Evolutionary perspectives on polygenic selection, missing heritability, and GWAS

LH Uricchio - Human genetics, 2020 - Springer
Genome-wide association studies (GWAS) have successfully identified many trait-
associated variants, but there is still much we do not know about the genetic basis of …

Ultrarare variants drive substantial cis heritability of human gene expression

RD Hernandez, LH Uricchio, K Hartman, C Ye, A Dahl… - Nature …, 2019 - nature.com
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 …

Human demographic history has amplified the effects of background selection across the genome

R Torres, ZA Szpiech, RD Hernandez - PLoS genetics, 2018 - journals.plos.org
Natural populations often grow, shrink, and migrate over time. Such demographic processes
can affect genome-wide levels of genetic diversity. Additionally, genetic variation in …

Exploiting selection at linked sites to infer the rate and strength of adaptation

LH Uricchio, DA Petrov, D Enard - Nature ecology & evolution, 2019 - nature.com
Genomic data encode past evolutionary events and have the potential to reveal the strength,
rate and biological drivers of adaptation. However, joint estimation of adaptation rate (α) and …

Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants

LH Uricchio, NA Zaitlen, CJ Ye, JS Witte… - Genome …, 2016 - genome.cshlp.org
The role of rare alleles in complex phenotypes has been hotly debated, but most rare variant
association tests (RVATs) do not account for the evolutionary forces that affect genetic …

A model of compound heterozygous, loss-of-function alleles is broadly consistent with observations from complex-disease GWAS datasets

JS Sanjak, AD Long, KR Thornton - PLoS genetics, 2017 - journals.plos.org
The genetic component of complex disease risk in humans remains largely unexplained. A
corollary is that the allelic spectrum of genetic variants contributing to complex disease risk …

Singleton variants dominate the genetic architecture of human gene expression

RD Hernandez, LH Uricchio, K Hartman, C Ye, A Dahl… - BioRxiv, 2017 - biorxiv.org
The vast majority of human mutations have minor allele frequencies (MAF) under 1%, with
the plurality observed only once (ie,“singletons”). While Mendelian diseases are …

SFS_CODE: more efficient and flexible forward simulations

RD Hernandez, LH Uricchio - bioRxiv, 2015 - biorxiv.org
Modern implementations of forward population genetic simulations are efficient and flexible,
enabling the exploration of complex models that may otherwise be intractable. Here we …

Population genetic simulation study of power in association testing across genetic architectures and study designs

DMH Tong, RD Hernandez - Genetic epidemiology, 2020 - Wiley Online Library
While it is well established that genetics can be a major contributor to population variation of
complex traits, the relative contributions of rare and common variants to phenotypic variation …

PGsim: a comprehensive and highly customizable personal genome simulator

L Juan, Y Wang, J Jiang, Q Yang, Q Jiang… - … in Bioengineering and …, 2020 - frontiersin.org
Although genome sequencing has become increasingly popular, the simulation of individual
genomes is still important. This is because sequencing a large number of individual …