Whole Exome Sequencing of Pediatric Gastric Adenocarcinoma: A Germline and Somatic Mutation Analysis
- Author(s): Chang, Vivian Y.
- Advisor(s): Nelson, Stanley F
- et al.
Gastric adenocarcinoma is a rare diagnosis in childhood. A 14-year old male patient presented with metastatic gastric adenocarcinoma, and a strong family history of colon cancer. Clinical sequencing of FAP and APC1 were negative. Whole exome sequencing was used to capture the majority of protein-coding regions for the identification of single-nucleotide variants, small insertion/deletions, and copy number abnormalities in the patient's germline as well as primary tumor.
Materials and Methods
DNA was extracted from the patient's blood, primary tumor, and the unaffected mother's blood. DNA libraries were constructed and sequenced on Illumina HiSeq2000. Data were analyzed with the Genome Analysis Toolkit. Variants were annotated using an in-house Ensembl-based program. Copy number was assessed using ExomeCNV.
Each sample was sequenced to a mean depth of coverage of greater than 120x. A rare non-synonymous coding SNV in TP53 was identified in the germline. There were 10 somatic cancer protein-damaging variants. ExomeCNV comparing tumor to the patient's germline, identified abnormal copy number, spanning 6,946 genes.
We present an unusual case of Li-Fraumeni detected by whole exome sequencing. There were also likely driver somatic mutations in the gastric adenocarcinoma. These results highlight the need for more thorough and broad scale germline and cancer analyses to accurately inform
patients of inherited risk to cancer and to identify somatic mutations.