ArticleBMC genomics2017
Interpreting whole genome and exome sequencing data of individual gastric cancer samples.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- GNAS drives gastric cancer progression via pyrimidine metabolic reprogramming and immune-microenvironment remodeling.Apoptosis : an international journal on programmed cell death · 2026Article
- The molecular profile of gastric intraepithelial foveolar type neoplasia based on somatic copy number alterations and multiple mutation analysis.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2024Article
- Sequence variants contributing to dysregulated inflammatory responses across keratoconic cone surface in adolescent patients with keratoconus.Frontiers in immunology · 2023Article
- Clinicopathological characteristics, survival outcomes, and genetic alterations of younger patients with gastric cancer: Results from the China National Cancer Center and cBioPortal datasets.Cancer medicine · 2022Article
- Analysis on the desert adaptability of indigenous sheep in the southern edge of Taklimakan Desert.Scientific reports · 2022Article
- Identification of key miRNA-gene pairs in gastric cancer through integrated analysis of mRNA and miRNA microarray.American journal of translational research · 2021Article
- An LCM-based genomic analysis of SPEM, Gastric Cancer and Pyloric Gland Adenoma in an Asian cohort.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2020Article
- A novel knowledge-derived data potentizing method revealed unique liver cancer-associated genetic variants.Human genomics · 2019Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGastric cancer is the fourth most common cancer and the second leading cause of cancer death worldwide. In order to understand the genetic background, we sequenced the whole exome and the whole genome of one microsatellite stable as well as one microsatellite unstable tumor and the matched healthy tissue on two different NGS platforms. We here aimed to provide a comparative approach for individual clinical tumor sequencing and annotation using different sequencing technologies and mutation calling algorithms.
resultsWe applied a population-based whole genome resource as a novel pathway-based filter for interpretation of genomic alterations from single nucleotide variations (SNV), indels, and large structural variations. In addition to a comparison with tumor genome database resources and a filtering approach using data from the 1000 Genomes Project, we performed pyrosequencing analysis and immunohistochemistry in a large cohort of 428 independent gastric cancer cases.
conclusionWe here provide an example comparing the usefulness and potential pitfalls of different technologies for a clinical interpretation of genomic sequence data of individual gastric cancer samples. Using different filtering approaches, we identified a multitude of novel potentially damaging mutations and could show a validated association between a mutation in GNAS and gastric cancer.
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