Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits

BC Zhang, A Biddanda, ÁF Gunnarsson, F Cooper… - Nature Genetics, 2023 - nature.com
Genome-wide genealogies compactly represent the evolutionary history of a set of genomes
and inferring them from genetic data has the potential to facilitate a wide range of analyses …

Cross-trait assortative mating is widespread and inflates genetic correlation estimates

R Border, G Athanasiadis, A Buil, AJ Schork, N Cai… - Science, 2022 - science.org
The observation of genetic correlations between disparate human traits has been
interpreted as evidence of widespread pleiotropy. Here, we introduce cross-trait assortative …

A review of SNP heritability estimation methods

M Tang, T Wang, X Zhang - Briefings in bioinformatics, 2022 - academic.oup.com
Over the past decade, statistical methods have been developed to estimate single
nucleotide polymorphism (SNP) heritability, which measures the proportion of phenotypic …

Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure

L Balagué-Dobón, A Cáceres… - Briefings in …, 2022 - academic.oup.com
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation
and the most accessible to genotype in large cohorts. However, they individually explain a …

[PDF][PDF] Low and differential polygenic score generalizability among African populations due largely to genetic diversity

L Majara, A Kalungi, N Koen, K Tsuo, Y Wang… - Human Genetics and …, 2023 - cell.com
African populations are vastly underrepresented in genetic studies but have the most
genetic variation and face wide-ranging environmental exposures globally. Because …

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

AS Findley, A Monziani, AL Richards, K Rhodes… - Elife, 2021 - elifesciences.org
Genetic effects on gene expression and splicing can be modulated by cellular and
environmental factors; yet interactions between genotypes, cell type, and treatment have not …

The lingering effects of Neanderthal introgression on human complex traits

X Wei, CR Robles, A Pazokitoroudi, A Ganna, A Gusev… - Elife, 2023 - elifesciences.org
The genetic variants introduced into the ancestors of modern humans from interbreeding
with Neanderthals have been suggested to contribute an unexpected extent to complex …

[PDF][PDF] Inferring gene-by-environment interactions with a Bayesian whole-genome regression model

M Kerin, J Marchini - The American Journal of Human Genetics, 2020 - cell.com
The contribution of gene-by-environment (GxE) interactions for many human traits and
diseases is poorly characterized. We propose a Bayesian whole-genome regression model …

[PDF][PDF] A robust method uncovers significant context-specific heritability in diverse complex traits

A Dahl, K Nguyen, N Cai, MJ Gandal, J Flint… - The American Journal of …, 2020 - cell.com
Gene-environment interactions (GxE) can be fundamental in applications ranging from
functional genomics to precision medicine and is a conjectured source of substantial …

[PDF][PDF] Quantifying the contribution of dominance deviation effects to complex trait variation in biobank-scale data

A Pazokitoroudi, AM Chiu, KS Burch, B Pasaniuc… - The American Journal of …, 2021 - cell.com
The proportion of variation in complex traits that can be attributed to non-additive genetic
effects has been a topic of intense debate. The availability of biobank-scale datasets of …