In total, 9912 participants were genotyped using the Illumina HumanHap550 quad genome-wide SNP genotyping platform by 23andMe subcontracting the Wellcome Trust Sanger Institute, Cambridge, UK, and the Laboratory Corporation of America, Burlington, NC, USA. Individuals were excluded from analyses on the basis of excessive or minimal heterozygosity, gender mismatch, individual missingness (>3%), cryptic relatedness as measured by identity by descent (genome-wide IBD >10%) and sample duplication. Individuals were assessed for population stratification using multi-dimensional scaling modelling seeded with HapMap Phase II release 22 reference populations. Individuals of non-European ancestry were removed from further analysis. SNPs with a final call rate of <95%, minor allele frequency (MAF) <1% and evidence of departure from Hardy–Weinberg equilibrium (HWE) (P < 5 × 10−7) were also excluded from analyses. After data cleaning, 5998 and 6609 individuals had complete phenotype and genotype data for the analysis of ‘age at first tooth’ and ‘number of teeth’, respectively. Individuals were imputed to HapMap Phase II (Build 36, release 22) using the Markov Chain Haplotyping software (MACH v.1.0.16) (32). X chromosome imputation was carried out on the non-pseudo
