The Illumina HumanCNV370-Duo DNA Analysis BeadChip was used for genotyping NFBC1966. SNPs were excluded from the analysis if the call rate in the final sample was <95%, if there was a lack of HWE (P < 5 × 10−4) or if the MAF was <1%; more details of genotyping and quality control procedures can be found in Sabatti et al. (53). After quality control, 328 077 SNPs were available for imputation. Imputation was carried out using IMPUTEv1 with CEU haplotypes from HapMap Phase II (release 21) as the reference panel. X chromosome imputation was carried out in the non-pseudo-autosomal region of the X chromosome (54). Only SNPs exceeding an ‘info’ metric of 0.3 and an MAF of >1% were included in subsequent analyses. After data cleaning, 5120 and 4904 individuals had complete phenotype and genotype data for the analysis of ‘age at first tooth’ and ‘number of teeth’, respectively.
