Table Summary of observation studies of single molecular diagnostic testing undertaken as a requested or routine pathology service with a view of treatment management Lead author/Year Citation type Country Diagnostic test and test population Context of study Data collection Test method(s) Use of archive tissues Outcomes reported potentially relevant to this submission Bibeau 2010a,b,c Conference abstract France KRAS mutation testing in mCRC A retrospective one year observation study of KRAS mutation testing in clinical practice 575 samples Tests between May 2008-May 2009 Not reported Reviewed archival FFPE tissues; Test failures Ciardiello 2011 Full journal article Europe (6 countries); Latin America (5 countries); Asia (2 countries) KRAS mutation testing in mCRC Yearly survey (quantitative questionnaire of physicians including review of the records of 4 a priori designated mCRC patients (last seen, last seen in first, second and third line settings) 2008: 113 tests 2009: 1775 tests 2010: 2619 tests Survey years: 2008-2010 Not reported Not specified whether testing was on newly acquired, archive tissue or either TATO Test failures Bibeau 2012 Full journal article France KRAS mutation testing in mCRC study of access to KRAS mutation testing of patients with mCRC across 66 institutions 329 patients Testing undertaken Oct 2008-Oct 2009 Mostly RT-PCR; sequencing; pyrosequencing Testing was on primary tissue and surgical samples TATO Test failures
Lapeyrere 2012 Full journal article France KRAS mutation testing in CRC Retrospective study of KRAS analysis management in KRAS mutation testing laboratories (Acquitaine); 302 analyses Jan 2009 2009 Not specified FFPE archival tissue used TATO Chretien 2013 Full journal article France KRAS mutation testing in mCRC Review of analysis of tissues by single testing centre for routine testing 674 samples Collected for assessment between Jan 2008 – Dec 2009 High resolution melting; allelic discrimination PCR Reviewed FFPE tissues; mainly primary tissue Test failures TATo Lievre 2013; Artu 2012; Ducreux 2011 Flash-KRAS study Full journal article; Conference abstract France KRAS mutation testing in mCRC Observational retrospective study of initial management of mCRC in 160 hospital centres 538 cases/ 433 test requests Tests requested during a period in March 2011 Mostly sequencing; pyrosequencing; SNaPshot; allelic discrimination; high resolution melting Testing was mainly (86.1%) on the primary tumour tissue; 14.5% of testing was prior to the diagnosis of first metastases TATO TATRS TATRR Test failure Biomarker directed treatment management Scott 2014 Full journal article Australia KRAS mutation testing in mCRC Audit of routine KRAS testing in by 9 major NATA accredited molecular pathology service providers 3688 cases (TAT available for 2531 cases [4 of the 9 testing facilities]) Tests requested between Sept 2011-Oct 2013 Various: Sanger direct (3 sites); pyrosequencing (2 sites); single nucleotide base extension using Sequenom Massarray (2 sites); Sanger sequencing, then SNaPshot (1site); HRM then Sanger ~25% from biopsy; 75% surgically resected tissue from FFPE blocks of the primary tissue (i.e., 75% archive tissue TATO; TATRS; TATRR; Proportion of cases with a given TATO; 2011- Apr
sequencing (1 site) Boleij 2015 Conference abstract 24 countries in Europe RAS- mutation testing in mCRC Survey of 96 pathology laboratories undertaking RAS testing in clinical practice in Europe; information provided on approximately 20-30 of the most recent tested mCRC patients 3,972 patients Survey took place Oct 2014-Dec 2014 Various Included FFPE tissue; not specified whether testing was on newly acquired, archive tissue or either TATO Lievre 2015 Flash-RAS study Conference abstract France KRAS mutation testing in mCRC Observational multi-centre retrospective study of RAS testing in mCRC in clinical practice; 104 centres 375 patients Mar 2014 Not specified Not specified whether testing was on newly acquired, archive tissue or either TATO Lowe 2016 Conference abstract US KRAS, NRAS and BRAF mutation testing in mCRC Retrospective review of testing in community cancer centres (OSCER database) 1550 patients Diagnosed between Jan 2011-Aug 2015 Not specified Not specified whether testing was on newly acquired, archive tissue or either TATO Gracia 2011 Conference abstract Spain EGFR mutation testing in NSCLC Prospective epidemiological study to gain insight into variables that affect the 1009 patients with available sample 6-month study; date not reported Various Biopsy and cytological sample; not specified whether testing was on TATO Test failures June
