Members about Netherlands Dual Check in (van Beijsterveldt mais aussi al

Note: a this particular variable incontri omone ner casuali are Blond hair + blue-eyes throughout the 1908 analysis and you can Blond tresses + blue/grey eyes throughout the 2004 research.

Steps

, Site van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and you may Lamb 2013; Willemsen ainsi que al., Source Willemsen, Vink, Abdellaoui, den Braber, van Beek and Draisma 2013) was indeed included in this research in accordance with the presence off worry about-claimed research on sheer hair and you can eye colour in addition to visibility of genotype data towards an Illumina 370, 660, 1M otherwise Affymetrix Perlegen-5.0, otherwise six.0 system. There were seven,063 genotyped Dutch-origins players, clustered within the step three,407 family members having research on the eye colour, and you will 6,965 genotyped somebody got research to the each other locks and vision color. On hereditary organization analysis out of attention colour (see Supplementary thing) all the investigation have been analyzed. To have bivariate hereditary analyses inside GCTA, the unrelated people were chose, based on a hereditary relatedness matrix (GRM) cut-away from 0.025 (Yang et al., Site Yang, Lee, Goddard and you may Visscher 2011). So it remaining 3,619 anyone on bivariate analyses, with a genetic relatedness comparable to lower than third otherwise 4th cousin.

, Source Willemsen, Vink, Abdellaoui, den Braber, van Beek and Draisma 2013). Adult members said their absolute tresses color from one off five alternatives: ‘fair/blond‘, ‘hazel‘, ‘red/auburn‘, ‘dark brown‘, and you can ‘black‘ and eye color which have certainly one of around three solutions: ‘blue/gray‘, ‘green/hazel‘ and ‘brown‘. A comparable inquiries on the vision colour and you can tresses colour have been replied of the adolescent (14- so you can 18-year-old) twins after they complete the latest Dutch Health and Behavior Survey in 2005 or 2006 (van Beijsterveldt et al., Resource van Beijsterveldt, Groen-Blokhuis, Hottenga, Franic, Hudziak and you will Lamb 2013). To the statistical analyses, i joint the fresh new black colored, light brownish, and dark brown tresses color to ‘dark‘, because simply very few some body claimed a black locks colour (Lin et al., Site Lin, Mbarek, Willemsen, Dolan, Fedko and you can Abdellaoui 2015). Written told consent are extracted from the people.

Age, intercourse, absolute hair, and you can vision color had been taken from Mature NTR survey seven, that was collected inside 2004 (Willemsen ainsi que 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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