Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL

Zandra C Deans¹, Jose Luis Costa², Ian Cree³, Els Dequeker⁴, Anders Edsjö⁵, Shirley Henderson⁶, Michael Hummel⁷, Marjolijn Jl Ligtenberg⁸, Marco Loddo⁹, Jose Carlos Machado², Antonio Marchetti¹⁰, Katherine Marquis⁹, Joanne Mason⁶, Nicola Normanno¹¹, Etienne Rouleau¹², Ed Schuuring¹³, Keeda-Marie Snelson⁹, Erik Thunnissen¹⁴, Bastiaan Tops⁸, Gareth Williams⁹, Han van Krieken⁸, Jacqueline A Hall^{15

16}; IQN Path ASBL

Affiliations

¹ UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK. sandi.deans@ed.ac.uk.
² i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
³ Department of Pathology, University Hospital Coventry and Warwickshire, Coventry, CV2 2DX, UK.
⁴ Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven-University of Leuven, Leuven, Belgium.
⁵ Clinical Pathology, Laboratory Medicine, Medical Services, Region Skåne, Lund, Sweden.
⁶ Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK.
⁷ Institute of Pathology, Berlin, Germany and the DGP, German Society of Pathology, Charite, University Medicine Berlin, Berlin, Germany.
⁸ Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
⁹ Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK.
¹⁰ Center of Predictive Molecular Medicine, CeSI-MeT, University of Chieti, Chieti, Italy.
¹¹ Cell Biology and Biotherapy Unit, Istituto Nazionale Tumouri "Fondazione Giovanni Pascale" IRCCS, Naples, Italy.
¹² Department of Medical Biology and Pathology, Genetic and Pathology Molecular Service, Gustave Roussy, 114 Rue Edouard Vaillant, 94800, Villejuif, France.
¹³ Department of Pathology, University of Groningen, University Medical Center of Groningen, Groningen, The Netherlands.
¹⁴ Pathology, VU University Medical Center, Amsterdam, the Netherlands.
¹⁵ International Quality Network for Pathology (IQN Path) Association Sans But Lucratif (A.S.B.L), 17 Boulevard Royal, L2449, Luxembourg City, Luxembourg.
¹⁶ Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK.

PMID: 27678269
PMCID: PMC5243883
DOI: 10.1007/s00428-016-2025-7

Review

Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL

Zandra C Deans et al. Virchows Arch. 2017 Jan.

. 2017 Jan;470(1):5-20.

doi: 10.1007/s00428-016-2025-7. Epub 2016 Sep 27.

Authors

Affiliations

¹ UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK. sandi.deans@ed.ac.uk.
² i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
³ Department of Pathology, University Hospital Coventry and Warwickshire, Coventry, CV2 2DX, UK.
⁴ Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven-University of Leuven, Leuven, Belgium.
⁵ Clinical Pathology, Laboratory Medicine, Medical Services, Region Skåne, Lund, Sweden.
⁶ Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK.
⁷ Institute of Pathology, Berlin, Germany and the DGP, German Society of Pathology, Charite, University Medicine Berlin, Berlin, Germany.
⁸ Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
⁹ Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK.
¹⁰ Center of Predictive Molecular Medicine, CeSI-MeT, University of Chieti, Chieti, Italy.
¹¹ Cell Biology and Biotherapy Unit, Istituto Nazionale Tumouri "Fondazione Giovanni Pascale" IRCCS, Naples, Italy.
¹² Department of Medical Biology and Pathology, Genetic and Pathology Molecular Service, Gustave Roussy, 114 Rue Edouard Vaillant, 94800, Villejuif, France.
¹³ Department of Pathology, University of Groningen, University Medical Center of Groningen, Groningen, The Netherlands.
¹⁴ Pathology, VU University Medical Center, Amsterdam, the Netherlands.
¹⁵ International Quality Network for Pathology (IQN Path) Association Sans But Lucratif (A.S.B.L), 17 Boulevard Royal, L2449, Luxembourg City, Luxembourg.
¹⁶ Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK.

PMID: 27678269
PMCID: PMC5243883
DOI: 10.1007/s00428-016-2025-7

Abstract

The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guidelines establish consensus standards for somatic diagnostic testing, specifically for identifying and reporting mutations in solid tumours. These guidelines cover the testing strategy, implementation of testing within clinical service, sample requirements, data analysis and reporting of results. In conjunction with appropriate staff training and international standards for laboratory testing, these consensus standards for the use of NGS in molecular pathology of solid tumours will assist laboratories in implementing NGS in clinical services.

Keywords: Best practice; Molecular pathology; Next-generation sequencing; Quality; Solid tumours.

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Conflict of interest statement

Compliance with ethical standards This guideline does not contain any studies with human participants or animals performed by any of the authors. For this type of work, human subjects were not used and formal consent is not required. Funding IQN Path provided administration support for the project; no industry funds were used in the development of these guidelines. Conflict of interest Deans, ZC has received financial support for educational programmes from Astra Zeneca, Roche and Qiagen and is a member of advisory boards for Amgen, Astra Zeneca, Pfizer, Merck Serono and Roche. Cree, I has received grant income from Novartis and speaker fees from Welcome Trust and Novartis. He is on the Advisory Board for Life Technologies/Thermofisher and Novartis. Dequeker, E has received research grants from Pfizer and Amgen. Edsjö, A has received research grants and speaker Honoraria from Astra Zeneca and Amgen. Hall, JA owns stock in Vivactiv Ltd. Ligtenberg, M has received research grants from: research project MLDS 13-19 and research project KWF KUN2015-7740 and has Honoraria for speaking at symposia; consultation and research grant with Astra Zeneca and is a member of the onconetwork consortium of Life Technologies. Normanno, N Is on Advisory Boards and has Research funds from Qiagen and Roche. Schuuring, E is on the Advisory Board of Honoraria from Amgen, Abbott, Astra Zeneca, Biocartis, Roche, Novartis and Pfizer. He has received speaker’s fees from Biocartis, Astrazeneca, Novartis, Roche and Abbott and travel reimbursements from Abbott and Roche. He has also received grants from Hologic, Roche and Boehringer Ingelheim. Van Krieken, H has received research grants and speaker’s fees from Amgen and Merck Serono and speaker’s fees from Roche Diagnostics. Costa, HL, Henderson, S, Hummel, M, Loddo, M, Machado, HL, Marchetti, A, Marquis, K, Mason, J, Rouleau, Snelson, KM, Thunnissen, E, Tops, B, Williams, G declare that they have no conflict of interest.

References

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Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL

Affiliations

Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL

Authors

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Molecular Biology Databases