in females. Sex obtained from genotyping was compared to the sex recorded in the Danish Civil Registration System and mismatches were excluded. It is extremely unlikely to observe errors in recorded sex in the Danish Civil Registration System.26 About 0.25% (N=224) of the sample did not match the expected sex. Half of the failures (N=119) were due to abnormal structural variation on chromosome X (aneuploidy and loss of heterozygosity). The other half were due to sample mix-ups (N=103). In this study we describe the sample QC only and not the subsequent single-nucleotide polymorphism QC, which vary between studies.
