1 Multi-drug, genetic-marker-directed, non-comparative, multi-centre, multi-arm phase II trial in non-small cell lung cancer Sponsor: University of Birmingham Chief Investigator: Gary Middleton Chief Biostatistician: Lucinda Billingham Lead Investigators: Sanjay Popat, Timothy Yap, Yvonne Summers, James Spicer Trial Management Team at CRCTU: Laura Llewellyn, Dee Wherton, Susannah Brown, Kate Davies, Maria Sharif, Peter Fletcher, Ylenia Vigo, Ian Nutt SMP2 Team at Cancer Research UK: led by Rowena Sharpe and Catrin Middleton Trial Management Group: chaired by Sanjay Popat Trial Steering Committee: chaired by Richard Kaplan Current Pharma partners: AstraZeneca, Pfizer Contact: [email protected]Website: www.birmingham.ac.uk/lungmatrix
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Multi-drug, genetic-marker-directed, non-comparative, multi-centre, multi-arm phase II trial in non-small cell lung cancer
Sponsor: University of Birmingham
Chief Investigator: Gary Middleton
Chief Biostatistician: Lucinda Billingham
Lead Investigators: Sanjay Popat, Timothy Yap, Yvonne Summers, James Spicer
Trial Management Team at CRCTU: Laura Llewellyn, Dee Wherton, Susannah Brown,
Kate Davies, Maria Sharif, Peter Fletcher, Ylenia Vigo, Ian Nutt
SMP2 Team at Cancer Research UK: led by Rowena Sharpe and Catrin Middleton
Trial Management Group: chaired by Sanjay Popat
Trial Steering Committee: chaired by Richard Kaplan
• The question – how many slices of the molecular pie are there in non-small cell lung cancer (NSCLC)?
• Overarching design – adaptive umbrella for economies of scale
• Endpoints – big hitters versus small fry
• An embedded programme – integration of SMP2 with standard NHS practice and making do with what we have
What we wanted to achieve, and how we have
tried to achieve it
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Single test that requires less DNA, analyses more genes, all types of mutational events, better quality result
– Developed in partnership with Illumina
– Panel linked to National Lung Matrix Trial
– Increased gene spectrum
– Increased mutation spectrum
AKT1 ALK BRAF CCND1
CCND2 CCND3 CCNE1 CDK2
CDK4 CDKN2A EGFR FGFR2
FGFR3 Her2* HRAS KRAS
MET NF1 NRAS NTRK1
PIK3CA PTEN RB1 RET
ROS1 STK11 TSC1 TSC2
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Recruiting Sites
• The National Lung Matrix Trial (NLMT) is being run through all 18 UK Experimental Cancer Medicine Centres (ECMC) with each participating centre operating a hub and spoke model with patients being referred in from nearby hospitals (feeder sites) to the centre.
• Each centre is linked with one of the 3 Technology Hubs (TH).
• 10 additional centres have been approved for inclusion in areas of the UK with large populations of lung cancer patients not currently represented in the trial.
How actionability is called – the tiering algorithm
Carr TH et al. Nature Reviews Cancer 16, 319–329 (2016)
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• Arm F (AZD5363): PIK3CA, PTEN and AKT aberrations:
• No concomitant KRAS mutations or gene failures
• Davies BR et al. Mol Cancer Ther 2012;11:873-887
• Arm C (palbociclib) cohorts:
• Proven Rb proficiency is required (no gene failures or aberrations)
• Cohort C6 (palbociclib: KRAS mutation)
• Rb Proficient and no activation of PI3K/AKT/MTOR signaling (no concomitant STK11/LKB1, PIK3CA, PTEN, AKT, EGFR, FGFR, TSC1/2 or HER2 aberrations)
Puyol M et al. Cancer Cell, 2010; 18: 63 – 73
Kennedy AL et al Mol Cell. Apr 8, 2011; 42(1): 36–49
Molecular Exclusion Rules – Enhancing the
Likelihood of Clinical Success by Attention to
the pre-Clinical data
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Ensuring Genes are Wildtype Tumour
%
Variant present at 10% frequency –
what % of reads would be mutant
Mutant
reads
10 mutant reads minimum so minimum read
depth required is
5% 0.5% 1/200 2000
10% 1% 1/100 1000
20% 2% 1/50 500
40% 4% 1/25 250
50% 5% 1/20 200
100% 10% 1/10 100 Tumour % information critical for analysis
Really important to define this to the nearest 10%.
Coverage calculator works out % of bases within gene covered to the depth required
Gene is passed or failed based on criteria below
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Statistical Design The aim of the trial is to determine whether there is sufficient signal of activity in any drug-biomarker combination to warrant further investigation. A Bayesian adaptive design that gives a more realistic approach to decision-making, and flexibility to make conclusions without fixing the sample size, was chosen. Target recruitment in each drug-biomarker cohort is 30 patients with interim analysis at 15.
