Genetic Similarity Assessment of Twin-Family Populations by Custom-Designed Genotyping Array

Jeffrey J Beck, Jouke Jan Hottenga, Hamdi Mbarek, Casey T Finnicum, Erik A Ehli, Yoon-Mi Hur, Nicholas G Martin, Eco J.C. de Geus, D.I. Boomsma, Gareth E Davies

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Twin registries often take part in large collaborative projects and are major contributors to genome-wide association (GWA) meta-analysis studies. In this article, we describe genotyping of twin-family populations from Australia, the Midwestern USA (Avera Twin Register), the Netherlands (Netherlands Twin Register), as well as a sample of mothers of twins from Nigeria to assess the extent, if any, of genetic differences between them. Genotyping in all cohorts was done using a custom-designed Illumina Global Screening Array (GSA), optimized to improve imputation quality for population-specific GWA studies. We investigated the degree of genetic similarity between the populations using several measures of population variation with genotype data generated from the GSA. Visualization of principal component analysis (PCA) revealed that the Australian, Dutch and Midwestern American populations exhibit negligible interpopulation stratification when compared to each other, to a reference European population and to globally distant populations. Estimations of fixation indices (FST values) between the Australian, Midwestern American and Netherlands populations suggest minimal genetic differentiation compared to the estimates between each population and a genetically distinct cohort (i.e., samples from Nigeria genotyped on GSA). Thus, results from this study demonstrate that genotype data from the Australian, Dutch and Midwestern American twin-family populations can be reasonably combined for joint-genetic analysis.

Original languageEnglish
Pages (from-to)210-219
Number of pages10
JournalTwin research and human genetics : the official journal of the International Society for Twin Studies
Volume22
Issue number4
DOIs
Publication statusPublished - Aug 2019

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Population
Netherlands
Genome-Wide Association Study
Nigeria
Genotype
Principal Component Analysis
Registries
Meta-Analysis
Joints

Cite this

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title = "Genetic Similarity Assessment of Twin-Family Populations by Custom-Designed Genotyping Array",
abstract = "Twin registries often take part in large collaborative projects and are major contributors to genome-wide association (GWA) meta-analysis studies. In this article, we describe genotyping of twin-family populations from Australia, the Midwestern USA (Avera Twin Register), the Netherlands (Netherlands Twin Register), as well as a sample of mothers of twins from Nigeria to assess the extent, if any, of genetic differences between them. Genotyping in all cohorts was done using a custom-designed Illumina Global Screening Array (GSA), optimized to improve imputation quality for population-specific GWA studies. We investigated the degree of genetic similarity between the populations using several measures of population variation with genotype data generated from the GSA. Visualization of principal component analysis (PCA) revealed that the Australian, Dutch and Midwestern American populations exhibit negligible interpopulation stratification when compared to each other, to a reference European population and to globally distant populations. Estimations of fixation indices (FST values) between the Australian, Midwestern American and Netherlands populations suggest minimal genetic differentiation compared to the estimates between each population and a genetically distinct cohort (i.e., samples from Nigeria genotyped on GSA). Thus, results from this study demonstrate that genotype data from the Australian, Dutch and Midwestern American twin-family populations can be reasonably combined for joint-genetic analysis.",
author = "Beck, {Jeffrey J} and Hottenga, {Jouke Jan} and Hamdi Mbarek and Finnicum, {Casey T} and Ehli, {Erik A} and Yoon-Mi Hur and Martin, {Nicholas G} and {de Geus}, {Eco J.C.} and D.I. Boomsma and Davies, {Gareth E}",
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Genetic Similarity Assessment of Twin-Family Populations by Custom-Designed Genotyping Array. / Beck, Jeffrey J; Hottenga, Jouke Jan ; Mbarek, Hamdi; Finnicum, Casey T; Ehli, Erik A; Hur, Yoon-Mi; Martin, Nicholas G; de Geus, Eco J.C.; Boomsma, D.I.; Davies, Gareth E.

In: Twin research and human genetics : the official journal of the International Society for Twin Studies, Vol. 22, No. 4, 08.2019, p. 210-219.

Research output: Contribution to JournalArticleAcademicpeer-review

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