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A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.

Nicholson, G, Rantalainen, M, Li, JV, Maher, AD, Malmodin, D, Ahmadi, KR, Faber, JH, Barrett, A, Min, JL, Rayner, NW , Toft, H, Krestyaninova, M, Viksna, J, Neogi, SG, Dumas, ME, Sarkans, U, MolPAGE Consortium, , Donnelly, P, Illig, T, Adamski, J, Suhre, K, Allen, M, Zondervan, KT, Spector, TD, Nicholson, JK, Lindon, JC, Baunsgaard, D, Holmes, E, McCarthy, MI and Holmes, CC (2011) A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet, 7 (9).

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Abstract

We have performed a metabolite quantitative trait locus (mQTL) study of the (1)H nuclear magnetic resonance spectroscopy ((1)H NMR) metabolome in humans, building on recent targeted knowledge of genetic drivers of metabolic regulation. Urine and plasma samples were collected from two cohorts of individuals of European descent, with one cohort comprised of female twins donating samples longitudinally. Sample metabolite concentrations were quantified by (1)H NMR and tested for association with genome-wide single-nucleotide polymorphisms (SNPs). Four metabolites' concentrations exhibited significant, replicable association with SNP variation (8.6×10(-11)<p<2.8×10(-23)). Three of these-trimethylamine, 3-amino-isobutyrate, and an N-acetylated compound-were measured in urine. The other-dimethylamine-was measured in plasma. Trimethylamine and dimethylamine mapped to a single genetic region (hence we report a total of three implicated genomic regions). Two of the three hit regions lie within haplotype blocks (at 2p13.1 and 10q24.2) that carry the genetic signature of strong, recent, positive selection in European populations. Genes NAT8 and PYROXD2, both with relatively uncharacterized functional roles, are good candidates for mediating the corresponding mQTL associations. The study's longitudinal twin design allowed detailed variance-components analysis of the sources of population variation in metabolite levels. The mQTLs explained 40%-64% of biological population variation in the corresponding metabolites' concentrations. These effect sizes are stronger than those reported in a recent, targeted mQTL study of metabolites in serum using the targeted-metabolomics Biocrates platform. By re-analysing our plasma samples using the Biocrates platform, we replicated the mQTL findings of the previous study and discovered a previously uncharacterized yet substantial familial component of variation in metabolite levels in addition to the heritability contribution from the corresponding mQTL effects.

Item Type: Article
Authors :
NameEmailORCID
Nicholson, GUNSPECIFIEDUNSPECIFIED
Rantalainen, MUNSPECIFIEDUNSPECIFIED
Li, JVUNSPECIFIEDUNSPECIFIED
Maher, ADUNSPECIFIEDUNSPECIFIED
Malmodin, DUNSPECIFIEDUNSPECIFIED
Ahmadi, KRk.ahmadi@surrey.ac.ukUNSPECIFIED
Faber, JHUNSPECIFIEDUNSPECIFIED
Barrett, AUNSPECIFIEDUNSPECIFIED
Min, JLUNSPECIFIEDUNSPECIFIED
Rayner, NWUNSPECIFIEDUNSPECIFIED
Toft, HUNSPECIFIEDUNSPECIFIED
Krestyaninova, MUNSPECIFIEDUNSPECIFIED
Viksna, JUNSPECIFIEDUNSPECIFIED
Neogi, SGUNSPECIFIEDUNSPECIFIED
Dumas, MEUNSPECIFIEDUNSPECIFIED
Sarkans, UUNSPECIFIEDUNSPECIFIED
MolPAGE Consortium, UNSPECIFIEDUNSPECIFIED
Donnelly, PUNSPECIFIEDUNSPECIFIED
Illig, TUNSPECIFIEDUNSPECIFIED
Adamski, JUNSPECIFIEDUNSPECIFIED
Suhre, KUNSPECIFIEDUNSPECIFIED
Allen, MUNSPECIFIEDUNSPECIFIED
Zondervan, KTUNSPECIFIEDUNSPECIFIED
Spector, TDUNSPECIFIEDUNSPECIFIED
Nicholson, JKUNSPECIFIEDUNSPECIFIED
Lindon, JCUNSPECIFIEDUNSPECIFIED
Baunsgaard, DUNSPECIFIEDUNSPECIFIED
Holmes, EUNSPECIFIEDUNSPECIFIED
McCarthy, MIUNSPECIFIEDUNSPECIFIED
Holmes, CCUNSPECIFIEDUNSPECIFIED
Date : September 2011
Identification Number : 10.1371/journal.pgen.1002270
Uncontrolled Keywords : Acetyltransferases, Dimethylamines, Female, Genome-Wide Association Study, Haplotypes, Humans, Isobutyrates, Magnetic Resonance Spectroscopy, Metabolic Networks and Pathways, Metabolome, Methylamines, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Selection, Genetic
Depositing User : Symplectic Elements
Date Deposited : 17 May 2017 09:48
Last Modified : 17 May 2017 14:44
URI: http://epubs.surrey.ac.uk/id/eprint/825175

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