feasibility and implementation of EGFR mutation testing in routine clinical practice; 39 Spanish centres using two central testing centres and 7 on-site testing facilities newly acquired, archive tissue or either Tao 2011 Conference abstract Canada EGFR mutation testing in advanced NSCLC Result from pilot routine testing network NSCLC involving 5 testing laboratories 1869 requests March 2010 – Nov 2010 Not specified Reviewed, archive FFPE includes tissue and cytology samples Test failures TATRS TATRR Leary 2012 Full journal article UK EGFR mutation testing in advanced NSCLC Study of the feasibility of prospective EGFR testing in routine clinical practice; single testing centre Year 1: 152 samples (144 cases) Year 2: 755 cases Screening period: Jan 2009 - Jan 2010; Jan 2010 - Jan 2011 Year 1: TheraScreen EGFR29 ARMS mutation kit; Year 2: Combination of ARMS; fragment analysis; direct sequencing Blocks or slides; not specified whether testing was on newly acquired, archive tissue or either; some samples were from external sources Test failures TATO TATRS 2012 Conference abstract US EGFR and ALK mutation testing in NSCLC Retrospective observation study to determine the utility of a reflex testing policy for the mutations: 63 prior to policy; 123 post 6 months before and 6 months after introduction of reflex policy Not specified FFPE archival tissue used TATO
Baldotto 2013 Conference abstract Brazil EGFR mutation testing in NSCLC Retrospective study of EGFR testing in one centre after introduction of reflex testing; single centre 189 of 336 screened May May 2013 PCR; Sanger sequencing Cytological samples and tumour tissue; unclear how much was archival TATO Cankovic 2013a, b Conference abstract US EGFR mutation and ALK translocation testing in NSCLC Four phase exercise to streamline process from pre-analytic to reporting phase of molecular testing for EGFR/ALK mutations 111 cases tested Mar 2011-Sept 2012 Not reported Not reported TATO Ellis 2013 Full journal article Canada EGFR mutation testing in advanced NSCLC Prospective validation/QC exercise for implementation of routine EGFR testing strategy in NSCLC involving 5 testing laboratories 2104 test requests Tests requested between Mar 2010-Dec 2010 RT-PCR Blocks or slides; not specified whether testing was on newly acquired, archive tissue or either Test failures TATO RATRS TATRR Arriola 2014 Conference abstract Spain EGFR mutation in advanced NSCLC Retrospective observation study of the management patterns of advanced EGFR mutated NSCLC pts in 181 evaluable patients Patients diagnosed 2010-Dec 2011 RT-PCR Mainly biopsy material TATO
Spain; 8 centres; Testing mainly done in external laboratories Janssens 2014 Full journal article Belgium EGFR mutation testing in NSCLC Data collection from testing of patients in clinical care by two central testing facilities 107 samples tested Not specified Not specified Tissues collected prospectively; not archival tissue Test failures TATO Lim 2015 Full journal article Canada EGFR mutation and ALK rearrangement testing in advanced NSCLC Retrospective chart review of EGFR mutation and ALK rearrangement testing of a random sample of 25% of patients with advanced NSCLC in a single centre 300 cases of which focus was on 258 cases of non-squamous NSCLC of which 126 underwent diagnostic testing at the institution of which 99 testing requests were initiated by the oncologist at the initial consultation (27 cases already had test results available) Referrals from April 2010 – March 2013 EGRM mutation testing by PCR fragment analysis; ALK testing by IHC confirmed by FISH Included testing of archival and new tissue; 27/126 (21%) of results available at first consultation; 99/126 978.65) not available at initial consultation Test failures Cases where repeat biopsies undertaken Cases where rebiopsy provided adequate tissue for analysis TATO Biomarker directed treatment management Fergusson 2009 Conference abstract UK HER2 testing in breast cancer Retrospective observation study of length of time of testing process; single centre (tests undertaken centrally) 49 cases Apr 2006-Apr 2007 Not specified Not specified whether testing was on newly acquired, archive tissue or either TATO
