Quantitative evaluation of MSI testing using NGS detects the imperceptible microsatellite changed caused by MSH6 deficiency
| Autor: | Akemi Takahashi, Tetsuhiko Tachikawa, Shigeki Yamaguchi, Miho Kakuta, Kiwamu Akagi, Gou Yamamoto, Yukiko Osanai, Takanori Washio, Masato Kamiyama, Michio Shiibashi, Takashi Takenoya |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Genetic Markers Cancer Research Computational biology 030105 genetics & heredity Biology DNA Mismatch Repair Sensitivity and Specificity 03 medical and health sciences 0302 clinical medicine Multiplex polymerase chain reaction Genetics medicine Humans Genetic Testing neoplasms Genetics (clinical) Genetic testing medicine.diagnostic_test Microsatellite instability High-Throughput Nucleotide Sequencing medicine.disease Colorectal Neoplasms Hereditary Nonpolyposis digestive system diseases Lynch syndrome MSH6 DNA-Binding Proteins Oncology 030220 oncology & carcinogenesis Microsatellite DNA mismatch repair Microsatellite Instability Colorectal Neoplasms Reference genome |
| Zdroj: | Familial cancer. 20(2) |
| ISSN: | 1573-7292 |
| Popis: | Microsatellite instability (MSI) is an effective biomarker for diagnosing Lynch syndrome (LS) and predicting the responsiveness of cancer therapy. MSI testing is conventionally performed by capillary electrophoresis, and MSI status is judged by visual assessment of allele size change. Here, we attempted to develop a quantitative evaluation model of MSI using next-generation sequencing (NGS). Microsatellite markers were analyzed in tumor and non-tumor tissues of colorectal cancer patients by NGS after a single multiplex polymerase chain reaction amplification. The read counts corresponding to microsatellite loci lengths were calculated independently of mapping against a reference genome, and their distribution was digitized by weighted mean. Weighted mean differences between tumor and non-tumor samples with different MSI status were assessed, and cut-off values for each marker in the discovery cohort were determined. Each microsatellite maker was defined as unstable if the weighted mean difference was greater than the cut-off value. In the discovery cohort, the evaluation model demonstrated sensitivity and specificity of 100% for all markers. In the validation cohort, MSI status determined by the new model was consistent with the outcome of the conventional method in 29/30 cases (97%). The single inconsistent case was classified as low-frequency MSI by the conventional method but considered MSI-high by NGS. Genetic testing for mismatch repair genes revealed a pathogenic variant in MSH6 in the discordant case. We successfully developed a quantitative evaluation method for determining MSI status using NGS. This is a robust and sensitive method and could improve LS diagnosis. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full text from SpringerLink