Analysis of tumor mutational burden: correlation of five large gene panels with whole exome sequencing

[1]  S. Sleijfer,et al.  Impact of panel design and cut-off on tumour mutational burden assessment in metastatic solid tumour samples , 2020, British Journal of Cancer.

[2]  Olaf Neumann,et al.  Measurement of tumor mutational burden (TMB) in routine molecular diagnostics: in silico and real‐life analysis of three larger gene panels , 2019, International journal of cancer.

[3]  C. Brennan,et al.  Tumor mutational load predicts survival after immunotherapy across multiple cancer types , 2019, Nature Genetics.

[4]  F. López-Ríos,et al.  Implementing TMB measurement in clinical practice: considerations on assay requirements , 2019, ESMO Open.

[5]  Olaf Neumann,et al.  Implementing tumor mutational burden (TMB) analysis in routine diagnostics-a primer for molecular pathologists and clinicians. , 2018, Translational lung cancer research.

[6]  T A Chan,et al.  Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[7]  Jacob Silterra,et al.  Blood-based tumor mutational burden as a predictor of clinical benefit in non-small-cell lung cancer patients treated with atezolizumab , 2018, Nature Medicine.

[8]  Isabelle Salmon,et al.  Methods of measurement for tumor mutational burden in tumor tissue. , 2018, Translational lung cancer research.

[9]  K. Yamaguchi,et al.  Molecular profiling and sequential somatic mutation shift in hypermutator tumours harbouring POLE mutations , 2018, Scientific Reports.

[10]  Arun Ahuja,et al.  Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer , 2018, Cancer cell.

[11]  J. Szustakowski,et al.  Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden , 2018, The New England journal of medicine.

[12]  M. Berger,et al.  Alterations in DNA Damage Response and Repair Genes as Potential Marker of Clinical Benefit From PD-1/PD-L1 Blockade in Advanced Urothelial Cancers. , 2018, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[13]  I. Petersen,et al.  Interlaboratory concordance of PD‐L1 immunohistochemistry for non‐small‐cell lung cancer , 2018, Histopathology.

[14]  E. Jaffee,et al.  Tumor Mutational Burden and Response Rate to PD-1 Inhibition. , 2017, The New England journal of medicine.

[15]  B. Levy,et al.  Beyond PD-L1 testing-emerging biomarkers for immunotherapy in non-small cell lung cancer. , 2017, Annals of translational medicine.

[16]  L. Rubinstein,et al.  The Challenge for Development of Valuable Immuno-oncology Biomarkers , 2017, Clinical Cancer Research.

[17]  J. Taube,et al.  A Prospective, Multi-institutional, Pathologist-Based Assessment of 4 Immunohistochemistry Assays for PD-L1 Expression in Non–Small Cell Lung Cancer , 2017, JAMA oncology.

[18]  Ludmila V. Danilova,et al.  Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade , 2017, Science.

[19]  M. Socinski,et al.  First‐Line Nivolumab in Stage IV or Recurrent Non–Small‐Cell Lung Cancer , 2017, The New England journal of medicine.

[20]  Y. Sasaki,et al.  Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation , 2017, PloS one.

[21]  Marina N Nikiforova,et al.  Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. , 2017, The Journal of molecular diagnostics : JMD.

[22]  Levi Garraway,et al.  Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden , 2017, Genome Medicine.

[23]  M. Atkins,et al.  Predictive biomarkers for checkpoint inhibitor-based immunotherapy. , 2016, The Lancet. Oncology.

[24]  Daniel G. MacArthur,et al.  The ExAC browser: displaying reference data information from over 60 000 exomes , 2016, bioRxiv.

[25]  Nikhil Wagle,et al.  The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine , 2016, Genome Medicine.

[26]  D. Carbone,et al.  Predictive Markers for the Efficacy of Anti-PD-1/PD-L1 Antibodies in Lung Cancer. , 2016, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[27]  J. Sosman,et al.  Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma , 2016, Cell.

[28]  Tudung T Nguyen,et al.  Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS) , 2015, Molecular oncology.

[29]  C. Rudin,et al.  Nivolumab versus Docetaxel in Advanced Nonsquamous Non-Small-Cell Lung Cancer. , 2015, The New England journal of medicine.

[30]  R. Goswami,et al.  Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies , 2015, Cancers.

[31]  T. Schumacher,et al.  Neoantigens in cancer immunotherapy , 2015, Science.

[32]  Martin L. Miller,et al.  Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer , 2015, Science.

[33]  Edwin Cuppen,et al.  Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..

[34]  J. Wolchok,et al.  Genetic basis for clinical response to CTLA-4 blockade in melanoma. , 2014, The New England journal of medicine.

[35]  Shuifang Zhu,et al.  Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads , 2014, BMC Bioinformatics.

[36]  David M. Thomas,et al.  Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing , 2014, BMC Medical Genomics.

[37]  Adam Kiezun,et al.  Whole-exome sequencing and clinical interpretation of FFPE tumor samples to guide precision cancer medicine , 2013, Nature Medicine.

[38]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[39]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[40]  Pablo Cingolani,et al.  Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift , 2012, Front. Gene..

[41]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[42]  D. Schadendorf,et al.  Improved survival with ipilimumab in patients with metastatic melanoma. , 2010, The New England journal of medicine.

[43]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[44]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[45]  F. Pontén,et al.  A high frequency of sequence alterations is due to formalin fixation of archival specimens. , 1999, The American journal of pathology.

[46]  Alexander Dobrovic,et al.  Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization. , 2015, Clinical chemistry.