Goom 2012 Conference abstract UK HER2 testing in breast cancer Internal audit of testing timelines in a single testing facility serving 10 hospitals 814 test requests Not specified Not specified Biopsy material (not archival material) TATO Lim 2013 Full journal article US HER2 testing in breast cancer Review of previously testing Single centre 101 selected cases Samples identified in archive between May 2010 – Nov 2011 FISH Archival FFPE tissue TATO Shabaan 2014 Full journal article UK HER2 testing in breast cancer Process mapping from three recognised laboratories Not reported Not reported ICH and FISH Core biopsy and/or resected material; not specified whether testing was on newly acquired, archive tissue or either TAT Steinmetz 2014 Conference abstract US HER2 testing tumour type not specified Multiple phase exercise to streamline process from pre-analytic to reporting; single test lab study Not applicable Not applicable FISH FFPE tissue; Not specified whether testing was on newly acquired, archive tissue or either TATO Butt 2013 Conference abstract UK HER2 testing in tumours Review of previous testing over 2.5 years; single referral laboratory 844 test referrals Not specified F/DDISH FFPE tissue; Not specified whether testing was on newly acquired, Adequacy of sample TATRR i
archive tissue or either Reddy 2010 Conference abstract US Biomarker testing in tumour tissues Review of routine biomarker testing (various including KRAS BRAF and EGRF) in various cancers including CRC, lung and other in a community setting 104 consecutive patients Review undertaken between Aug 2008-Dec 2009 RT-PCR FFPE tissue; Not specified whether testing was on newly acquired, archive tissue or either TATO TATRS Test failures Abbreviations: ALK, anaplastic lymphoma kinase; CRC, colorectal cancer; EGFR, epidermal growth factor receptor; FISH, fluorescence in situ hybridisation; FFPE, formalin-fixed paraffin-embedded; HER2, human epidermal growth factor receptor 2; IHC, immunohistochemistry; KRAS, Kirsten rat sarcoma; mCRC, metastatic colorectal cancer; NSCLC, non-small cell lung cancer; TATo = Overall turnaround time from ordering of test to reporting of test result; includes time of retrieval and review of archival tissue where applicable; TATRS = Time from ordering of test to receipt of sample at test facility, includes time of retrieval and review of archival tissue where applicable TATRR= Time from receipt of sample at test facility to reporting of test result
Table 14 Summary of studies of evaluating gene panel testing of tumours, with a view of treatment management or placing patients into early phase clinical trials Lead author/Year Citation type Country Diagnostic test Context/Study type Date Test method(s) Use of archive tissue Outcomes reported potentially relevant to this submission Tran 2011 Conference abstract Canada Multi-platform molecular profiling in patients with advanced solid tumours Feasibility of prospective molecular profiling of tumours; 5 centre study 15 enrolled patients (14 tested) (preliminary report) Not reported Targeted mutation analysis (Sequenom Mass Array); Targeted exome sequencing; confirmed by Sanger sequencing FFPE and snap frozen; new and archive tissue Test failures TATO TATRR Biopsy failure rate Biopsy adverse events Bedard 2013 Conference abstract Canada Targeted gene testing panel of various advanced solid cancers Trial screening program to match patients with target therapies; Single institution 485 patients Patients enrolled between Mar 2012 – Jan 2013 Next generation sequencing Exclusively testing in archival FFPE tissue Test failures