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Litchfield K, Stanislaw S, Spain L, Gallegos LL, Rowan A, Schnidrig D, Rosenbaum H, Harle A, Au L, Hill SM, Tippu Z, Thomas J, Thompson L, Xu H, Horswell S, Barhoumi A, Jones C, Leith KF, Burgess DL, Watkins TBK, Lim E, Birkbak NJ, Lamy P, Nordentoft I, Dyrskjøt L, Pickering L, Hazell S, Jamal-Hanjani M, Larkin J, Swanton C, Alexander NR, Turajlic S. Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue. Cell Rep 2020; 31:107550. [PMID: 32375028 DOI: 10.1016/j.celrep.2020.107550] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/17/2019] [Accepted: 04/01/2020] [Indexed: 01/10/2023] Open
Abstract
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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Affiliation(s)
- Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stacey Stanislaw
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Lavinia Spain
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Lisa L Gallegos
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Desiree Schnidrig
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Heidi Rosenbaum
- Roche Sequencing Solutions, Madison, 500 S. Rosa Road, Madison, WI 53719, USA
| | - Alexandre Harle
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000 Nancy, France
| | - Lewis Au
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Samantha M Hill
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA; Department of Cancer Biology, University of Arizona Cancer Center, Tucson, AZ 85724, USA
| | - Zayd Tippu
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Jennifer Thomas
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Lisa Thompson
- The Centre for Molecular Pathology, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Aoune Barhoumi
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Carol Jones
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Katherine F Leith
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Daniel L Burgess
- Roche Sequencing Solutions, Madison, 500 S. Rosa Road, Madison, WI 53719, USA
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emilia Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lisa Pickering
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Stephen Hazell
- Histopathology Department, Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
| | - Nelson R Alexander
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA.
| | - Samra Turajlic
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK.
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Cortés JM, de Petris G, López JI. Detection of Intratumor Heterogeneity in Modern Pathology: A Multisite Tumor Sampling Perspective. Front Med (Lausanne) 2017; 4:25. [PMID: 28321395 PMCID: PMC5337957 DOI: 10.3389/fmed.2017.00025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/20/2017] [Indexed: 12/30/2022] Open
Abstract
Current sampling protocols of neoplasms along the digestive tract and in the urinary bladder have to be updated, as they do not respond to the necessities of modern personalized medicine. We show here that an adapted version of multisite tumor sampling (MSTS) is a sustainable model to overcome current deficiencies in digestive and bladder tumors when they are large enough so as to make unaffordable a total sampling. The new method is based on the divide-and-conquer algorithm and includes a slight modification of the MSTS, which proved to be useful very recently in clear cell renal cell carcinoma. This in silico analysis confirms the usefulness of MSTS for detecting intratumor heterogeneity (ITH) in tumors arising in hollow viscera. However, MSTS does not seem to improve routine traditional sampling in detecting tumor budding, extramural venous invasion, and perineural invasion. We conclude that (1) MSTS is the best method for tumor sampling to detect ITH balancing high performance and sustainable cost, (2) MSTS must be adapted to tumor shape and tumor location for an optimal performance.
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Affiliation(s)
- Jesús M Cortés
- Quantitative Biomedicine Unit, Biocruces Research Institute, Barakaldo, Spain; Ikerbasque: The Basque Foundation for Science, Bilbao, Spain; Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Giovanni de Petris
- Department of Pathology and Laboratory Medicine, Penrose St Francis Hospital , Colorado Springs, CO , USA
| | - José I López
- Department of Pathology, Cruces University Hospital, Barakaldo, Spain; Biomarkers in Cancer Unit, Biocruces Research Institute, Barakaldo, Spain; University of the Basque Country (UPV/EHU), Leioa, Spain
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Guarch R, Cortés JM, Lawrie CH, López JI. Multi-site tumor sampling (MSTS) improves the performance of histological detection of intratumor heterogeneity in clear cell renal cell carcinoma (CCRCC). F1000Res 2016; 5:2020. [PMID: 27635226 PMCID: PMC5007747 DOI: 10.12688/f1000research.9419.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2016] [Indexed: 12/23/2022] Open
Abstract
Current standard-of-care tumor sampling protocols for CCRCC (and other cancers) are not efficient at detecting intratumoural heterogeneity (ITH). We have demonstrated in silico that an alternative protocol, multi-site tumor sampling (MSTS) based upon the divide and conquer (DAC) algorithm, can significantly increase the efficiency of ITH detection without extra costs. Now we test this protocol on routine hematoxylin-eosin (HE) sections in a series of 38 CCRCC cases. MSTS was found to outperform traditional sampling when detecting either high grade (p=0.0136) or granular/eosinophilic cells (p=0.0114). We therefore propose that MSTS should be used in routine clinical practice.
