Whole genome sequencing of matched primary and metastatic acral melanomas

Abstract

Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here, we used whole genome sequencing to characterize somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis. Our data show that the somatic mutational rates in this acral melanoma sample pair were more comparable to the rates reported in cancer genomes not associated with mutagenic exposure than in the genome of a melanoma cell line or the transcriptome of melanoma short-term cultures. Despite the perception that acral skin is sun-protected, the dominant mutational signature in these samples is compatible with damage due to ultraviolet light exposure. A nonsense mutation in ERCC5 discovered in both the primary and metastatic tumors could also have contributed to the mutational signature through accumulation of unrepaired dipyrimidine lesions. However, evidence of transcription-coupled repair was suggested by the lower mutational rate in the transcribed regions and expressed genes. The primary and the metastasis are highly similar at the level of global gene copy number alterations, loss of heterozygosity and single nucleotide variation (SNV). Furthermore, the majority of the SNVs in the primary tumor were propagated in the metastasis and one nonsynonymous coding SNV and one splice site mutation appeared to arise de novo in the metastatic lesion.

Figure 1.

Summary of lesions found in acral melanoma. Shown are primary and metastasis Circos plots (Krzywinski et al. 2009) of somatic mutations in the primary (A) and metastatic (B) tumors. The outer circle contains whole genome high-confidence SNVs (black dots) and nonsynonymous SNVs (orange dots; annotated with HGNC/Ensembl gene symbols). Copy number alterations are shown in the inner two plots (green circle shows gains and blue shows losses). Validated structural variations are depicted as links in the interior of the plot.

Figure 2.

Somatic SNVs analysis in acral melanoma samples. (A) Somatic SNV mutation rates of all SNVs and C>T/G>A transitions for expressed genes in the primary (P-EXP) and metastatic tumors (M-EXP) and nonexpressed genes (P-NON and M-NON). (B) Proportion of somatic SNVs by class in the primary and metastatic tumors for the whole genome (WG) and coding regions (CDS). (C) Frequency of bases ±5 bp of whole genome C>T/G>A transitions in the primary tumors. (D) Frequency of bases ±5 bp of whole genome C>T/G>A transitions in the metastatic tumors.

Figure 3.

Copy number alterations in the primary tumor. SNP array plots showing somatic copy number alteration (CNA) in the primary tumor detected by genome-wide SNP arrays (left column) and whole-genome (WG) sequencing normalized read-depth per 10 kb (right column) for chromosomes 4, 11, and 17.

Figure 4.

Loss of heterozygosity in the primary tumor. SNP array plots showing loss of heterozygosity (LOH) in the primary tumor as detected by allele B frequency from SNP array (left column) and whole-genome sequencing LOH rate in 100-kb windows (right column) for chromosomes 4, 11, and 17.