Note: a that this variable was Blond hair + blue-eyes on the 1908 studies and Blond tresses + blue/grey eyes throughout the 2004 analysis.
Procedures
, Site van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and you will Lamb 2013; Willemsen ainsi que al., Site Willemsen, Vink, Abdellaoui, den Braber, van Beek and you can Draisma 2013) were among them research in line with the visibility of mind-reported research towards natural tresses and you may vision colour and presence regarding genotype analysis on a keen Illumina 370, 660, 1M otherwise Affymetrix Perlegen-5.0, otherwise six.0 system. There had been eight,063 genotyped Dutch-ancestry members, clustered inside the step three,407 family having data on vision colour, and you may six,965 genotyped people got data to the one another tresses and you will eye colour. Towards the genetic relationship analysis out of eyes colour (discover Second situation) most of the study was basically assessed. For bivariate hereditary analyses when you look at the GCTA, the unrelated individuals were chose, predicated on an inherited relatedness matrix (GRM) cut-from 0.025 (Yang et al., Resource Yang, Lee, Goddard and you can Visscher 2011). It kept step 3,619 individuals with the bivariate analyses, with a hereditary relatedness equivalent to less than 3rd otherwise fourth relative.
, Source Willemsen, Vink, Abdellaoui, den Braber, van Beek and you may Draisma 2013). Adult participants reported their particular sheer tresses color from one of five choices: ‘fair/blond’, ‘hazel’, ‘red/auburn’, ‘dark brown’, and you can ‘black’ and you can eyes colour which have certainly three selection: ‘blue/gray’, ‘green/hazel’ and you will ‘brown’. The same inquiries for the vision color and you may locks color had been replied by the teenage (14- so you can 18-year-old) twins when they complete new Dutch Health insurance and Choices Questionnaire for the 2005 otherwise 2006 (van Beijsterveldt mais aussi al. migliori siti incontri elite, Reference van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and you will Lamb 2013). Into statistical analyses, we joint the fresh new black, white brownish, and you will brownish tresses tone to help you ‘dark’, while the merely very few anybody stated a black hair color (Lin et al., Resource Lin, Mbarek, Willemsen, Dolan, Fedko and Abdellaoui 2015). Created informed consent are obtained from all users.
Decades, intercourse, natural tresses, and you will vision colour was basically taken from Mature NTR survey eight, that was accumulated when you look at 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.
