Extended Data Fig. 3: Copy-number alteration analysis of Patient 10 whole-exome sequencing data.

a, Genome plots show B (minor) allele frequencies (left) and read coverage (right) for single-nucleotide variants (SNVs) detected in the Patient 10 germline sample using whole-exome sequencing. Heterozygous SNVs (A/B) are indicated in red, homozygous SNVs (B/B) are indicated in green. The same SNVs are shown for bone marrow and skin tumour sample #1 and #2, indicating copy-number alterations specific to the skin tumours. A homozygous deletion of the CDKN2A gene locus is indicated by arrows. An additional focal loss on chr4q in skin tumour #2 is also indicated. b, Genome plots show SNVs detected in the relapse skin tumour and bone marrow samples of Patient 10 collected after receiving an allogeneic stem cell transplant. SNVs homozygous in the host germline sample are indicated in blue (A/A) and green (B/B). Heterozygous SNVs are indicated in red (A/B). A low level of donor DNA is detected in the relapse skin tumour sample (<5%). The estimated percentage of donor DNA is 60% in the relapse bone marrow sample. Copy-number alterations specific to the skin tumours (i.e. loss of chr9, chr3p, and copy-number neutral LOH of chr6p) are detected in both relapse samples. The only additional alteration is a focal loss on chr1q. Related to Fig. 1.