
School of Medicine Publications and Presentations
Document Type
Article
Publication Date
3-1-2015
Abstract
Initial results from sequencing studies suggest that there are relatively few low-frequency (<5%) variants associated with large effects on common phenotypes. We performed low-pass whole-genome sequencing in 680 individuals from the InCHIANTI study to test two primary hypotheses: (i) that sequencing would detect single low-frequency–large effect variants that explained similar amounts of phenotypic variance as single common variants, and (ii) that some common variant associations could be explained by low-frequency variants. We tested two sets of disease-related common phenotypes for which we had statistical power to detect large numbers of common variant–common phenotype associations—11 132 cis-gene expression traits in 450 individuals and 93 circulating biomarkers in all 680 individuals. From a total of 11 657 229 high-quality variants of which 6 129 221 and 5 528 008 were common and low frequency (<5%), respectively, low frequency–large effect associations comprised 7% of detectable cis-gene expression traits [89 of 1314 cis-eQTLs at P < 1 × 10−06 (false discovery rate ∼5%)] and one of eight biomarker associations at P < 8 × 10−10. Very few (30 of 1232; 2%) common variant associations were fully explained by low-frequency variants. Our data show that whole-genome sequencing can identify low-frequency variants undetected by genotyping based approaches when sample sizes are sufficiently large to detect substantial numbers of common variant associations, and that common variant associations are rarely explained by single low-frequency variants of large effect.
Recommended Citation
Wood, A. R., Tuke, M. A., Nalls, M., Hernandez, D., Gibbs, J. R., Lin, H., Xu, C. S., Li, Q., Shen, J., Jun, G., Almeida, M., Tanaka, T., Perry, J. R., Gaulton, K., Rivas, M., Pearson, R., Curran, J. E., Johnson, M. P., Göring, H. H., Duggirala, R., … Frayling, T. M. (2015). Whole-genome sequencing to understand the genetic architecture of common gene expression and biomarker phenotypes. Human molecular genetics, 24(5), 1504–1512. https://doi.org/10.1093/hmg/ddu560
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
First Page
1504
Last Page
1512
Publication Title
Human Molecular Genetics
DOI
10.1093/hmg/ddu560
Academic Level
faculty
Mentor/PI Department
Office of Human Genetics
Comments
© The Author 2014. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.