ArticleBMC medical genomics2019
Next-generation sequencing with comprehensive bioinformatics analysis facilitates somatic mosaic APC gene mutation detection in patients with familial adenomatous polyposis.
Article in BMC medical genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 2 of them syntheses that pooled it.
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Who cites it
19 citing papers in PubMed, 2 syntheses or guidelines pooled it, 30 citations in OpenAlex.
- Japanese society for cancer of the colon and rectum (JSCCR) guidelines 2024 for the clinical practice of hereditary colorectal cancer.International journal of clinical oncology · 2026Guideline
- Genomic mosaicism in colorectal cancer and polyposis syndromes: a systematic review and meta-analysis.International journal of colorectal disease · 2024Pooled it
- Evaluation of ACMG/AMP guidelines for classifying APC variants in Korean patients with suspected familial adenomatous polyposis.Cancer cell international · 2026Article
- Mutational profile of a Saudi patient with Familial adenomatous polyposis that progressed to colon cancer: A case report.World journal of clinical oncology · 2025Article
- Hereditary Colorectal Cancer: Clinical Implications of Genomic Medicine and Precision Oncology.Journal of the anus, rectum and colon · 2025Review
- Screening and surveillance for hereditary colorectal cancer.Intestinal research · 2024Review
- Antitumor effect of neoantigen-reactive T cells combined with PD1 inhibitor therapy in mouse lung cancer.Journal of cancer research and clinical oncology · 2023Article
- Diffuse gastric polyposis in a young patient with a giant retroperitoneal mass: A case report.Experimental and therapeutic medicine · 2023Article
- Neoantigen-reactive T cells exhibit effective anti-tumor activity against colorectal cancer.Human vaccines & immunotherapeutics · 2022Article
- Article
- Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1.Oncotarget · 2022Article
- Use of sanger and next-generation sequencing to screen for mosaic and intronic APC variants in unexplained colorectal polyposis patients.Familial cancer · 2022Article
- Anti-tumour effect of neo-antigen-reactive T cells induced by RNA mutanome vaccine in mouse lung cancer.Journal of cancer research and clinical oncology · 2021Article
- APC germline variant analysis in the adenomatous polyposis phenotype in Japanese patients.International journal of clinical oncology · 2021Article
- Japanese Society for Cancer of the Colon and Rectum (JSCCR) guidelines 2020 for the Clinical Practice of Hereditary Colorectal Cancer.International journal of clinical oncology · 2021Article
- Article
- Two cases of somatic STK11 mosaicism in Danish patients with Peutz-Jeghers syndrome.Familial cancer · 2021Article
- Candidate Gene Discovery in Hereditary Colorectal Cancer and Polyposis Syndromes-Considerations for Future Studies.International journal of molecular sciences · 2020Review
- Association of Pathogenic Missense and Nonsense Mutations in Mitochondrial COII Gene with Familial Adenomatous Polyposis (FAP).International journal of molecular and cellular medicine · 2020Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFamilial adenomatous polyposis (FAP) is an autosomal dominant colorectal tumor characterized by numerous adenomatous colonic polyps that often lead to colon cancer. Although most patients with FAP harbored germline mutations in APC gene, it was recently recognized that patients with clinical FAP, but without detectable pathogenic mutations, could be associated with somatic mosaic APC mutation.
methodsWe reanalyzed the nest-generation sequencing (NGS) gene panel testing results of patients who were diagnosed with FAP, but did not have APC mutations, at Yonsei Cancer Prevention Center between July 2016 and March 2018. We tested several variant calling algorithms to identify low level mosaic variants. In one patient with a low frequency APC mutation, NGS analysis was performed together with endoscopic biopsy. Variant calling tools HaplotypeCaller, MuTect2, VarScan2, and Pindel were used. We also used 3'-Modified Oligonucleotides (MEMO)-PCR or conventional PCR for confirmation.
resultsAmong 28 patients with clinical suspicion of FAP but no detectable pathogenic variants of colonic polyposis associated genes, somatic mosaic pathogenic variants were identified in seven patients. The variant allele frequency ranged from 0.3 to 7.7%. These variants were mostly detected through variant caller MuTect2 and Pindel, and were further confirmed using mutant enrichment with MEMO-PCR.
conclusionsThe NGS with an adequate combination of bioinformatics tools is effective to detect low level somatic variants in a single assay. Because mosaic APC mutations are more frequent than previously thought, the presence of mosaic mutations must be considered when analyzing genetic tests of patients with FAP.
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