학술논문
The functional impact of rare variation across the regulatory cascade
Document Type
article
Author
Taibo Li; Nicole Ferraro; Benjamin J. Strober; Francois Aguet; Silva Kasela; Marios Arvanitis; Bohan Ni; Laurens Wiel; Elliot Hershberg; Kristin Ardlie; Dan E. Arking; Rebecca L. Beer; Jennifer Brody; Thomas W. Blackwell; Clary Clish; Stacey Gabriel; Robert Gerszten; Xiuqing Guo; Namrata Gupta; W. Craig Johnson; Tuuli Lappalainen; Henry J. Lin; Yongmei Liu; Deborah A. Nickerson; George Papanicolaou; Jonathan K. Pritchard; Pankaj Qasba; Ali Shojaie; Josh Smith; Nona Sotoodehnia; Kent D. Taylor; Russell P. Tracy; David Van Den Berg; Matthew T. Wheeler; Stephen S. Rich; Jerome I. Rotter; Alexis Battle; Stephen B. Montgomery
Source
Cell Genomics, Vol 3, Iss 10, Pp 100401- (2023)
Subject
Language
English
ISSN
2666-979X
Abstract
Summary: Each human genome has tens of thousands of rare genetic variants; however, identifying impactful rare variants remains a major challenge. We demonstrate how use of personal multi-omics can enable identification of impactful rare variants by using the Multi-Ethnic Study of Atherosclerosis, which included several hundred individuals, with whole-genome sequencing, transcriptomes, methylomes, and proteomes collected across two time points, 10 years apart. We evaluated each multi-omics phenotype’s ability to separately and jointly inform functional rare variation. By combining expression and protein data, we observed rare stop variants 62 times and rare frameshift variants 216 times as frequently as controls, compared to 13–27 times as frequently for expression or protein effects alone. We extended a Bayesian hierarchical model, “Watershed,” to prioritize specific rare variants underlying multi-omics signals across the regulatory cascade. With this approach, we identified rare variants that exhibited large effect sizes on multiple complex traits including height, schizophrenia, and Alzheimer’s disease.