Detection of somatic genomic loss in BM failure syndromes using SNP-A analysis. (A) At the top, a whole-genome view is shown for patient 57. Individual dots represent the raw signal intensity of a specific SNP, which indicates the copy number at that locus. In general, the copy number is around 2N. Each chromosome is represented by a different color, from chromosome 1 on the left to the X chromosome on the right. Loss of chromosome 7, as well as the “physiologic” loss of the X chromosome in this male patient can be seen. At a higher level of resolution, the total and allele-specific copy numbers can be investigated for individual chromosomes. In the middle, Affymetrix 250K array karyograms for chromosomes 7 and X are displayed. The blue line represents smoothed total copy number, while the green ticks below the ideogram represent heterozygous calls. Although both chromosomes 7 and X show a reduced copy number, indicating loss of the entire chromosome, the presence of a large number of heterozygous calls along the length of chromosome 7 is consistent with the clonal nature of this lesion, compared with the X chromosome which has almost no heterozygous calls. Those that remain most likely reflect technical artifacts. At the bottom, karyograms from Affymetrix 6.0 array analysis of the same patient are shown. Raw and smoothed copy number tracks, as well as allele calls (blue dots), are shown. A reduction in the total copy number, as well as loss of heterozygous calls, are seen for both chromosomes, indicative of deletion. (B) Large clonal lesions were detectable in patients with AA by SNP-A. The results are shown for an exemplary patient (no. 96). On the short arm of chromosome 6, loss of heterozygous calls (heterozygous SNP call and allele-specific copy number tracks) with a normal diploid copy number marked a region of copy-neutral loss of heterozygosity in the somatic (BM) but not germline (CD3⁺) configuration. Similarly, clonal monosomy 7 was identified in this patient.