BACKGROUND: 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 CDH1 and APC were 
negative. Whole exome sequencing was therefore applied 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 post-processed using Picard and 
Samtools, then analyzed with the Genome Analysis Toolkit. Variants were 
annotated using an in-house Ensembl-based program. Copy number was assessed 
using ExomeCNV.
RESULTS: Each sample was sequenced to a mean depth of coverage of greater than 
120×. A rare non-synonymous coding single-nucleotide variant (SNV) in TP53 was 
identified in the germline. There were 10 somatic cancer protein-damaging 
variants that were not observed in the unaffected mother genome. ExomeCNV 
comparing tumor to the patient's germline, identified abnormal copy number, 
spanning 6,946 genes.
CONCLUSION: 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.