Takahashi 2013 Conference abstract Japan Pan-cancer gene panel screening for advanced solid tumours Feasibility study of multiplex screening; single centre 105 patients Patients enrolled between Jul 2012-Feb 2013 Next generation sequencing FFPE tissues, mainly archive Test failures Biopsy adverse events Re-biopsy rate Yardley 2013 Conference abstract US Cancer gene panel screening in metastatic breast cancer Community based molecular profiling initiative for identifying candidates for targeted therapies 101 samples Samples profiled between Oct 2012 – May 2013 Next generation sequencing Exclusively testing in archival FFPE tissue Test failures Morris 2014 Conference abstract US Cancer gene panel screening Feasibility study of large scale screening in 400 cases Patients enrolled between Aug IHC, gene sequencing, Not specified whether testing was on newly Test failures TATRS
NSCLC considered inadequate for mutation analysis samples Dingemans 2011 Conference abstract Netherlands EGFR and KRAS mutation analysis in NSCLC Retrospective testing of patients with chemo-naive advanced NSCLC treated with a platinum doublet 188 cases where tissue avilable Not reported High resolution melting following sequencing Archival FFPE tissue Test failures Halblass 2011 Conference abstract Germany EGFR, ALK, BRAF and KRAS mutation analysis in NSCLC Part prospective, part retrospective testing of patients 88 patients Not reported Various Reviewed archival FFPE tissue Test failures Subramonia 2012 Conference abstract US EGFR mutation testing in NSCLC Retrospective chart review of patients with NSCLC; single centre; 64 cases Diagnosed during 2010; reviewed 2011 Not applicable Archival tissue On review. adequacy of biopsy samples for potential testing Wu 2014 Conference abstract US EGFR and KRAS mutation testing in NSCLC Method development using previously tested tissue; Single centre 15 samples Not reported Cell enriched transfer; PCR Reviewed archive FFPE tumour tissue Test failures Madrid 2004 Full journal article Philippines HER2-/neu testing in breast cancer Evaluation of CISH assay; single centre study 160 randomly selected HER2+ cases Testing between CISH Archival FFPE primary breast tumour tissue Test failures Penault-Llorca 2008 Full journal article France HER2 testing in breast cancer Retrospective testing of tissues 710 Cases Cases between 1982-2004 Not reported Archival FFPE primary breast Availability of usable sample
Table 16 Summary of studies of genomic panel testing undertaken as part of method development, assessment of test performance or tumour characterisation for research purposes Lead author/Year Citation type Country Diagnostic test Context/Study type Date Test method(s) Use of archive tissue Outcomes reported potentially relevant to this submission Peeters 2010 Conference abstract Mulit-national Multi-cancer gene testing for profiling mCRC Re-examination of clinical trial participants previously tested for KRAS mutations 320 patients Not reported Next generation sequencing; pyrosequncing Archival tumour tissue used Test failures Walthier 2012 Conference abstract US Multi-cancer gene testing for profiling solid tumours Method development and experience of a single testing facility Not applicable Not reported Parallel Taqman array system; pyrosequencing Not specified whether testing was on newly acquired, archive tissue or either Estimated TATO Wagle 2013 Conference abstract US Multi-cancer gene testing in various tumour types Method development; feasibility study Tissues from 15 patients Not reported Whole exome sequencing Archive FFPE tissue, TATRR Hagermann 2015 Full journal article US Targeted sequencing of 23 genes in NSCLC Feasibility study of routine targeted gene profiling; single testing centre 381 consecutive samples Mar 2012-Oct 2013 Next generation sequencing Archival FFPE tissues Test failures TATO Melchior 2015 Full journal article Multi-national; 6 centres BRAF mutation testing in malignant melanoma Evaluation of test performance compared to original assessments made by several routine 148 left over samples Not reported RT-PCR (Idylla) Reviewed archive FFPE tissue Test failures TATRT