Article ; Online: A calibrated cell-based functional assay to aid classification of MLH1 DNA mismatch repair gene variants.
2022 Volume 43, Issue 12, Page(s) 2295–2307
Abstract: Functional assays provide important evidence for classifying the disease significance of germline variants in DNA mismatch repair genes. Numerous laboratories, including our own, have developed functional assays to study mismatch repair gene variants. ... ...
| Abstract | Functional assays provide important evidence for classifying the disease significance of germline variants in DNA mismatch repair genes. Numerous laboratories, including our own, have developed functional assays to study mismatch repair gene variants. However, previous assays are limited due to the model system employed, the manner of gene expression, or the environment in which function is assessed. Here, we developed a human cell-based approach for testing the function of variants of uncertain significance (VUS) in the MLH1 gene. Using clustered regularly interspaced short palindromic repeats gene editing, we knocked in MLH1 VUS into the endogenous MLH1 loci in human embryonic stem cells. We examined their impact on RNA and protein, including their ability to prevent microsatellite instability and instigate a DNA damage response. A statistical clustering analysis determined the range of functions associated with known pathogenic or benign variants, and linear regression was performed using existing odds in favor of pathogenicity scores for these control variants to calibrate our functional assay results. By converting the functional outputs into a single odds in favor of pathogenicity score, variant classification expert panels can use these results to readily reassess these VUS. Ultimately, this information will guide proper diagnosis and disease management for suspected Lynch syndrome patients. |
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| MeSH term(s) | Humans ; DNA Mismatch Repair/genetics ; MutL Protein Homolog 1/genetics ; Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; Colorectal Neoplasms, Hereditary Nonpolyposis/pathology ; Microsatellite Instability ; Germ-Line Mutation/genetics ; Mismatch Repair Endonuclease PMS2/genetics | |||||
| Chemical Substances | MutL Protein Homolog 1 (EC 3.6.1.3) ; Mismatch Repair Endonuclease PMS2 (EC 3.6.1.3) ; MLH1 protein, human | |||||
| Language | English | |||||
| Publishing date | 2022-09-12 | |||||
| Publishing country | United States | |||||
| Document type | Journal Article ; Research Support, N.I.H., Extramural | |||||
| ZDB-ID | 1126646-6 | |||||
| ISSN | 1098-1004 ; 1059-7794 | |||||
| ISSN (online) | 1098-1004 | |||||
| ISSN | 1059-7794 | |||||
| DOI | 10.1002/humu.24462 | |||||
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| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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