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.
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.
UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK. sandi.deans@ed.ac.uk.
Zandra C
ZC
Deans
i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
Jose Luis
JL
Costa
Department of Pathology, University Hospital Coventry and Warwickshire, Coventry, CV2 2DX, UK.
Ian
I
Cree
Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven-University of Leuven, Leuven, Belgium.
Els
E
Dequeker
Clinical Pathology, Laboratory Medicine, Medical Services, Region Skåne, Lund, Sweden.
Anders
A
Edsjö
Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK.
Shirley
S
Henderson
Institute of Pathology, Berlin, Germany and the DGP, German Society of Pathology, Charite, University Medicine Berlin, Berlin, Germany.
Michael
M
Hummel
Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
Marjolijn Jl
MJ
Ligtenberg
Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK.
Marco
M
Loddo
i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.
Jose Carlos
JC
Machado
Center of Predictive Molecular Medicine, CeSI-MeT, University of Chieti, Chieti, Italy.
Antonio
A
Marchetti
Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK.
Katherine
K
Marquis
Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK.
Joanne
J
Mason
Cell Biology and Biotherapy Unit, Istituto Nazionale Tumouri "Fondazione Giovanni Pascale" IRCCS, Naples, Italy.
Nicola
N
Normanno
Department of Medical Biology and Pathology, Genetic and Pathology Molecular Service, Gustave Roussy, 114 Rue Edouard Vaillant, 94800, Villejuif, France.
Etienne
E
Rouleau
Department of Pathology, University of Groningen, University Medical Center of Groningen, Groningen, The Netherlands.
Ed
E
Schuuring
Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK.
Keeda-Marie
KM
Snelson
Pathology, VU University Medical Center, Amsterdam, the Netherlands.
Erik
E
Thunnissen
Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
Bastiaan
B
Tops
Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK.
Gareth
G
Williams
Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
Han
H
van Krieken
International Quality Network for Pathology (IQN Path) Association Sans But Lucratif (A.S.B.L), 17 Boulevard Royal, L2449, Luxembourg City, Luxembourg.|Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK.
Jacqueline A
JA
Hall
D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation / Q000235:genetics*; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D057089:Pathology, Molecular / Q000379:methods
Best practice; Molecular pathology; Next-generation sequencing; Quality; Solid tumours
J Clin Pathol. 2014 Nov;67(11):923-31
25012948
Sci Rep. 2015 Dec 07;5:17875
26639839
BMC Clin Pathol. 2015 Mar 24;15:5
25859162
Cancers (Basel). 2015 Oct 14;7(4):2023-36
26473927
Anticancer Res. 2011 Dec;31(12):4207-10
22199282
Genet Med. 2015 May;17(5):405-24
25741868
Genome Res. 1998 Mar;8(3):186-94
9521922
Genet Med. 2013 Sep;15(9):733-47
23887774
PLoS One. 2013 Jul 26;8(7):e69604
23922754
BMC Genomics. 2012 Jul 24;13:341
22827831
Arch Pathol Lab Med. 2015 Apr;139(4):481-93
25152313
Genome Res. 1998 Mar;8(3):175-85
9521921
J Clin Pathol. 2015 Feb;68(2):111-8
25430497
Eur J Hum Genet. 2016 Jan;24(1):2-5
26508566
Nat Biotechnol. 2012 Nov;30(11):1033-6
23138292
Clin Cancer Res. 2013 Feb 1;19(3):691-8
23243218
Cancer Cytopathol. 2013 Jul;121(7):370-6
23408463
Clin Cancer Res. 2015 May 15;21(10):2227-35
25979929
Lancet Oncol. 2015 Oct;16(13):1324-34
26342236
Genes Chromosomes Cancer. 2016 Jun;55(6):505-21
26917275
Hum Mutat. 2008 Nov;29(11):1282-91
18951446
J Natl Cancer Inst. 2015 Apr 11;107(7):
25863335
Nat Med. 2014 Jun;20(6):682-8
24836576
J Mol Diagn. 2016 Mar;18(2):299-315
26801070
Nat Med. 2015 Jun;21(6):560-2
25939061
J Mol Diagn. 2012 Nov;14(6):525-40
22918138
Lab Invest. 2011 Aug;91(8):1253-61
21519325
Ann Oncol. 2014 Dec;25(12):2295-2303
25344359
Nat Med. 2012 Jan 22;18(2):221-3
22270724
BMC Cancer. 2015 Jan 31;15:26
25637035
Biotech Histochem. 2012 Jan;87(1):14-7
21732745
Genome Biol. 2014 Mar 25;15(3):R53
24667040
Biomed Res Int. 2015;2015:456479
26539496
N Engl J Med. 2015 Jun 25;372(26):2499-508
26061753
BMC Genomics. 2014 Jun 24;15:516
24962530
Cancer Cytopathol. 2013 Jun;121(6):311-9
23225576
Oncotarget. 2012 May;3(5):546-58
22643842
Am J Pathol. 2002 Sep;161(3):1051-60
12213734
N Engl J Med. 2006 Feb 2;354(5):526-8; author reply 526-8
16452569
Genome Med. 2013 Sep 27;5(9):89
24070238
J Pathol Transl Med. 2015 May;49(3):236-42
26018515
Lung Cancer. 2017 May;107:22-35
27316470