A combination of multiple test platforms was used to determine the MSI or MMR status of the profiled samples, including fragment analysis (FA, Promega, Madison, WI), IHC (MLH1, M1 antibody; MSH2, G2191129 antibody; MSH6, 44 antibodies; and PMS2, EPR3947 antibody (Ventana Medical Systems, Inc., Tucson, AZ) and NGS (7000 target microsatellite loci were examined and compared to the reference genome hg19 from the University of California). The three platforms generated highly concordant results as previously reported41 (link) and in the rare cases of discordant results, the MSI or MMR status of the tumor was determined in the order of IHC, FA, and NGS.
Zimmer K., Kocher F., Untergasser G., Kircher B., Amann A., Baca Y., Xiu J., Korn W.M., Berger M.D., Lenz H.J., Puccini A., Fontana E., Shields A.F., Marshall J.L., Hall M., El-Deiry W.S., Hsiehchen D., Macarulla T., Tabernero J., Pichler R., Khushman M., Manne U., Lou E., Wolf D., Sokolova V., Schnaiter S., Zeimet A.G., Gulhati P., Widmann G, & Seeber A. (2023). PBRM1 mutations might render a subtype of biliary tract cancers sensitive to drugs targeting the DNA damage repair system. NPJ Precision Oncology, 7, 64.
Other organizations :
University Hospital of Bern, University of Bern, University of Southern California, Ospedale Policlinico San Martino, Sarah Cannon Research Institute, The Barbara Ann Karmanos Cancer Institute, Wayne State University, Georgetown University, Georgetown University Medical Center, Temple University Health System, Fox Chase Cancer Center, Brown University, The University of Texas Southwestern Medical Center, Vall d'Hebron Hospital Universitari, Innsbruck Medical University, Universität Innsbruck, University of Alabama at Birmingham, University of Minnesota Medical Center, Ospedale di Bolzano, Rutgers, The State University of New Jersey
IHC (MLH1, M1 antibody; MSH2, G2191129 antibody; MSH6, 44 antibodies; and PMS2, EPR3947 antibody (Ventana Medical Systems, Inc., Tucson, AZ))
NGS (7000 target microsatellite loci were examined and compared to the reference genome hg19 from the University of California)
dependent variables
MSI or MMR status of the profiled samples
control variables
The three platforms generated highly concordant results as previously reported
In the rare cases of discordant results, the MSI or MMR status of the tumor was determined in the order of IHC, FA, and NGS
Annotations
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