Note: a that varying is Blond hair + blue eyes in the 1908 research and you may Blond locks + blue/gray vision on the 2004 study.
Steps
, Resource van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and you can Lamb 2013; Willemsen mais aussi al., Source Willemsen, Vink, Abdellaoui, den Braber, van Beek and Draisma 2013) were one of them research in line with the exposure out of notice-advertised studies to your natural tresses and you will attention color and also the exposure regarding genotype data into a keen Illumina 370, 660, 1M or Affymetrix Perlegen-5.0, otherwise six.0 platform. There had been seven,063 genotyped Dutch-ancestry members, clustered during the step 3,407 parents which have analysis into the eye colour, and 6,965 genotyped somebody got research towards each other locks and you may eyes colour. Towards hereditary association analysis off eye color (find Supplementary topic) the research was in fact assessed. Getting bivariate genetic analyses when you look at the GCTA, the unrelated citizens were chose, according to a hereditary relatedness matrix (GRM) cut-off of 0.025 (Yang mais aussi al., Site Yang, Lee, Goddard and Visscher 2011). That it remaining step three,619 people to your bivariate analyses, that have a genetic relatedness comparable to below 3rd otherwise 4th cousin.
, Site Willemsen, Vink, Abdellaoui, den https://datingranking.net/de/heterosexuelles-dating/ Braber, van Beek and you will Draisma 2013). Adult professionals stated their natural tresses colour in one from five possibilities: ‘fair/blond’, ‘hazel’, ‘red/auburn’, ‘black brown’, and you will ‘black’ and you will eye colour that have certainly about three solutions: ‘blue/gray’, ‘green/hazel’ and you will ‘brown’. An equivalent issues to the eye color and tresses colour were replied by the adolescent (14- to help you 18-year-old) twins once they finished this new Dutch Health and Choices Survey when you look at the 2005 otherwise 2006 (van Beijsterveldt et al., Reference van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and you can Lamb 2013). Into mathematical analyses, we joint new black, white brownish, and you can dark brown locks colors so you can ‘dark’, due to the fact just few somebody reported a black hair colour (Lin ainsi que al., Source Lin, Mbarek, Willemsen, Dolan, Fedko and you will Abdellaoui 2015). Created informed consent is actually obtained from most of the participants.
Decades, sex, sheer hair, and you will eye color have been obtained from Adult NTR survey 7, that was collected inside the 2004 (Willemsen et 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.
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