Affymetrix SNP 6.0 array data for ACRG Gastric Cancer Study

Gastric cancer, a leading cause of cancer related deaths, is a heterogeneous disease, with little consensus on molecular subclasses and their clinical relevance. We describe four molecular subtypes linked with distinct patterns of molecular alterations, disease progression and prognosis via: a) Microsatellite Instable: hypermutated intestinal subtype tumors occurring in antrum, best overall prognosis, lower frequency of recurrence (22%), with liver metastasis in 23% of recurred cases; b) Mesenchymal-like: diffuse tumors with worst prognosis, a tendency to occur at an earlier age and highest recurrence (63%) with peritoneal seeding in 64% of recurred cases, low frequency of molecular alterations; c) TP53-inactive with TP53 loss, presence of focal amplifications and chromosomal instability; d) TP53-active marked by EBV infection and PIK3CA mutations. The key molecular mechanisms and associated survival patterns are validated in multiple independent cohorts, to provide a consistent and unified framework for further preclinical and clinical research. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 277 stomach cancer samples and 14 matching adjacent stomach normal tissue sample. PICNIC (Predicting Integer Copy Number In Cancer) analysis was performed on all 291 samples. One normal and six tumor samples failed in PICNIC. Copy number segments were generated for 284 smaples. To access tumor's purity and ploidy, ASCAT (Allele-Specific Copy number Analysis of Tumors) analysis were performa on 277 tumors, with the matching 14 normals. ASCAT analysis successfully completed cauculated tumor's ploidy and purity for 190 tumor samples.