Note: a that this variable try Blonde hair + blue-eyes on the 1908 analysis and you can Blond locks + blue/grey attention throughout the 2004 analysis.
Steps
, Source van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and you can Lamb 2013; Willemsen et al., Resource Willemsen, Vink, Abdellaoui, den Braber, van Beek and you can Draisma 2013) was one of them investigation according to research by the exposure from self-reported research with the pure locks and eyes colour as well as the visibility away from genotype studies for the an enthusiastic Illumina 370, 660, 1M or Affymetrix Perlegen-5.0, otherwise 6.0 program. There had been seven,063 genotyped Dutch-origins users, clustered inside step three,407 parents that have data toward eyes colour, and you will 6,965 genotyped some body had investigation to the both tresses and you can eyes color. To the hereditary association data away from eyes color (find Additional topic) all of the research had been reviewed. To have bivariate hereditary analyses within the GCTA, the unrelated people were picked, according to a hereditary relatedness matrix (GRM) cut-from 0.025 (Yang et al., Source Yang, Lee, Goddard and you can Visscher 2011). It left 3,619 anyone with the bivariate analyses, having an inherited relatedness comparable to less than 3rd otherwise 4th cousin.
, Resource Willemsen, Vink, Abdellaoui, den Braber, van Beek and you may Draisma 2013). Adult professionals claimed their sheer locks colour from off five solutions: ‘fair/blond’, ‘hazel’, ‘red/auburn’, ‘ebony brown’, and you will ‘black’ and eyes colour with among three alternatives: ‘blue/gray’, ‘green/hazel’ and ‘brown’. An equivalent inquiries into eye color and locks colour was basically answered by the adolescent (14- to help you 18-year-old) https://datingranking.net/fr/rencontres-thai-fr/ twins once they accomplished the fresh new Dutch Health and Behavior Survey in the 2005 otherwise 2006 (van Beijsterveldt mais aussi al., Source van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and Lamb 2013). On the statistical analyses, we mutual brand new black colored, white brown, and darkish locks colors so you’re able to ‘dark’, while the merely not many someone claimed a black locks color (Lin ainsi que al., Reference Lin, Mbarek, Willemsen, Dolan, Fedko and you will Abdellaoui 2015). Authored informed concur is obtained from all the participants.
Age, intercourse, pure locks, and eye colour was basically taken from Adult NTR questionnaire eight, that has been built-up in the 2004 (Willemsen mais aussi al
DNA extraction, purification, and genotype calling of the samples were performed at various points in time following the manufacturer’s protocols and genotype calling programs (Lin et al., Reference Lin, Mbarek, Willemsen, Dolan, Fedko and Abdellaoui 2015). For each platform, the individual SNPs were remapped on the build 37 (HG19), ALL 1000 Genomes Phase 1 imputation reference dataset (Auton et al., Reference Auton, Brooks, Durbin, Garrison, Kang and Korbel 2015). SNPs that failed unique mapping and SNPs with an allele frequency difference over 0.20 with the reference data were removed. SNPs with a minor allele frequency (MAF) < 0.01 were also removed, as well as SNPs that were out of Hardy–Weinberg Equilibrium (HWE) with p < 10 ?5 . The platform data were then merged into a single genotype set and the above SNP QC filters were reapplied. Samples were excluded from the data when their DNA was discordant with their expected sex or IBD status, the genotype missing rate was above 10%, the Plink F-inbreeding value was either larger than 0.10 or smaller than ?0.10, or they were an ethnic outlier based on EIGENSTRAT PCs calculated from the 1000G imputed data (Auton et al., Reference Auton, Brooks, Durbin, Garrison, Kang and Korbel 2015). Phasing of the samples and imputing cross-missing platform SNPs was done with MACH 1 (Li Abecasis, Reference Li and Abecasis 2006). The phased data were then imputed with MINIMAC to the 1000G reference. After imputation, SNPs were filtered, based on Mendelian error rate (>2%), a R 2 imputation quality value of <0.80, MAF <0.01 and a difference of more than 0.15 between the allele frequency and the reference (Howie et al., Reference Howie, Fuchsberger, Stephens, ). We tested the effect of different platforms and removed SNPs showing platform effects. This was done by defining individuals on a specific platform as cases and the others as controls. If the allelic association between the specific platform allele frequency and the other platform's allele frequency was significant (p < 10 ?5 ) SNPs were removed. This left 5,987,253 SNPs, which were all used to construct a GRM.