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Affiliation(s)
- Rosa Guarch
- Department of Pathology, Complejo Hospitalario B de Navarra, Pamplona, Navarra, 31008, Spain
| | - Jesús M Cortés
- Quantitative Biomedicine Unit, Biocruces Research Institute, Barakaldo, 48903, Spain; Ikerbasque: The Basque Foundation for Science, Bilbao, 48013, Spain; Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Charles H Lawrie
- Ikerbasque: The Basque Foundation for Science, Bilbao, 48013, Spain; Molecular Oncology Group, Biodonostia Research Institute, San Sebastian, 20014, Spain; Department of Physiology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain; Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - José I López
- Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, 48903, Spain; Biomarkers in Cancer Unit, Biocruces Research Institute, Barakaldo, 48903, Spain
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5
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Guarch R, Cortés JM, Lawrie CH, López JI. Multi-site tumor sampling (MSTS) improves the performance of histological detection of intratumor heterogeneity in clear cell renal cell carcinoma (CCRCC). F1000Res 2016. [PMID: 27635226 DOI: 10.12688/f1000research.9419.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Current standard-of-care tumor sampling protocols for CCRCC (and other cancers) are not efficient at detecting intratumoural heterogeneity (ITH). We have demonstrated in silico that an alternative protocol, multi-site tumor sampling (MSTS) based upon the divide and conquer (DAC) algorithm, can significantly increase the efficiency of ITH detection without extra costs. Now we test this protocol on routine hematoxylin-eosin (HE) sections in a series of 38 CCRCC cases. MSTS was found to outperform traditional sampling when detecting either high grade (p=0.0136) or granular/eosinophilic cells (p=0.0114). We therefore propose that MSTS should be used in routine clinical practice.
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Affiliation(s)
- Rosa Guarch
- Department of Pathology, Complejo Hospitalario B de Navarra, Pamplona, Navarra, 31008, Spain
| | - Jesús M Cortés
- Quantitative Biomedicine Unit, Biocruces Research Institute, Barakaldo, 48903, Spain; Ikerbasque: The Basque Foundation for Science, Bilbao, 48013, Spain; Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain
| | - Charles H Lawrie
- Ikerbasque: The Basque Foundation for Science, Bilbao, 48013, Spain; Molecular Oncology Group, Biodonostia Research Institute, San Sebastian, 20014, Spain; Department of Physiology, University of the Basque Country (UPV/EHU), Leioa, 48940, Spain; Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - José I López
- Department of Pathology, Cruces University Hospital, University of the Basque Country (UPV/EHU), Barakaldo, 48903, Spain; Biomarkers in Cancer Unit, Biocruces Research Institute, Barakaldo, 48903, Spain
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Lopez JI, Cortes JM. A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma. F1000Res 2016; 5:385. [PMID: 27127618 DOI: 10.12688/f1000research.8196.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/17/2016] [Indexed: 12/17/2022] Open
Abstract
Intratumor heterogeneity (ITH) is an inherent process in cancer development which follows for most of the cases a branched pattern of evolution, with different cell clones evolving independently in space and time across different areas of the same tumor. The determination of ITH (in both spatial and temporal domains) is nowadays critical to enhance patient treatment and prognosis. Clear cell renal cell carcinoma (CCRCC) provides a good example of ITH. Sometimes the tumor is too big to be totally analyzed for ITH detection and pathologists decide which parts must be sampled for the analysis. For such a purpose, pathologists follow internationally accepted protocols. In light of the latest findings, however, current sampling protocols seem to be insufficient for detecting ITH with significant reliability. The arrival of new targeted therapies, some of them providing promising alternatives to improve patient survival, pushes the pathologist to obtain a truly