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Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue
- Source :
- PEACE Consortium & Blackhall, F 2020, ' Representative Sequencing : Unbiased Sampling of Solid Tumor Tissue ', Cell Reports, vol. 31, no. 5, 107550, pp. 107550 . https://doi.org/10.1016/j.celrep.2020.107550, Cell Reports, Cell Reports, Elsevier Inc, 2020, 31 (5), pp.107550. ⟨10.1016/j.celrep.2020.107550⟩, Litchfield, K, Stanislaw, S, Spain, L, Gallegos, L L, Rowan, A, Schnidrig, D, Rosenbaum, H, Harle, A, Au, L, Hill, S M, Tippu, Z, Thomas, J, Thompson, L, Xu, H, Horswell, S, Barhoumi, A, Jones, C, Leith, K F, Burgess, D L, Watkins, T B K, Lim, E, Birkbak, N J, Lamy, P, Nordentoft, I, Dyrskjøt, L, Pickering, L, Hazell, S, Jamal-Hanjani, M, PEACE Consortium, Larkin, J, Swanton, C, Alexander, N & Turajlic, S 2020, ' Representative Sequencing : Unbiased Sampling of Solid Tumor Tissue ', Cell Reports, vol. 31, no. 5, 107550 . https://doi.org/10.1016/j.celrep.2020.107550, Cell Reports, Vol 31, Iss 5, Pp-(2020), Litchfield, K, Stanislaw, S, Spain, L, Gallegos, L L, Rowan, A, Schnidrig, D, Rosenbaum, H, Harle, A, Au, L, Hill, S M, Tippu, Z, Thomas, J, Thompson, L, Xu, H, Horswell, S, Barhoumi, A, Jones, C, Leith, K F, Burgess, D L, Watkins, T B K, Lim, E, Birkbak, N J, Lamy, P, Nordentoft, I, Dyrskjøt, L, Pickering, L, Hazell, S, Jamal-hanjani, M, Larkin, J, Swanton, C, Alexander, N, Turajlic, S, Abbosh, C, Shiu, K, Bridgewater, J, Hochhauser, D, Forster, M, Lee, S, Ahmad, T, Papadatos-pastos, D, Janes, S, Van Loo, P, Enfield, K, Mcgranahan, N, Huebner, A, Quezada, S, Beck, S, Parker, P, Walczak, H, Enver, T, Hynds, R, Falzon, M, Proctor, I, Sinclair, R, Lok, C, Rhodes, Z, Moore, D, Marafioti, T, Borg, E, Mitchison, M, Khiroya, R, Trevisan, G, Ellery, P, Linch, M, Brandner, S, Hiley, C, Veeriah, S, Razaq, M, Shaw, H, Attard, G, Akther, M A, Naceur-lombardelli, C, Manzano, L, Al-bakir, M, Summan, S, Kanu, N, Ward, S, Asghar, U, Lim, E, Gishen, F, Tookman, A, Stone, P, Stirling, C, Furness, A, Edmonds, K, Hunter, N, Sarker, S, Vaughan, S, Mangwende, M, Pearce, K, Spain, L, Shepherd, S, Yan, H, Shum, B, Carlyle, E, Hazell, S, Fendler, A, Byrne, F, Yousaf, N, Popat, S, Curtis, O, Stamp, G, Toncheva, A, Nye, E, Murra, A, Korteweg, J, Sheikh, N, Josephs, D, Chandra, A, Spicer, J, Mahadeva, U, Green, A, Stewart, R, Iredale, L, Mackay, T, Deakin, B, Enting, D, Rudman, S, Ghosh, S, Karapagniotou, L, Pintus, E, Tutt, A, Howlett, S, Michalarea, V, Brenton, J, Caldas, C, Fitzgerald, R, Jimenez-linan, M, Provenzano, E, Cluroe, A, Stewart, G, Watts, C, Gilbertson, R, Mcdermott, U, Tavare, S, Beddowes, E, Roxburgh, P, Biankin, A, Chalmers, A, Fraser, S, Oien, K, Kidd, A, Blyth, K, Krebs, M, Blackhall, F, Summers, Y, Dive, C, Marais, R, Gomes, F, Carter, M, Dransfield, J, Le Quesne, J, Fennell, D, Shaw, J, Naidu, B, Baijal, S, Tanchel, B, Langman, G, Robinson, A, Collard, M, Cockcroft, P, Ferris, C, Bancroft, H, Kerr, A, Middleton, G, Webb, J, Kadiri, S, Colloby, P, Olisemeke, B, Wilson, R, Tomlinson, I, Jogai, S, Ottensmeier, C, Harrison, D, Loda, M, Flanagan, A, Mckenzie, M, Hackshaw, A, Ledermann, J, Sharp, A, Farrelly, L & Bridger, H 2020, ' Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue ', Cell Reports, vol. 31, no. 5, pp. 107550 . https://doi.org/10.1016/j.celrep.2020.107550, CELL REPORTS, Cell Reports, 2020, 31 (5), pp.107550. ⟨10.1016/j.celrep.2020.107550⟩
- Publication Year :
- 2020
- Publisher :
- Elsevier BV, 2020.
-
Abstract
- International audience; Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias isinherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mmbiopsy), 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 butlow 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.
