MSI-XGNN: an explainable GNN computational framework integrating transcription- and methylation-level biomarkers for microsatellite instability detection

MSIMEP: predicting microsatellite instability from microarray DNA methylation tumor profiles

(2023) Martín Santamarina-García et al.   iScience

A novel cuproptosis-related gene model predicts outcomes and treatment responses in pancreatic adenocarcinoma

(2023) Qixian Liu et al.   BMC CANCER

Multi‐omic analysis in normal colon organoids highlights MSH4 as a novel marker of defective mismatch repair in Lynch syndrome and microsatellite instability

(2023) Matthew Devall et al.   Cancer Medicine

Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA

(2022) Smita S. Chandran et al.   NATURE MEDICINE

Homologous recombination deficiency is inversely correlated with microsatellite instability and identifies immunologically cold tumors in most cancer types

(2022) Jan Budczies et al.   Journal of Pathology Clinical Research

Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes

(2022) Aleksandr Zaitsev et al.   CANCER CELL

Genomic and transcriptomic determinants of response to neoadjuvant therapy in rectal cancer

(2022) Walid K. Chatila et al.   NATURE MEDICINE

PD-1 Blockade in Mismatch Repair–Deficient, Locally Advanced Rectal Cancer

(2022) Andrea Cercek et al.   NEW ENGLAND JOURNAL OF MEDICINE

Alternative RNA splicing modulates ribosomal composition and determines the spatial phenotype of glioblastoma cells

(2022) Tatyana D. Larionova et al.   NATURE CELL BIOLOGY

Multi-omics characterization and validation of MSI-related molecular features across multiple malignancies

(2021) Yuansheng Zheng et al.   LIFE SCIENCES

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

(2021) Alexander Bagaev et al.   CANCER CELL

EPM2AIP1 Immunohistochemistry Can Be Used as Surrogate Testing for MLH1 Promoter Methylation in Endometrial Cancer

(2021) Miralem Mrkonjic et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

Phase Separation mediates NUP98 Fusion Oncoprotein Leukemic Transformation

(2021) Bappaditya Chandra et al.   Cancer Discovery

Proteogenomic Characterization of Endometrial Carcinoma

(2020) Yongchao Dou et al.   CELL

Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability

(2020) Noam Auslander et al.   Nature Communications

Complete response to anti-PD-L1 antibody in a metastatic bladder cancer associated with novel MSH4 mutation and microsatellite instability

(2020) Yuanquan Yang et al.   Journal for ImmunoTherapy of Cancer

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability

(2020) Peng Jia et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Detection of microsatellite instability in a panel of solid tumours with the Idylla MSI Test using extracted DNA

(2020) Adrien Pécriaux et al.   JOURNAL OF CLINICAL PATHOLOGY

Molecular Characterization of Astrocytoma Progression Towards Secondary Glioblastomas Utilizing Patient-Matched Tumor Pairs

(2020) Michael Seifert et al.   Cancers

Pembrolizumab in Microsatellite-Instability–High Advanced Colorectal Cancer

(2020) Thierry André et al.   NEW ENGLAND JOURNAL OF MEDICINE

TSC22D2 identified as a candidate susceptibility gene of multi-cancer pedigree using genome-wide linkage analysis and whole exome sequencing

(2019) Lan Xiao et al.   CARCINOGENESIS

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

(2019) Suhas Vasaikar et al.   CELL

Individual Patient Data Meta-Analysis of the Value of Microsatellite Instability As a Biomarker in Gastric Cancer

(2019) Filippo Pietrantonio et al.   JOURNAL OF CLINICAL ONCOLOGY

Efficacy of Pembrolizumab in Patients With Noncolorectal High Microsatellite Instability/Mismatch Repair–Deficient Cancer: Results From the Phase II KEYNOTE-158 Study

(2019) Aurelien Marabelle et al.   JOURNAL OF CLINICAL ONCOLOGY

Clinically relevant molecular subtypes and genomic alteration-independent differentiation in gynecologic carcinosarcoma

(2019) Osamu Gotoh et al.   Nature Communications

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Analysis of DNA methylation in cancer: location revisited

(2018) Alexander Koch et al.   Nature Reviews Clinical Oncology

Analysis of the Prevalence of Microsatellite Instability in Prostate Cancer and Response to Immune Checkpoint Blockade

(2018) Wassim Abida et al.   JAMA Oncology

Microsatellite Instability and Promoter Hypermethylation of DNA repair genes in Hematologic Malignancies: a forthcoming direction toward diagnostics

(2017) Priyanjali Bhattacharya et al.   Hematology

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

(2017) Teresa Davoli et al.   SCIENCE

A molecular portrait of microsatellite instability across multiple cancers

(2017) Isidro Cortes-Ciriano et al.   Nature Communications

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Microsatellite Instability as a Biomarker for PD-1 Blockade

(2016) J. C. Dudley et al.   CLINICAL CANCER RESEARCH

Frequent PIK3CA Mutations in Colorectal and Endometrial Tumors With 2 or More Somatic Mutations in Mismatch Repair Genes

(2016) Stacey A. Cohen et al.   GASTROENTEROLOGY

Reliable Detection of Mismatch Repair Deficiency in Colorectal Cancers Using Mutational Load in Next-Generation Sequencing Panels

(2016) Zsofia K. Stadler et al.   JOURNAL OF CLINICAL ONCOLOGY

Classification and characterization of microsatellite instability across 18 cancer types

(2016) Ronald J Hause et al.   NATURE MEDICINE

Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS

(2016) Esko A. Kautto et al.   Oncotarget

Highly Expressed Genes in Rapidly Proliferating Tumor Cells as New Targets for Colorectal Cancer Treatment

(2015) S. Bazzocco et al.   CLINICAL CANCER RESEARCH

Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes

(2015) Razvan Cristescu et al.   NATURE MEDICINE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Microsatellite Instable Subset of Colorectal Cancer Is a Particularly Good Candidate for Checkpoint Blockade Immunotherapy

(2015) Yanping Xiao et al.   Cancer Discovery

Microsatellite Instability Detection by Next Generation Sequencing

(2014) S. J. Salipante et al.   CLINICAL CHEMISTRY

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value

(2013) Laetitia Marisa et al.   PLOS MEDICINE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Dominantly Inherited Constitutional Epigenetic Silencing of MLH1 in a Cancer-Affected Family Is Linked to a Single Nucleotide Variant within the 5′UTR

(2011) Megan P. Hitchins et al.   CANCER CELL

Microsatellite instability in colorectal cancer—the stable evidence

(2010) Eduardo Vilar et al.   Nature Reviews Clinical Oncology

Association of survival and disease progression with chromosomal instability: A genomic exploration of colorectal cancer

(2009) M. Sheffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Copy-Number Alterations Underlie Gene Expression Differences between Microsatellite Stable and Unstable Colorectal Cancers

(2008) R. N. Jorissen et al.   CLINICAL CANCER RESEARCH