Targeted Cancer Next-Generation Sequencing as a Primary Screening Tool for Microsatellite Instability and Lynch Syndrome in Upper Gastrointestinal Tract Cancers

PURPOSE Mutations in DNA mismatch repair genes and PTEN, diagnostic of Lynch and Cowden syndromes, respectively, represent the only established inherited predisposition genes in endometrial cancer to date. The prevalence of other cancer predisposition genes remains unclear. We determined the prevalence of pathogenic germline variants in unselected patients with endometrial cancer scheduled for surgical consultation. PATIENTS AND METHODS Patients prospectively consented (April 2016 to May 2017) to an institutional review board–approved protocol of tumor-normal sequencing via a custom next-generation sequencing panel—the Memorial Sloan Kettering–Integrated Mutation Profiling of Actionable Cancer Targets—that yielded germline results for more than 75 cancer predisposition genes. Tumors were assessed for microsatellite instability. Per institutional standards, all tumors underwent Lynch syndrome screening via immunohistochemistry (IHC) for mismatch repair proteins. RESULTS Of 156 patients who consented to germline genetic testing, 118 (76%) had stage I disease. In 104 patients (67%), tumors were endometrioid, and 60 (58%) of those tumors were grade 1. Twenty-four pathogenic germline variants were identified in 22 patients (14%): seven (4.5%) had highly penetrant cancer syndromes and 15 (9.6%) had variants in low-penetrance, moderate-penetrance, or recessive genes. Of these, five (21%) were in Lynch syndrome genes (two MSH6, two PMS2, and one MLH1). All five tumors had concordant IHC staining; two (40%) were definitively microsatellite instability–high by next-generation sequencing. One patient had a known BRCA1 mutation, and one had an SMARCA4 deletion. The remaining 17 variants (71%) were incremental findings in low- and moderate-penetrance variants or genes associated with recessive disease. CONCLUSION In unselected patients with predominantly low-risk, early-stage endometrial cancer, germline multigene panel testing identified cancer predisposition gene variants in 14%. This finding may have implications for future cancer screening and risk-reduction recommendations. Universal IHC screening for Lynch syndrome successfully identifies the majority (71%) of high-penetrance germline mutations.

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Screening for Lynch syndrome in young Saudi colorectal cancer patients using microsatellite instability testing and next generation sequencing

Familial Cancer ◽

10.1007/s10689-017-0015-9 ◽

2017 ◽

Vol 17 (2) ◽

pp. 197-203 ◽

Cited By ~ 1

Author(s):

Masood Alqahtani ◽

Caitlin Edwards ◽

Natasha Buzzacott ◽

Karen Carpenter ◽

Khalid Alsaleh ◽

...

Keyword(s):

Colorectal Cancer ◽

Next Generation Sequencing ◽

Lynch Syndrome ◽

Microsatellite Instability ◽

Cancer Patients ◽

Next Generation ◽

Colorectal Cancer Patients ◽

Generation Sequencing

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A Novel Method for Microsatellite Instability Detection by Liquid Biopsy Based on Next- Generation Sequencing

Current Bioinformatics ◽

10.2174/1574893615666200324133451 ◽

2020 ◽

Vol 15 ◽

Author(s):

Zheng Jiang ◽

Hui Liu ◽

Siwen Zhang ◽

Jia Liu ◽

Weitao Wang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Liquid Biopsy ◽

Tumor Tissue ◽

High Sensitivity ◽

Next Generation ◽

Tissue Samples ◽

Next Generation Sequencing Technology ◽

Medication Selection ◽

Generation Sequencing

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

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Tumor Mutational Burden Calculation and Microsatellite Instability Detection in Clinical Next-Generation Sequencing Assays

Advances in Molecular Pathology ◽

10.1016/j.yamp.2021.07.008 ◽

2021 ◽

Vol 4 ◽

pp. 199-204

Author(s):

Ashkan Bigdeli ◽

Amanda Oran ◽

Robyn Sussman

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Next Generation ◽

Mutational Burden ◽

Tumor Mutational Burden ◽

Generation Sequencing

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Adoption of universal next generation sequencing for lynch syndrome screening in endometrial cancer

Gynecologic Oncology ◽

10.1016/j.ygyno.2021.10.056 ◽

2022 ◽

Vol 164 (1) ◽

pp. 4-5

Author(s):

Isabel Rodriguez ◽

Sarah Strickland ◽

David Wells ◽

Enna Manhardt ◽

Eric Konnick ◽

...

