Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue.

Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias is inherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mm biopsy), which becomes grossly under-powered as tumor volume scales. Here, we demonstrate representative sequencing (Rep-Seq) as a new method to achieve unbiased tumor tissue sampling. Rep-Seq uses fixed residual tumor material, which is homogenized and subjected to next-generation sequencing. Analysis of intratumor tumor mutation burden (TMB) variability shows a high level of misclassification using current single-biopsy methods, with 20% of lung and 52% of bladder tumors having at least one biopsy with high TMB but low clonal TMB overall. Misclassification rates by contrast are reduced to 2% (lung) and 4% (bladder) when a more representative sampling methodology is used. Rep-Seq offers an improved sampling protocol for tumor profiling, with significant potential for improved clinical utility and more accurate deconvolution of clonal structure.

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Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of Interests S.T. reports grants from Roche Tissue Diagnostics. K.L., S.T., and C.S. report speaker fees from Roche Tissue Diagnostics. K.L., S.S., S.T., and N.R.A. report a patent pending using Rep-Seq profiling to support detection of MRD. N.R.A., S.S., L.G., A.B., K.F.L., and S.H. have patents pending on representative sampling of solid tumors. C.S. receives grant support from Pfizer, AstraZeneca (AZ), Bristol-Myers Squibb (BMS), Roche-Ventana, Boehringer Ingelheim, and Ono. C.S. has consulted for Pfizer, Novartis, GlaxoSmithKline (GSK), Merck Sharpe & Dohme (MSD), BMS, Celgene, AZ, Illumina, Genentech, Roche-Ventana, GRAIL, Medicxi, and the Sarah Cannon Research Institute. C.S. is a shareholder of Apogen Biotechnologies, Epic Bioscience, and GRAIL and has stock options in and is co-founder of Achilles Therapeutics. Outside of the submitted work, K.L., S.T., and C.S. have a patent pending on indel burden and CPI response and a patent pending on targeting of frameshift neoantigens for personalized immunotherapy. J.L. reports institutional research support from BMS, MSD, Novartis, Pfizer, Achilles Therapeutics, Roche, Nektar Therapeutics, Covance, Immunocore, Pharmacyclics, and Aveo and consultancy support from Achilles, AZ, Boston Biomedical, BMS, Eisai, EUSA Pharma, GSK, Ipsen, Imugene, Incyte, iOnctura, Kymab, Merck Serono, MSD, Nektar, Novartis, Pierre Fabre, Pfizer, Roche/Genentech, Secarna, and Vitaccess. S.T. has received speaking fees from Astra Zeneca, Novartis, and Ipsen. S.T., K.L., and C.S. have the following patents filed: Clear Cell Renal Cell Carcinoma BiomarkersP113326GB.