provide clearer guidance, but individual
assays performed only after the discovery of the variant are both time and
resource intensive. Here, we discuss how multiplex assays of variant effect
(MAVEs) can be used to measure the functional consequences of all possible
variants in disease-relevant loci for a variety of molecular and cellular
phenotypes. The resulting large-scale functional data can be combined with
machine learning and clinical knowledge for the development of "lookup tables" of
accurate pathogenicity predictions. A coordinated effort to produce, analyze, and
disseminate large-scale functional data generated by multiplex assays could be
essential to addressing the variant-interpretation crisis.