Colorectal Adenocarcinoma (Genentech, Nature 2012)
Overview
74 primary colon tumour-normal pairs collected from commercial sources (fresh-frozen) and characterised by multi-platform genomic profiling at Genentech. Published in Nature 2012. The cohort identified recurrent RSPO2/RSPO3 gene fusions as an alternative mechanism of Wnt pathway activation in colorectal cancer. PMID:22895193
Composition
- 74 tumour-normal pairs total: 72 by exome sequencing, 68 by RNA-seq, 74 by Illumina 2.5M SNP arrays, 2 by whole-genome sequencing.
- 15 MSI samples (mean 47 mutations/Mb; 764–3,113 coding mutations per sample); 57 MSS samples (mean 2.8 mutations/Mb; 31–149 coding mutations per sample).
- Cancer types: COAD / COADREAD.
- Mean exome coverage: 179x (SeqCap EZ v2.0/NimbleGen capture; HiSeq 2000 sequencing). PMID:22895193
Assays / panels (linked)
- whole-exome-seq — 72 tumour-normal pairs
- rna-seq — 68 tumour-normal pairs
- whole-genome-seq — 2 tumour-normal pairs
- Illumina 2.5M SNP arrays — 74 pairs (copy number)
Papers using this cohort
- PMID:22895193 — primary characterisation study (Seshagiri et al., Nature 2012)
Notable findings derived from this cohort
- RSPO2 fusions (EIF3E-RSPO2) in 3% (2/68) of tumours and RSPO3 fusions (PTPRK-RSPO3) in 8% (5/68), combined ~10%; mutually exclusive with APC mutations (P = 0.038, Fisher’s exact test). PMID:22895193
- 23 significantly mutated genes in MSS samples (FDR ≤ 5%) including KRAS, APC, TP53, SMAD4, FBXW7, PIK3CA, and ATM. PMID:22895193
- IGF2 focal amplification and upregulation in 12% (8/68) of samples. PMID:22895193
- MYC amplification (8q) in 23% and KRAS amplification in 13%. PMID:22895193
- ERBB3 mutated in 8% with multiple oncogenic hotspot mutations; novel recurrent mutations in TCF7L2, TET2, and TET3. PMID:22895193
Sources
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