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Genes 2018, 9(1), 45; https://doi.org/10.3390/genes9010045

Using Y-Chromosomal Haplogroups in Genetic Association Studies and Suggested Implications

1
Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
2
MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
*
Author to whom correspondence should be addressed.
Received: 23 October 2017 / Revised: 16 January 2018 / Accepted: 16 January 2018 / Published: 22 January 2018
(This article belongs to the Special Issue Complex Genetic Loci)
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Abstract

Y-chromosomal (Y-DNA) haplogroups are more widely used in population genetics than in genetic epidemiology, although associations between Y-DNA haplogroups and several traits, including cardiometabolic traits, have been reported. In apparently homogeneous populations defined by principal component analyses, there is still Y-DNA haplogroup variation which will result from population history. Therefore, hidden stratification and/or differential phenotypic effects by Y-DNA haplogroups could exist. To test this, we hypothesised that stratifying individuals according to their Y-DNA haplogroups before testing for associations between autosomal single nucleotide polymorphisms (SNPs) and phenotypes will yield difference in association. For proof of concept, we derived Y-DNA haplogroups from 6537 males from two epidemiological cohorts, Avon Longitudinal Study of Parents and Children (ALSPAC) (n = 5080; 816 Y-DNA SNPs) and the 1958 Birth Cohort (n = 1457; 1849 Y-DNA SNPs), and studied the robust associations between 32 SNPs and body mass index (BMI), including SNPs in or near Fat Mass and Obesity-associated protein (FTO) which yield the strongest effects. Overall, no association was replicated in both cohorts when Y-DNA haplogroups were considered and this suggests that, for BMI at least, there is little evidence of differences in phenotype or SNP association by Y-DNA structure. Further studies using other traits, phenome-wide association studies (PheWAS), other haplogroups and/or autosomal SNPs are required to test the generalisability and utility of this approach. View Full-Text
Keywords: Y-DNA; haplogroups; body mass index; Avon Longitudinal Study of Parents and Children; 1958 Birth Cohort Y-DNA; haplogroups; body mass index; Avon Longitudinal Study of Parents and Children; 1958 Birth Cohort
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Erzurumluoglu, A.M.; Baird, D.; Richardson, T.G.; Timpson, N.J.; Rodriguez, S. Using Y-Chromosomal Haplogroups in Genetic Association Studies and Suggested Implications. Genes 2018, 9, 45.

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