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Detection of Mismatch Repair Deficiency in Endometrial Cancer: Assessment of IHC, Fragment Length Analysis, and Amplicon Sequencing Based MSI Testing.
Cancers (Basel)
November 2024
Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
Mismatch repair (MMR) deficiency can be indicative of Lynch syndrome (LS) and guide treatment with immune checkpoint inhibitors. Colorectal cancers (CRCs) and endometrial cancers (ECs) are routinely screened to identify LS, primarily using immunohistochemistry (IHC) or microsatellite instability (MSI) testing, but concordance between these methods is variable in ECs. Here, we investigate this variability in 361 ECs from the Ohio OCCPI/OPTEC ( = 196) and Manchester PETALS ( = 165) trials, where concordance between assays differed significantly.
View Article and Find Full Text PDFMismatch Repair Proficient Colorectal Adenocarcinoma in Two Patients With Lynch Syndrome.
Clin Genet
December 2024
Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA.
Screening for Lynch syndrome (LS) is essential in colorectal carcinoma (CRC) diagnosis. The hallmark of CRC in LS is mismatch repair (MMR) deficiency, a vital biomarkers assessed by microsatellite instability (MSI) analysis and/or immunohistochemistry (IHC) staining of the MMR proteins in the tumor, that also predict response to immune checkpoint inhibitors. We report two LS patients who developed MMR proficient CRCs.
View Article and Find Full Text PDFStableLift: Optimized Germline and Somatic Variant Detection Across Genome Builds.
bioRxiv
November 2024
Department of Human Genetics, University of California, Los Angeles.
Reference genomes are foundational to modern genomics. Our growing understanding of genome structure leads to continual improvements in reference genomes and new genome "builds" with incompatible coordinate systems. We quantified the impact of genome build on germline and somatic variant calling by analyzing tumour-normal whole-genome pairs against the two most widely used human genome builds.
View Article and Find Full Text PDFAssessing pathogenicity of mismatch repair variants of uncertain significance by molecular tumor analysis.
Exp Mol Pathol
December 2024
Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands. Electronic address:
Functional analyses are the main method to classify mismatch repair (MMR) gene variants of uncertain significance (VUSs). However, the pathogenicity remains unclear for many variants because of conflicting results between clinical, molecular, and functional data. In this study, we evaluated whether whole exome sequencing (WES) could add another layer of evidence to elucidate the pathogenicity of MMR variants with conflicting interpretations.
View Article and Find Full Text PDFEvaluation of Bayesian point-based system on the variant classification of hereditary cancer predisposition genes.
Genet Med
December 2024
Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN.
Purpose: To assess the differences in variant classifications using the American College of Medical Genetics and Genomics and the Association for Molecular Pathology 2015 guidelines and the Bayesian point-based classification system (here referred to as the point system) in 115 hereditary cancer predisposition genes and explore variant sub-tiering by the point system.
Methods: Germline variant classifications for 721 pediatric patients from an in-house panel were retrospectively evaluated using the 2 scoring systems.
Results: A total of 2376 unique variants were identified, with ∼23.
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