representative sampling of tumor diversity in routine practice. How large this sampling must be and how this must be performed are unanswered questions so far. Here we present a very simple method for tumor sampling that enhances ITH detection without increasing costs. This method follows a divide-and-conquer (DAC) strategy, that is, rather than sampling a small number of large-size tumor-pieces as the routine protocol (RP) advises, we suggest sampling many small-size pieces along the tumor. We performed a computational modeling approach to show that the usefulness of the DAC strategy is twofold: first, we show that DAC outperforms RP with similar laboratory costs, and second, DAC is capable of performing similar to total tumor sampling (TTS) but, very remarkably, at a much lower cost. We thus provide new light to push forward a shift in the paradigm about how pathologists should sample tumors for achieving efficient ITH detection.
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Affiliation(s)
- José I Lopez
- Department of Pathology, Cruces University Hospital, Biocruces Research Institute, University of the Basque Country (UPV/EHU), Barakaldo, Spain
| | - Jesús M Cortes
- Quantitative Biomedicine Unit, Biocruces Research Institute, Barakaldo, Spain; Ikerbasque: The Basque Foundation for Science, Bilbao, Spain; Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Spain
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7
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Lopez JI, Cortes JM. A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma. F1000Res 2016; 5:385. [PMID: 27127618 PMCID: PMC4830216 DOI: 10.12688/f1000research.8196.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2016] [Indexed: 12/18/2022] Open
Abstract
Intratumor heterogeneity (ITH) is an inherent process in cancer development which follows for most of the cases a branched pattern of evolution, with different cell clones evolving independently in space and time across different areas of the same tumor. The determination of ITH (in both spatial and temporal domains) is nowadays critical to enhance patient treatment and prognosis. Clear cell renal cell carcinoma (CCRCC) provides a good example of ITH. Sometimes the tumor is too big to be totally analyzed for ITH detection and pathologists decide which parts must be sampled for the analysis. For such a purpose, pathologists follow internationally accepted protocols. In light of the latest findings, however, current sampling protocols seem to be insufficient for detecting ITH with significant reliability. The arrival of new targeted therapies, some of them providing promising alternatives to improve patient survival, pushes the pathologist to obtain a truly representative sampling of tumor diversity in routine practice. How large this sampling must be and how this must be performed are unanswered questions so far. Here we present a very simple method for tumor sampling that enhances ITH detection without increasing costs. This method follows a divide-and-conquer (DAC) strategy, that is, rather than sampling a small number of large-size tumor-pieces as the routine protocol (RP) advises, we suggest sampling many small-size pieces along the tumor. We performed a computational modeling approach to show that the usefulness of the DAC strategy is twofold: first, we show that DAC outperforms RP with similar laboratory costs, and second, DAC is capable of performing similar to total tumor sampling (TTS) but, very remarkably, at a much lower cost. We thus provide new light to push forward a shift in the paradigm about how pathologists should sample tumors for achieving efficient ITH detection.
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Affiliation(s)
- José I Lopez
- Department of Pathology, Cruces University Hospital, Biocruces Research Institute, University of the Basque Country (UPV/EHU), Barakaldo, Spain
| | - Jesús M Cortes
- Quantitative Biomedicine Unit, Biocruces Research Institute, Barakaldo, Spain; Ikerbasque: The Basque Foundation for Science, Bilbao, Spain; Department of Cell Biology and Histology, University of the Basque Country (UPV/EHU), Leioa, Spain
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