Keyword(s):

Endometrial Cancer ◽

Next Generation Sequencing ◽

Lynch Syndrome ◽

Next Generation ◽

Generation Sequencing

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MICROBIOMA: AMIGO O ENEMIGO EN PACIENTES CON COVID - 19

SCIENTIARVM ◽

10.26696/sci.epg.0115 ◽

2015 ◽

Vol 1 (1) ◽

pp. 15-21

Author(s):

Katherine Milagros Quispe Medina ◽

◽

Angel Sixto Mamani Ruelas ◽

Brenda Jasmin Alvarez Vera ◽

Yasmin Yessenia Silvestre Gutierrez ◽

...

Keyword(s):

Next Generation Sequencing ◽

Gastrointestinal Tract ◽

Molecular Biology ◽

Gut Microbiome ◽

Next Generation ◽

Multiple Factors ◽

Lung Microbiome ◽

The Relationship ◽

Generation Sequencing ◽

Clinical Cases

The research of the microbiome concerning various diseases has grown in the last ten years due to the advances in molecular biology and next-generation sequencing, finding interactions with various pathologies. The new coronavirus 19 (SARS-COV 2) pandemic has aroused interest in the study of multiple factors that could influence in the development of symptoms mainly due to the interaction of the microbiome whether of the respiratory or gastrointestinal tract finally in the prognosis. Therefore, in this study, we focus on reviewing and analyzing the current bibliography of research and clinical cases about the relationship between the lung and gut microbiome and COVID-19, highlighting its effect on infected patients, aiming to contribute to this new line of research. Keywords: Microbiome, COVID-19, SARS-COV 2, gut microbiome, lung microbiome.

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Mutation Burden and I Index for Detection of Microsatellite Instability in Colorectal Cancer by Targeted Next-Generation Sequencing

Journal of Molecular Diagnostics ◽

10.1016/j.jmoldx.2018.09.005 ◽

2019 ◽

Vol 21 (2) ◽

pp. 241-250 ◽

Cited By ~ 8

Author(s):

Jeong E. Kim ◽

Sung-Min Chun ◽

Yong S. Hong ◽

Kyu-pyo Kim ◽

Sun Y. Kim ◽

...

Keyword(s):

Colorectal Cancer ◽

Next Generation Sequencing ◽

Microsatellite Instability ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Mutation Burden ◽

Generation Sequencing

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Microsatellite instability detection using a large next-generation sequencing cancer panel across diverse tumour types

Journal of Clinical Pathology ◽

10.1136/jclinpath-2019-206136 ◽

2019 ◽

Vol 73 (2) ◽

pp. 83-89 ◽

Cited By ~ 6

Author(s):

Jiuhong Pang ◽

Tatyana Gindin ◽

Mahesh Mansukhani ◽

Helen Fernandes ◽

Susan Hsiao

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Instability ◽

Microsatellite Loci ◽

Clinical Samples ◽

Next Generation ◽

Diverse Range ◽

Tree Classifier ◽

Generation Sequencing ◽

Cancer Panel ◽

Clinical Cases

AimMicrosatellite instability (MSI), a hallmark of DNA mismatch repair deficiency, is a key molecular biomarker with multiple clinical implications including the selection of patients for immunotherapy, identifying patients who may have Lynch syndrome and predicting prognosis in patients with colorectal tumours. Next-generation sequencing (NGS) provides the opportunity to interrogate large numbers of microsatellite loci concurrently with genomic variants. We sought to develop a method to detect MSI that would not require paired normal tissue and would leverage the sequence data obtained from a broad range of tumours tested using our 467-gene NGS Columbia Combined Cancer Panel (CCCP).MethodsAltered mononucleotide and dinucleotide microsatellite loci across the CCCP region of interest were evaluated in clinical samples encompassing a diverse range of tumour types. The number of altered loci was used to develop a decision tree classifier model trained on the retrospectively collected cohort of 107 clinical cases sequenced by the CCCP assay.ResultsThe classifier was able to correctly classify all cases and was then used to analyse a test set of clinical cases (n=112) and was able to correctly predict their MSI status with 100% sensitivity and specificity. Analysis of recurrently altered loci identified alterations in genes involved in DNA repair, signalling and transcriptional regulation pathways, many of which have been implicated in MSI tumours.ConclusionThis study highlights the utility of this approach, which should be applicable to laboratories performing similar testing.

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