Whole-genome reconstruction and mutational signatures in gastric cancer

Abstract

Background: Gastric cancer is the second highest cause of global cancer mortality. To explore the complete repertoire of somatic alterations in gastric cancer, we combined massively parallel short read and DNA paired-end tag sequencing to present the first whole-genome analysis of two gastric adenocarcinomas, one with chromosomal instability and the other with microsatellite instability.

Results: Integrative analysis and de novo assemblies revealed the architecture of a wild-type KRAS amplification, a common driver event in gastric cancer. We discovered three distinct mutational signatures in gastric cancer--against a genome-wide backdrop of oxidative and microsatellite instability-related mutational signatures, we identified the first exome-specific mutational signature. Further characterization of the impact of these signatures by combining sequencing data from 40 complete gastric cancer exomes and targeted screening of an additional 94 independent gastric tumors uncovered ACVR2A, RPL22 and LMAN1 as recurrently mutated genes in microsatellite instability-positive gastric cancer and PAPPA as a recurrently mutated gene in TP53 wild-type gastric cancer.

Conclusions: These results highlight how whole-genome cancer sequencing can uncover information relevant to tissue-specific carcinogenesis that would otherwise be missed from exome-sequencing data.

Figure 1

Copy number of two gastric cancer genomes, mechanism of 12p amplification and creation of a fusion gene. (a) Somatic CNVs in the two gastric tumors (chromosomes are arranged on the x-axis, copy number is shown on the y-axis). (b) Copy number of chromosome 12 (top) and the amplicon on 12p (middle) are shown in orange (y-axis). Rearrangements identified by DNA-PET clusters with a size ≥ 45 are represented by arrows and connecting lines (bottom). Dark red and pink arrows represent 5' and 3' cluster regions, respectively, with the connection between the tip of the dark red and the blunt end of the pink arrows. Numbers represent cluster sizes. (c) Fusion between SOX5 and OVCH1 predicted by a rearrangement point with cluster size of 129 in (b).

Figure 2

Map of somatic alterations in two gastric cancer genomes. The Circos plots depict the following information in order from outer to inner rings: using WGS data (1) CNVs (gain in red capped at 10 copies and loss in gray), (2) indel density (indel frequency per 10 kbp in blue, capped at 5 indels/10 kbp), (3) SNV density (SNV frequency per 10 kbp in black, each ring is 5 SNVs/10 kbp, capped at 10), and using DNA-PET data, (4) deletions (in red), tandem duplications (green) and inversions (purple), (5) intra- and (6) inter-chromosomal, insertions (orange) and unpaired SVs (gray).

Figure 3

Genome-wide and exome-wide mutational fingerprint. (a) Frequency of various classes of somatic SNVs genome-wide. (b) Frequency of somatic SNVs exome-wide. (c) Mutational bias as a function of infection status using data from 34 exomes (bias for SNV class i was computed as (s_i - g_i)/g_i, where s_i and g_i are the somatic and germline SNV frequencies). Note that nearly identical results were obtained when MSI tumors were excluded from the analysis (*P-value < 0.1; **P-values < 0.01, respectively). (d) Size-distribution of germline and somatic indels genome-wide.