Exome-wide rare variant analyses of two bone mineral density phenotypes: The challenges of analyzing rare genetic variation

Jianping Sun, Karim Oualkacha, Vincenzo Forgetta, Hou Feng Zheng, J. Brent Richards, Daniel S. Evans, Eric Orwoll, Celia M.T. Greenwood

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Abstract

Performance of a recently developed test for association between multivariate phenotypes and sets of genetic variants (MURAT) is demonstrated using measures of bone mineral density (BMD). By combining individual-level whole genome sequenced data from the UK10K study, and imputed genome-wide genetic data on individuals from the Study of Osteoporotic Fractures (SOF) and the Osteoporotic Fractures in Men Study (MrOS), a data set of 8810 individuals was assembled; tests of association were performed between autosomal gene-sets of genetic variants and BMD measured at lumbar spine and femoral neck. Distributions of p-values obtained from analyses of a single BMD phenotype are compared to those from the multivariate tests, across several region definitions and variant weightings. There is evidence of increased power with the multivariate test, although no new loci for BMD were identified. Among 17 genes highlighted either because there were significant p-values in region-based association tests or because they were in well-known BMD genes, 4 windows in 2 genes as well as 6 single SNPs in one of these genes showed association at genome-wide significant thresholds with the multivariate phenotype test but not with the single-phenotype test, Sequence Kernel Association Test (SKAT).

Original languageEnglish (US)
Article number220
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018

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Exome
Bone Density
Phenotype
Osteoporotic Fractures
Genes
Genome
Femur Neck
Single Nucleotide Polymorphism
Spine

ASJC Scopus subject areas

  • General

Cite this

Sun, J., Oualkacha, K., Forgetta, V., Zheng, H. F., Richards, J. B., Evans, D. S., ... Greenwood, C. M. T. (2018). Exome-wide rare variant analyses of two bone mineral density phenotypes: The challenges of analyzing rare genetic variation. Scientific Reports, 8(1), [220]. https://doi.org/10.1038/s41598-017-18385-9

Exome-wide rare variant analyses of two bone mineral density phenotypes : The challenges of analyzing rare genetic variation. / Sun, Jianping; Oualkacha, Karim; Forgetta, Vincenzo; Zheng, Hou Feng; Richards, J. Brent; Evans, Daniel S.; Orwoll, Eric; Greenwood, Celia M.T.

In: Scientific Reports, Vol. 8, No. 1, 220, 01.12.2018.

Research output: Contribution to journalArticle

Sun, Jianping ; Oualkacha, Karim ; Forgetta, Vincenzo ; Zheng, Hou Feng ; Richards, J. Brent ; Evans, Daniel S. ; Orwoll, Eric ; Greenwood, Celia M.T. / Exome-wide rare variant analyses of two bone mineral density phenotypes : The challenges of analyzing rare genetic variation. In: Scientific Reports. 2018 ; Vol. 8, No. 1.
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