Mismatches between self-reported sex of each individual, and sex inferred from the relative intensity of markers on the Y and X chromosomes16, can be used as a way to detect possible sample mishandling or other types of clerical error. In a dataset of this size, some such mismatches would be expected due to transgender or intersex individuals, or instances of rare genetic variation, such as sex-chromosome aneuploidies17. Using information in the measured intensities of chromosomes X and Y (see Methods), we identified a set of 652 (0.134%) individuals with sex chromosome karyotypes that were putatively different from XY or XX (Fig. 2d, Supplementary Table 2).
