Table 3 Identification of mislabelled samples. Mislabelled samples NA11839 and NA11840 (father and mother of NA10854, respectively) were first identified visually via SNPscan based on anomalous X chromosome profiles (Fig. 9). Subsequent analysis of genotype calls and copy number values suggested that the NA11839 Hind and NA11840 Hind labels (as shown in the table) were reversed; upon switching labels (not shown here; see Fig. 9, bottom two tracks), male case NA11839 has zero AB calls on the X chromosome and an X chromosome copy number of 1.22 as expected for a male. After correcting the labels, female case NA11840 has 621 AB calls on the X chromosome, and an X chromosome copy number of 2.09 as expected for a female.

From: Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan