The vast majority of human mutations have minor allele frequencies under 1%, with the plurality observed only once (that is, ‘singletons’). While Mendelian diseases are predominantly caused by rare alleles, their cumulative contribution to complex phenotypes is largely unknown. We develop and rigorously validate an approach to jointly estimate the contribution of all alleles, including singletons, to phenotypic variation. We apply our approach to transcriptional regulation, an intermediate between genetic variation and complex disease. Using whole-genome DNA and lymphoblastoid cell line RNA sequencing data from 360 European individuals, we conservatively estimate that singletons contribute approximately 25% of cis heritability across genes (dwarfing the contributions of other frequencies). The majority (approximately 76%) of singleton heritability derives from ultrarare variants absent from thousands of additional samples. We develop an inference procedure to demonstrate that our results are consistent with pervasive purifying selection shaping the regulatory architecture of most human genes.
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RNA-seq gene expression data were downloaded from http://www.internationalgenome.org/data-portal/data-collection/geuvadis. This dataset contains 375 individuals of European descent from 4 locations. Each of these individuals are contained in the 1KGP and genome sequence data were downloaded from www.1000genomes.org (ref. 24).
Three open source software tools are being made available as part of this study; all are available on GitHub: (1) HEh2.R—R code that performs all the Haseman–Elston analyses and simulations discussed in this paper. It also implements the artificial intelligence algorithm for parameter inference of linear mixed models. It is available from https://github.com/hernrya/HEh2; (2) SingHer R package discussed in the Supplementary Note, with performance statistics and available from https://github.com/andywdahl/SingHer; and (3) rejection sampling: scripts demonstrating how we used rejection sampling to infer parameters of the phenotype model are available from https://github.com/uricchio/HE_scripts.
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We thank H. M. Kang, A. Auton and S. Gusev for discussions about possible confounders that improved our analysis; members of the Pritchard laboratory for comments on rejection sampling; J. Barrett and K. Karczewski for peer-reviewing our preprint; R. Torres for assistance with data analysis; J. Wall for assistance with the Neanderthal-introgressed alleles; and A. Hernandez for discussions on figure colors. Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health (award no. R01HG007644 to R.D.H. and award no. K25HL121295). L.H.U. was supported by an Institutional Research and Academic Career Development Award (National Institute of General Medical Sciences, grant no. K12GM088033). K.H. was supported by a Gilliam Fellowship for Advanced Study; A.D. was supported by NIH (award nos. U01HG009080 and R01HG006399).
The authors declare no competing interests.
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Hernandez, R.D., Uricchio, L.H., Hartman, K. et al. Ultrarare variants drive substantial cis heritability of human gene expression. Nat Genet 51, 1349–1355 (2019). https://doi.org/10.1038/s41588-019-0487-7
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