From GWAS to function: using functional genomics to identify the mechanisms underlying complex diseases

E Cano-Gamez, G Trynka - Frontiers in genetics, 2020 - frontiersin.org
Genome-wide association studies (GWAS) have successfully mapped thousands of loci
associated with complex traits. These associations could reveal the molecular mechanisms …

Integrative omics for health and disease

KJ Karczewski, MP Snyder - Nature Reviews Genetics, 2018 - nature.com
Advances in omics technologies—such as genomics, transcriptomics, proteomics and
metabolomics—have begun to enable personalized medicine at an extraordinarily detailed …

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

U Võsa, A Claringbould, HJ Westra, MJ Bonder… - Nature …, 2021 - nature.com
Trait-associated genetic variants affect complex phenotypes primarily via regulatory
mechanisms on the transcriptome. To investigate the genetics of gene expression, we …

[HTML][HTML] clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng… - The innovation, 2021 - cell.com
Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life
science. It is crucial for this type of tool to use the latest annotation databases for as many …

Atlas of the aging mouse brain reveals white matter as vulnerable foci

O Hahn, AG Foltz, M Atkins, B Kedir, P Moran-Losada… - Cell, 2023 - cell.com
Aging is the key risk factor for cognitive decline, yet the molecular changes underlying brain
aging remain poorly understood. Here, we conducted spatiotemporal RNA sequencing of …

CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores

P Rentzsch, M Schubach, J Shendure, M Kircher - Genome medicine, 2021 - Springer
Background Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate
synthesis of human proteins. Genetic variants impacting splicing underlie a substantial …

Exaggerated false positives by popular differential expression methods when analyzing human population samples

Y Li, X Ge, F Peng, W Li, JJ Li - Genome biology, 2022 - Springer
When identifying differentially expressed genes between two conditions using human
population RNA-seq samples, we found a phenomenon by permutation analysis: two …

A compendium of uniformly processed human gene expression and splicing quantitative trait loci

N Kerimov, JD Hayhurst, K Peikova, JR Manning… - Nature …, 2021 - nature.com
Many gene expression quantitative trait locus (eQTL) studies have published their summary
statistics, which can be used to gain insight into complex human traits by downstream …

Sequencing of 640,000 exomes identifies GPR75 variants associated with protection from obesity

P Akbari, A Gilani, O Sosina, JA Kosmicki, L Khrimian… - Science, 2021 - science.org
INTRODUCTION Obesity accounts for a substantial and growing burden of disease globally.
Body adiposity is highly heritable, and human genetic studies can lead to biological and …

The impact of sex on gene expression across human tissues

M Oliva, M Muñoz-Aguirre, S Kim-Hellmuth, V Wucher… - Science, 2020 - science.org
INTRODUCTION Many complex human phenotypes, including diseases, exhibit sex-
differentiated characteristics. These sex differences have been variously attributed to …