Small Intestine Neuroendocrine Tumors (Carcinoid Tumors)

The diagnosed incidence of small bowel neuroendocrine tumors (NETs) is increasing. While patients with localized disease can be treated surgically, those with metastatic disease currently have few treatment options. The success of biologically targeted therapies in other malignancies has led to interest in the molecular alterations underlying the pathogenesis of these NETs. To identify genetic aberrations in small intestine NETs, we generated copy number profiles from 31 primary and metastatic tumors and performed whole-exome sequencing on a subset of 29 primary small intestine NETs and 24 metastatic NETs in parallel with normal blood DNA. Whole-genome sequencing data was generated on 15 tumor/normal pairs and 5 primary/metastasis/normal trios. The global genetic landscape of small bowel NETs is relatively quiet. Consistent with previous studies, the overwhelming majority of tumors were characterized by loss of chromosome 18 and, to a lesser extent, other chromosome arm gains and losses. In stark contrast to arm-level alterations, recurrent high-level focal amplifications and deletions were much less prevalent in these tumors. High-throughput mutation screening and exome sequencing revealed similarly low rates of somatic mutation in NETs (median of 0.77 non-silent mutations per megabase (Mb) of coding DNA) compared to other recent cancer exome sequencing efforts. Our analysis of this cohort identified only a single, statistically significant recurrent somatic mutation targeting the cyclin-dependent kinase inhibitor gene, CDKN1B, encoding p27. ]]>
This dataset includes whole-exome sequencing data from 29 primary small intestine neuroendocrine tumors and 24 metastatic neuroendocrine tumors and matching normal blood DNA on Illumina HiSeq 2000. Whole-genome sequencing was performed on15 primary tumor/normal pairs, 5 metastatic tumor/normal pairs and 2 primary/metastatic/normal trios on Illumina HiSeq 2000. All samples with a pathological assessment of well-differentiated neuroendocrine tumors of the small intestine or metastasis of the small intestine and a signed informed consent were included as part of the study. Those samples with sufficient native genomic DNA were used for SNP arrays, whole-exome or whole-genome sequencing. Samples were removed from analysis when there was a poor concordance between tumor and normal SNPs. Samples that did not meet whole-exome capture and/or sequencing requirements were also removed from the analysis. ]]>