A Canadian guideline on the use of next-generation sequencing in oncology.

Rapid advancements in next-generation sequencing (ngs) technology have created an unprecedented opportunity to decipher the molecular profile of tumours to more effectively prevent, diagnose, and treat cancer. Oncologists now have the option to order molecular tests that can guide treatment decisions. However, to date, most oncologists have received limited training in genomics, and they are now faced with the challenge of understanding how such tests and their interpretation align with patient management. Guidance on how to effectively use ngs technology is therefore needed to aid oncologists in applying the results of genomic tests. The Canadian guideline presented here describes best practices and unmet needs related to ngs-based testing for somatic variants in oncology, including clinical application, assay and sample selection, bioinformatics and interpretation of reports performed by laboratories, patient communication, and clinical trials.

[1]  R. Yelensky,et al.  Cancer Therapy Directed by Comprehensive Genomic Profiling: A Single Center Study. , 2016, Cancer research.

[2]  Angie Duy Vo,et al.  Identifying fusion transcripts using next generation sequencing , 2016, Wiley interdisciplinary reviews. RNA.

[3]  Joon-Oh Park,et al.  The NEXT-1 (Next generation pErsonalized tX with mulTi-omics and preclinical model) trial: prospective molecular screening trial of metastatic solid cancer patients, a feasibility analysis , 2015, Oncotarget.

[4]  R. Bourgon,et al.  Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial , 2016, The Lancet.

[5]  P. Stephens,et al.  Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers , 2017, Molecular Cancer Therapeutics.

[6]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[7]  Matthew P. Goetz,et al.  NCCN CLINICAL PRACTICE GUIDELINES IN ONCOLOGY , 2019 .

[8]  M. Ladanyi,et al.  Broad, Hybrid Capture–Based Next-Generation Sequencing Identifies Actionable Genomic Alterations in Lung Adenocarcinomas Otherwise Negative for Such Alterations by Other Genomic Testing Approaches , 2015, Clinical Cancer Research.

[9]  A. Karsan,et al.  Evidence-based best practices for EGFR T790M testing in lung cancer in Canada. , 2018, Current oncology.

[10]  Steven J. M. Jones,et al.  Lessons learned from the application of whole-genome analysis to the treatment of patients with advanced cancers , 2015, Cold Spring Harbor molecular case studies.

[11]  Peter Horak,et al.  Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls , 2016, ESMO Open.

[12]  Steven J. M. Jones,et al.  FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. , 2014, American journal of human genetics.

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

[14]  S. Sleijfer,et al.  Molecular Tumor Boards: current practice and future needs , 2017, Annals of oncology : official journal of the European Society for Medical Oncology.

[15]  G. Otterson,et al.  Economic impact of next generation sequencing vs sequential single-gene testing modalities to detect genomic alterations in metastatic non-small cell lung cancer using a decision analytic model. , 2018 .

[16]  M. Tsao,et al.  Harmonization of PD-L1 testing in oncology: a Canadian pathology perspective. , 2018, Current oncology.

[17]  R. Butler,et al.  Inhibition of EGFR, HER2, and HER3 signalling in patients with colorectal cancer wild-type for BRAF, PIK3CA, KRAS, and NRAS (FOCUS4-D): a phase 2-3 randomised trial , 2018 .

[18]  Carl Virtanen,et al.  Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial , 2016, Genome Medicine.

[19]  Marie-Cécile Le Deley,et al.  High-Throughput Genomics and Clinical Outcome in Hard-to-Treat Advanced Cancers: Results of the MOSCATO 01 Trial. , 2017, Cancer discovery.

[20]  E. V. Van Allen,et al.  Next-generation sequencing to guide cancer therapy , 2015, Genome Medicine.

[21]  F. Chang,et al.  Microsatellite Instability: A Predictive Biomarker for Cancer Immunotherapy , 2017, Applied immunohistochemistry & molecular morphology : AIMM.

[22]  Marilyn M. Li,et al.  Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. , 2017, The Journal of molecular diagnostics : JMD.

[23]  S Senan,et al.  Metastatic non-small cell lung cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[24]  Steven R. Head,et al.  Next-generation sequencing , 2010, Nature Reviews Drug Discovery.

[25]  R. Kamps,et al.  Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification , 2017, International journal of molecular sciences.

[26]  S. Ogino,et al.  Detection of Mismatch Repair Deficiency and Microsatellite Instability in Colorectal Adenocarcinoma by Targeted Next-Generation Sequencing. , 2017, The Journal of molecular diagnostics : JMD.

[27]  Ahmet Zehir,et al.  Molecular Determinants of Response to Anti-Programmed Cell Death (PD)-1 and Anti-Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non-Small-Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing. , 2018, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[28]  J. Blay,et al.  Vemurafenib in Multiple Nonmelanoma Cancers with BRAF V600 Mutations. , 2015, The New England journal of medicine.

[29]  Région de la Capitale Nationale,et al.  Hoffmann-La Roche Limited , 2011 .

[30]  T. de Baère,et al.  Precision medicine for patients with advanced biliary tract cancers: An effective strategy within the prospective MOSCATO-01 trial. , 2017, European journal of cancer.

[31]  M. Stukan,et al.  Detection of BRCA1/2 mutations in circulating tumor DNA from patients with ovarian cancer , 2017, Oncotarget.

[32]  R. Govindan,et al.  ALCHEMIST: Bringing genomic discovery and targeted therapies to early‐stage lung cancer , 2015, Clinical pharmacology and therapeutics.

[33]  M. Choti,et al.  NCCN Clinical Practice Guidelines in Oncology: colon cancer. , 2009, Journal of the National Comprehensive Cancer Network : JNCCN.

[34]  Lackner,et al.  The Role of Next‐Generation Sequencing in Enabling Personalized Oncology Therapy , 2016, Clinical and translational science.

[35]  David J. Sims,et al.  Feasibility of molecular profiling based assignment of cancer treatment (MPACT): A randomized NCI precision medicine study. , 2016 .

[36]  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.

[37]  S. Dacic,et al.  Next-Generation Sequencing Approach to Non-Small Cell Lung Carcinoma Yields More Actionable Alterations. , 2017, Archives of pathology & laboratory medicine.

[38]  M. Tsao,et al.  Standardizing biomarker testing for Canadian patients with advanced lung cancer. , 2018, Current oncology.