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• >2400 patients with 1+ samples have now been sent for testing through SMP2
• 31% of SMP2 patients were molecularly eligible for NLMT Arms A-G (Arm G
only until 14th December 2016)
• 5.4% of SMP2 patients were recruited to NLMT Arms A-G (Arm G only until 14th
December 2016)
• SMP2 QC failure rate has reduced from 35% in 2015 to 15% in 2016 to 7% in Q1 2017
• SMP2 gene failure rate has reduced from 38% in 2015 to 33% in 2016
• Median Technology Hub Turnaround time is in 20 working days Q1 2017
Stratified Medicine Programme 2
(SMP2) at a Glance
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SMP2 Patient Attrition – 2015 vs 2016
35% of results reported = patients molecularly eligible for an open MATRIX (Arms A-G) 57% of results reported = patients molecularly eligible for an open MATRIX (Arms A-NA)
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SMP2 Results Analysis – all samples
(2015 vs 2016)
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Monthly SMP2 Testing Figures Month
Number of samples tested on the NGS
panel (includes NGS fail (6%), NGS pass
and NGS partial pass) – excludes QC fail.
Taken from TH KPIs.
Month
Number of samples tested on the NGS
panel (includes NGS fail (6%), NGS pass
and NGS partial pass) – excludes QC fail.
Taken from TH KPIs.
Jan-15 5 Jan-16 107
Feb-15 0 Feb-16 127
Mar-15 26 Mar-16 126
Apr-15 86 Apr-16 85
May-15 104 May-16 47
Jun-15 107 Jun-16 91
Jul-15 83 Jul-16 115
Aug-15 66 Aug-16 99
Sep-15 80 Sep-16 79
Oct-15 74 Oct-16 84
Nov-15 62 Nov-16 89
Dec-15 73 Dec-16 91
Total 2015 766 (64/month) Total 2016 1140 (95/month)
Excludes QC fails (15% in 2016) and samples with insufficient tissue to send to TH (39/97 samples at UHB in 2016)
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• A not insignificant problem due to the stringent requirements for calling wildtype.
Why were they occurring?
• Large regions of interest
• Extremes in GC content
• Low tumour content of samples
• Poor quality of tissue and DNA
What was done about it?
• Addition of probes to failing genes/exons
• Revision of gene coverage
• Pre-analytical steps & Sample processing steps – fixation time, reverse cross-linking temperature
Gene Failures
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Molecularly Eligible Results Released
per Month (Jan 2015 – Mar 2017 inclusive; Arms a-G up to Dec 2016, Arms A-F thereafter)
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Patients Molecularly Eligible for NLMT (Jan2015 – Mar 2017 inclusive; Arms A-G up to Dec 2016, Arms A-F thereafter)
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Birmingham transition data on 92 molecularly eligible patients:
• 3 lost to follow-up
• 19 enrolled onto the NLMT (21%), 1 in screening, 4 failed eligibility - 26% (21% of 28% = 6%)
• 28% not at 2L time-point (on first line, in remission, indolent disease or subsequent radical Rx)
• 43% not fit for 2L (or for 1L), progressed on 1L with poor PS or rapid PD after 1L (19) or brain mets (6)
2L attrition is the awful reality of advanced NSCLC – recruit at SD on 1L, particularly in an immunotherapy era
Why if 28% patients are molecularly eligible,
are only 6% being recruited?
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Cumulative & Monthly NLMT Recruitment [28% OF 1340 WITH 21% transition = 7/month]
• n=2000 screened with 23% fail due to inadequate DNA quality/quantity
• 39% potentially actionable in genotype matched trials 11% of these entered (4% total)
How does National Lung Matrix Trial compare?
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• SAFIR01 (Lancet Oncol, 2014)
• WG CGH and Sanger PIK3CA and AKT – 67% and 70% respectively low % cancer cells
• Not dependent on time of testing or volume
• 46% targetable
• 13% targeted therapy (=28% targetable group)
• 9% response rate with 21% SD>16/52
How does this compare with frozen?
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• Incorporation of 2 new treatment arms into protocol for 2 molecular cohorts (already on the NGS panel - an NTRK inhibitor and a BRAF inhibitor), both provided by a new pharmaceutical partner.
• An additional 2 treatment arms from another pharmaceutical partner for new molecular cohorts (RET, Ch4 12q amplifications, CBL mutation) and a further no-actionable genetic change cohort.
• 3 of these arms should open to recruitment before the end of 2017.
• Discussions are currently ongoing regarding further new arms to be submitted for funding consideration.
New Arms
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• Predictive biomarkers from tissue and ctDNA
• Resistance mechanisms from ctDNA and PDX
• Integrating the SMP-2 data with NHSE – molecular prognostication and SOC prediction
Translational and Other Outputs
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Trial Milestones Year Milestone
2017 August: Interim analyses of first 2 cohorts to reach n=15 July: Major improvements to trial website www.birmingham.ac,uk/lungmatrix June: 150th patient recruited & funding approved for 2 new cohorts February: 4th Trial Steering Committee (TSC) Interim analysis & funding approved for 2 new cohorts
2016 November: 100th patient recruited September: 3rd TSC Interim analysis June: Approval for funding for further 2 years & 2 new arms from CRUK March: 50th patient recruited February: 2nd TSC Interim analysis
2015 October: Arm F & G opened to recruitment September: 1st TSC interim analysis May: First patient recruited March: Central R&D approval and first site opened
2014 December: MHRA approval received November: Ethics approval received October: Protocol Version 1 submitted for regulatory approval August: Grant Activation Date
2013 September: Initial approval for CRUK Clinical Trials Unit at Birmingham to run the NLMT with Prof Middleton as the Chief Investigator & Prof Billingham as Lead Statistician