- Subjects :
- 0301 basic medicine
tumor sequencing
medicine.medical_specialty
Sampling protocol
tumor mutational burden
tumor sampling
Lung Neoplasms
molecular profiling
Biopsy
homogenization
Tissue sample
[SDV.CAN]Life Sciences [q-bio]/Cancer
Biology
General Biochemistry, Genetics and Molecular Biology
03 medical and health sciences
0302 clinical medicine
medicine
Biomarkers, Tumor
Humans
Solid tumor
lcsh:QH301-705.5
Representative sampling
medicine.diagnostic_test
Manchester Cancer Research Centre
ResearchInstitutes_Networks_Beacons/mcrc
Clonal structure
biomarkers
High-Throughput Nucleotide Sequencing
Tumor tissue
tumor hetereogeneity
Tumor Burden
030104 developmental biology
lcsh:Biology (General)
representative sampling
Urinary Bladder Neoplasms
Mutation
Radiology
030217 neurology & neurosurgery
Subjects
Details
- ISSN :
- 22111247
- Database :
- OpenAIRE
- Journal :
- PEACE Consortium & Blackhall, F 2020, ' Representative Sequencing : Unbiased Sampling of Solid Tumor Tissue ', Cell Reports, vol. 31, no. 5, 107550, pp. 107550 . https://doi.org/10.1016/j.celrep.2020.107550, Cell Reports, Cell Reports, Elsevier Inc, 2020, 31 (5), pp.107550. ⟨10.1016/j.celrep.2020.107550⟩, Litchfield, K, Stanislaw, S, Spain, L, Gallegos, L L, Rowan, A, Schnidrig, D, Rosenbaum, H, Harle, A, Au, L, Hill, S M, Tippu, Z, Thomas, J, Thompson, L, Xu, H, Horswell, S, Barhoumi, A, Jones, C, Leith, K F, Burgess, D L, Watkins, T B K, Lim, E, Birkbak, N J, Lamy, P, Nordentoft, I, Dyrskjøt, L, Pickering, L, Hazell, S, Jamal-Hanjani, M, PEACE Consortium, Larkin, J, Swanton, C, Alexander, N & Turajlic, S 2020, ' Representative Sequencing : Unbiased Sampling of Solid Tumor Tissue ', Cell Reports, vol. 31, no. 5, 107550 . https://doi.org/10.1016/j.celrep.2020.107550, Cell Reports, Vol 31, Iss 5, Pp-(2020), Litchfield, K, Stanislaw, S, Spain, L, Gallegos, L L, Rowan, A, Schnidrig, D, Rosenbaum, H, Harle, A, Au, L, Hill, S M, Tippu, Z, Thomas, J, Thompson, L, Xu, H, Horswell, S, Barhoumi, A, Jones, C, Leith, K F, Burgess, D L, Watkins, T B K, Lim, E, Birkbak, N J, Lamy, P, Nordentoft, I, Dyrskjøt, L, Pickering, L, Hazell, S, Jamal-hanjani, M, Larkin, J, Swanton, C, Alexander, N, Turajlic, S, Abbosh, C, Shiu, K, Bridgewater, J, Hochhauser, D, Forster, M, Lee, S, Ahmad, T, Papadatos-pastos, D, Janes, S, Van Loo, P, Enfield, K, Mcgranahan, N, Huebner, A, Quezada, S, Beck, S, Parker, P, Walczak, H, Enver, T, Hynds, R, Falzon, M, Proctor, I, Sinclair, R, Lok, C, Rhodes, Z, Moore, D, Marafioti, T, Borg, E, Mitchison, M, Khiroya, R, Trevisan, G, Ellery, P, Linch, M, Brandner, S, Hiley, C, Veeriah, S, Razaq, M, Shaw, H, Attard, G, Akther, M A, Naceur-lombardelli, C, Manzano, L, Al-bakir, M, Summan, S, Kanu, N, Ward, S, Asghar, U, Lim, E, Gishen, F, Tookman, A, Stone, P, Stirling, C, Furness, A, Edmonds, K, Hunter, N, Sarker, S, Vaughan, S, Mangwende, M, Pearce, K, Spain, L, Shepherd, S, Yan, H, Shum, B, Carlyle, E, Hazell, S, Fendler, A, Byrne, F, Yousaf, N, Popat, S, Curtis, O, Stamp, G, Toncheva, A, Nye, E, Murra, A, Korteweg, J, Sheikh, N, Josephs, D, Chandra, A, Spicer, J, Mahadeva, U, Green, A, Stewart, R, Iredale, L, Mackay, T, Deakin, B, Enting, D, Rudman, S, Ghosh, S, Karapagniotou, L, Pintus, E, Tutt, A, Howlett, S, Michalarea, V, Brenton, J, Caldas, C, Fitzgerald, R, Jimenez-linan, M, Provenzano, E, Cluroe, A, Stewart, G, Watts, C, Gilbertson, R, Mcdermott, U, Tavare, S, Beddowes, E, Roxburgh, P, Biankin, A, Chalmers, A, Fraser, S, Oien, K, Kidd, A, Blyth, K, Krebs, M, Blackhall, F, Summers, Y, Dive, C, Marais, R, Gomes, F, Carter, M, Dransfield, J, Le Quesne, J, Fennell, D, Shaw, J, Naidu, B, Baijal, S, Tanchel, B, Langman, G, Robinson, A, Collard, M, Cockcroft, P, Ferris, C, Bancroft, H, Kerr, A, Middleton, G, Webb, J, Kadiri, S, Colloby, P, Olisemeke, B, Wilson, R, Tomlinson, I, Jogai, S, Ottensmeier, C, Harrison, D, Loda, M, Flanagan, A, Mckenzie, M, Hackshaw, A, Ledermann, J, Sharp, A, Farrelly, L & Bridger, H 2020, ' Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue ', Cell Reports, vol. 31, no. 5, pp. 107550 . https://doi.org/10.1016/j.celrep.2020.107550, CELL REPORTS, Cell Reports, 2020, 31 (5), pp.107550. ⟨10.1016/j.celrep.2020.107550⟩
- Accession number :
- edsair.doi.dedup.....40f254410047db4d0807701fbc62a8f6
- Full Text :
- https://doi.org/10.1016/j.celrep.2020.107550