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.
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.
Authors: P Therasse; S G Arbuck; E A Eisenhauer; J Wanders; R S Kaplan; L Rubinstein; J Verweij; M Van Glabbeke; A T van Oosterom; M C Christian; S G Gwyther Journal: J Natl Cancer Inst Date: 2000-02-02 Impact factor: 13.506
Authors: J P Borg; S Marchetto; A Le Bivic; V Ollendorff; F Jaulin-Bastard; H Saito; E Fournier; J Adélaïde; B Margolis; D Birnbaum Journal: Nat Cell Biol Date: 2000-07 Impact factor: 28.824
Authors: J M Birch; A L Hartley; K J Tricker; J Prosser; A Condie; A M Kelsey; M Harris; P H Jones; A Binchy; D Crowther Journal: Cancer Res Date: 1994-03-01 Impact factor: 12.701
Authors: S Bamford; E Dawson; S Forbes; J Clements; R Pettett; A Dogan; A Flanagan; J Teague; P A Futreal; M R Stratton; R Wooster Journal: Br J Cancer Date: 2004-07-19 Impact factor: 7.640
Authors: Abdulkadir Abakir; Tom C Giles; Agnese Cristini; Jeremy M Foster; Nan Dai; Marta Starczak; Alejandro Rubio-Roldan; Miaomiao Li; Maria Eleftheriou; James Crutchley; Luke Flatt; Lorraine Young; Daniel J Gaffney; Chris Denning; Bjørn Dalhus; Richard D Emes; Daniel Gackowski; Ivan R Corrêa; Jose L Garcia-Perez; Arne Klungland; Natalia Gromak; Alexey Ruzov Journal: Nat Genet Date: 2019-12-16 Impact factor: 38.330