Department of Pediatrics, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA.
Pediatr Blood Cancer. 2013 Apr;60(4):570-4. doi: 10.1002/pbc.24316. Epub 2012 Sep 26.
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.
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.
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.
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.
胃腺癌在儿童中是一种罕见的诊断。一名 14 岁男性患者患有转移性胃腺癌，且有强烈的结肠癌家族史。CDH1 和 APC 的临床测序均为阴性。因此，应用外显子组测序来捕获患者种系和原发性肿瘤中大多数编码蛋白的区域，以鉴定单核苷酸变异、小插入/缺失和拷贝数异常。
从患者的血液、原发性肿瘤和未受影响的母亲的血液中提取 DNA。构建 DNA 文库并在 Illumina HiSeq2000 上进行测序。使用 Picard 和 Samtools 对数据进行后处理，然后使用基因组分析工具包进行分析。使用基于 Ensembl 的内部程序对变体进行注释。使用 ExomeCNV 评估拷贝数。
每个样本的测序深度平均超过 120×。在种系中发现了 TP53 中罕见的非同义编码单核苷酸变异（SNV）。有 10 个体细胞癌症蛋白损伤变异在未受影响的母亲基因组中未观察到。与肿瘤相比，外显子组 CNV 比较患者的种系，鉴定出异常的拷贝数，跨越 6946 个基因。
我们提出了一个通过全外显子组测序检测到的不寻常的 Li-Fraumeni 病例。胃腺癌中也可能存在驱动性体细胞突变。这些结果强调需要更全面和广泛的种系和癌症分析，以准确告知患者癌症的遗传风险，并识别体细胞突变。
