Computational protocol: Breastfeeding moderates FTO related adiposity: a birth cohort study with 30 years of follow-up

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Protocol publication

[…] Information on breastfeeding duration was collected in the 1984 and 1986 visit and the earliest information on the age at which breastfeeding stopped completely was used. Data on the age of introduction of complementary foods was also collected in childhood, and duration of predominant breastfeeding assessed the age at which foods other than breast milk, teas or water were introduced.In 2004–05, we tried to follow the whole cohort, and participants were interviewed and donated a blood sample. DNA was extracted and genotyped using the Illumina HumanOmni2.5-8v1 array. Individual samples were excluded on the basis of sex mismatches (only for non-pseudoautosomal X-chromosome SNPs; heterozygosity threshold: 0.02), minimal or excessive heterozygosis (outside the range of median ±1.5*IQR of heterozygosity rate), disproportionate levels of individual missingness (>3%) and cryptic relatedness (>0.1 kinship). The FTO SNP rs9939609 was imputed (INFO metric of imputation quality >0.99) as A-allele dosages (with T being the non-effect allele). Imputation was performed by pre-phasing using SHAPEIT and the actual imputation using IMPUTE2,. Hardy-Weinberg equilibrium was assessed using X2 test. […]

Pipeline specifications

Software tools SHAPEIT, IMPUTE
Application GWAS