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Genet Epidemiol. 2016 Sep;40(6):486-91. doi: 10.1002/gepi.21980. Epub 2016 Jun 3.

Identification of Rare Variants in Metabolites of the Carnitine Pathway by Whole Genome Sequencing Analysis.

Author information

1
Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America.
2
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America.

Abstract

We use whole genome sequence data and rare variant analysis methods to investigate a subset of the human serum metabolome, including 16 carnitine-related metabolites that are important components of mammalian energy metabolism. Medium pass sequence data consisting of 12,820,347 rare variants and serum metabolomics data were available on 1,456 individuals. By applying a penalization method, we identified two genes FGF8 and MDGA2 with significant effects on lysine and cis-4-decenoylcarnitine, respectively, using Δ-AIC and likelihood ratio test statistics. Single variant analyses in these regions did not identify a single low-frequency variant (minor allele count > 3) responsible for the underlying signal. The results demonstrate the utility of whole genome sequence and innovative analyses for identifying candidate regions influencing complex phenotypes.

KEYWORDS:

carnitine; linkage disequilibrium; metabolomics; penalization; rare variants

PMID:
27256581
PMCID:
PMC5609480
DOI:
10.1002/gepi.21980
[Indexed for MEDLINE]
Free PMC Article

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