Molecular profiling of colorectal cancers

1. Molecular profiling of colorectal cancers Dr Angela Silmon 12th September 2014 Colorectal NSSG Audit Day

2. Outline • Brief introduction to NewGene • Personalised Medicine • Molecular testing in colorectal cancer • Horizon scanning

3. NewGene Ltd Apioneer in developing, validating and delivering molecular diagnostics using the latest high throughput sequencing and genotyping technologies

4. Technology platforms

5. Genotyping • SequenomMassARRAY 4 • MALDI TOF mass spectrometer • Low cost • Rapid turn around • Targeted mutations

6. Sequenom Mass Array 4 PCR Extension reaction Resin MALDI TOF Data analysis Spotting SAP clean Detector F 5’end [C/G] 3’end [G/C] 3’end 5’end R extension into SNP site 5500Da C G Time of flight [C/G] Laser [G/C] 5800Da Allele 1 G 6100Da Allele 2 Sequenom chip C

7. Sequenom Mass Array 4 7000Da 7000Da 7000Da 5500Da Wild type allele only (TT) Wild type and mutant allele present (TC) Mutant allele only (CC)

8. Personalised medicine portfolio

9. Funding * IHC carried out at Cellular Pathology, RVI, FISH test carried out by Cytogenetics

10. Referral pathway Request CDF number T176 Refer for testing incld CDF number Refer for testing Check T176 box Automatic un-registration from CDF Test result Test result Therapy decision Therapy decision CDF number if req Funding: NHS England Funding: CDF

11. Molecular testing in mCRC • Mutation in the RAS genes offer prognostic value with patients with a mutation in the KRAS or NRAS gene having lower overall survival rates compared to wild type • Mutations predict lack of benefit from EGFR targeted therapies such as Cetuximab and Panitumumab • Mutations in codons 12 and 13 of KRAS most common, ~40% of mCRC patients • Mutations in RAS genes found in ~ 50% of patients

12. Association of Clinical Pathologists Molecular Pathology and Diagnostics Group  • Targeted mutations • KRAS codons 12, 13, 59, 61, 117 and 146 • NRAS codons 12, 13, 59 and 61 • Interpretation • Therapy license - wild type RAS genes only • BRAF prognostic indicator but guidelines may change Wong NACS, Gonzalez D, Salto-Tellez M, et al. J ClinPathol2014

13. Association of Clinical Pathologists Molecular Pathology and Diagnostics Group  • Primary or metastatic CRC tissue can be used • Biopsy or resection specimen tissue can be used • The minimum neoplastic cell content tested should be at least two times the assay’s LOD. • Audit • TAT ≤7 working days for >90% of samples • Incident rates • Failure rates Wong NACS, Gonzalez D, Salto-Tellez M, et al. J ClinPathol2014

14. NewGene Audit 2014 • Turn around time • Target 5 working days • Range 2 - 11 days • Average 3.4 days • 90% of reports issued within 5d • Incidence rate • Failure rate • < 1% • EQA • Participation since 2010 • All genotyping maximum marks, no poor performance Jan – June 2014 N = 500

15. Horizon scanning • Require a comprehensive joined up approach to molecular testing • Funding mechanism • Testing mechanism

16. Horizon scanning • OncoFocus • Comprehensive test for actionable mutations • UltraSeek • Circulating tumour DNA • 1% tumour content Gene AA ABL1 T3151 AKT1 E17K ALK F1174L BRAF V600E, V600K, V600R EGFR G719S, T790M, L861Q, E746- A750del FLT 1836del IDH1 R132H IDH2 R140Q, R172K JAK2 V617F KRAS G12A, G12D, G12V, G12C, G12S, G13D NRAS Q61K, Q61R PIK3CA E545K, E542K, H1047R

17. Horizon scanning • Pilot data generation • OncoFocus • UltraSeek • Business case for service delivery • Phase I Clinical trials • Clinical implementation

18. Thank you Contact: Angela.silmon@newgene.org.uk 0191 242 1923 www.newgene.org.uk