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

Molecular profiling of colorectal cancers

Dr Angela Silmon12th September 2014

Colorectal NSSG Audit Day

Outline

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

NewGene Ltd

A pioneer in developing, validating and delivering molecular diagnostics using the

latest high throughput sequencing and genotyping technologies

Technology platforms

Genotyping

• Sequenom MassARRAY 4– MALDI TOF mass spectrometer– Low cost– Rapid turn around– Targeted mutations

F

R

5’end

3’end

[C/G]

[G/C]3’end

5’end

[C/G]

[G/C]

extension into SNP site5500DaC

5800Da

G6100Da

G

C

Allele 1

Allele 2

PCR SAP clean

Extension reaction Resin Spotting MALDI TOF Data

analysis

Laser

Detector

Time of flight

Sequenom chip

Sequenom Mass Array 4

Sequenom Mass Array 4

5500Da 7000Da 7000Da 7000Da

Wild type allele only (TT)

Mutant allele only (CC)Wild type and mutant allele present (TC)

Personalised medicine portfolio

Gene Mutations

Non-small cell lung cancer

EGFR 17 point mutations Indels exon 19 and 20Inclds T790M

Metastatic colorectal cancer

KRAS, BRAF, NRAS 23 mutations in each RAS geneInclds BRAF V600E

Melanoma BRAF

GIST cKIT, PDGFRA Two step process

FundingGene Mutations

Non-small cell lung cancer

EGFR Astra Zeneca until Oct 2010CCGs

ALK* Pfizer2015, likely change

Metastatic colorectal cancer

KRAS, BRAF, NRAS Merck Serono until May 2014 NHS England

Melanoma BRAF Roche2015, TBD

GIST cKIT, PDGFRA Referring Trust

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

Referral pathway

Request CDF number

Refer for testing incld CDF number

Automatic un-registration from CDF

Test result

Therapy decisionCDF number if req

T176

Refer for testingCheck T176 box

Test result

Therapy decision

Funding: CDF

Funding: NHS England

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

• 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

Association of Clinical Pathologists Molecular Pathology and Diagnostics Group

Wong NACS, Gonzalez D, Salto-Tellez M, et al. J Clin Pathol 2014

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 Clin Pathol 2014

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

Wild type samples 42%Mutation positive samples 58%Gene NewGene Reported

KRAS 42.7% 40%

NRAS 6% 5%

BRAF 9.3% 10%

Jan – June 2014N = 500

Horizon scanning

• Require a comprehensive joined up approach to molecular testing– Funding mechanism– Testing mechanism

Gene Horizon

Non-small cell lung cancer

EGFR KRAS

Metastatic colorectal cancer

KRAS, BRAF, NRAS

Melanoma BRAF NRAS

Horizon scanning

• OncoFocus– Comprehensive test for actionable mutations

• UltraSeek– Circulating tumour DNA– 1% tumour content

Gene AAABL1 T3151AKT1 E17KALK F1174LBRAF V600E, V600K, V600REGFR G719S, T790M, L861Q, E746- A750delFLT 1836delIDH1 R132HIDH2 R140Q, R172KJAK2 V617FKRAS G12A, G12D, G12V, G12C, G12S, G13DNRAS Q61K, Q61RPIK3CA E545K, E542K, H1047R

Horizon scanning

• Pilot data generation– OncoFocus– UltraSeek– Business case for service delivery– Phase I Clinical trials– Clinical implementation

Thank you

Contact: [email protected]

0191 242 1923www.newgene.org.uk