Presentation on theme: "“Molecular Pathology past present & future”"— Presentation transcript:
1 “Molecular Pathology past present & future” Thomas KerrPrincipal Healthcare ScientistMolecular PathologyPathology DepartmentSouthern General Hospital
2 “Molecular Pathology past present & future” Thomas KerrPrincipal Healthcare ScientistMolecular DiagnosticsGeneticsSouthern General Hospital
3 Molecular Pathology ?The discipline involved in diagnostic, prognostic and predictive testing on samples (usually tumour) removed from the patient in the course of investigation and treatment of disease.
24 MGMT promoter status – clinical relevance valuable for patient counsellinguseful in deciding intensity of treatmentcan be used clinically to select patients likely to benefit from adjuvant temazolomide treatment.can potentially save half of patients from receiving chemotherapy.
26 Predictive & Prognostic markers in Neuro-oncology Molecular assays introduced to aid typing & grading of gliomasImproved understanding of these tumours at molecular levelEspecially presence/absence of combined 1p19q loss in oligodendroglial tumours, MGMT promoter gene methylation in glioblastoma, EGFR amplification in grade III astrocytic tumours & glioblastoma & IDH mutation analysisNow being used to tailor treatment decisions in patients, current therapy combination of surgery, radiotherapy & chemotherapy
27 49F frontal60F temp/parietal1p19qThree case reviews to follow.
28 Molecular Haematology 2008 Microsatellites for Chimaerism testing in post-BMT patientsBCRABL (t9;22)PMLRARA (t15;17) in AMLAML/ETO (t8;21) in AMLChromosome 16 inversion in AMLJAK 2 status in myeloproliferative diseasesFLT3 mutations
30 Purpose of Chimaerism testing post BMT To detect an identifiable difference between a patient and their donorAbility to measure the proportion of donor present in the blood or bone marrow post transplantFiona M Reid April 2011
31 Identification of chimaerism Microsatellites: Short Tandem RepeatsPrepare DNA from blood or marrowPCRA number of primer sets in useMust identify an “informative “ set of primers
35 Microsatellites Full donor Chimaerism Fiona M Reid April 2011
36 Microsatellites Mixed Chimaerism Fiona M Reid April 2011
37 The Calman review of genetics in relation to healthcare in Scotland Recommendations from the molecular pathology review group on the future of molecular pathology testing in Scotland. (2010)The Calman review of genetics in relation to healthcare in ScotlandBetter health better care action planBetter cancer care action planClinical trialsSPAN & Scottish cancer group networked approach to HER2 FISH testing37
38 Conclusions & recommendations A molecular pathology service should be developed and run as a NSD supported consortium, mirroring the Scottish genetics laboratory consortium for diagnosis of constitutional genetic abnormalities.To ensure the stability of the services, equity of access and service developmentLinked to the Scottish cancer taskforce, cancer networks and Scottish medicines consortium so that there is early coordinated planning for new testing.
41 Therapeutic monoclonal antibodies Target specific antigens on proteins-extracellular growth factors eg transmembrane receptorsMonoclonal antibodies end with the stem “mab” e.g. cetuximab which targets EGFR
42 Small moleculesPenetrate the cell membrane to interact with targets inside a cellInterfere with the enzymatic activity of the target proteinEnd with the stem “ib”, the agent has inhibitory properties e.g. imatinib in CML
43 Cost Targeted therapies £20000 per patient per year Molecular test EGFR £50
44 Current Treatment is the Same for Most Patients Outcomes can vary widely =PatientsTreatment+DiseaseDifferentoutcomes=Current treatment generally uses a ‘one size fits all’ approach. However, while a drug may be highly effective in one patient, it may have little or no response in another. Similarly, a drug may be well tolerated or cause severe or even life-threatening side effects depending on the individual.Different treatment outcomes affect patients’ safety, survival and quality of life44
45 The Alternative: Personalized Healthcare (PHC) Tailors treatment to the patient Personalized healthcare is a tailored approach to treatment based on the fact that people are different. Among patients with the same diagnosis, variations in response to treatment can be associated with differences in genetic make-up and/or the molecular nature of their disease.Personalized healthcare involves stratifying patients into subgroups, based on these differences, enabling the most appropriate known treatment for that subgroup to be chosen.At least in the foreseeable future, personalized healthcare does not mean developing a unique drug for every patient; rather, rational and optimal use of treatment options.Molecular diagnostic testing can stratify patients according to their specific genetic makeup and/or the nature of their disease or conditionThis approach improves drug safety, may increase patient survival, and may improve quality of life45
46 Personalized Healthcare Provides benefits for all stakeholders PatientHealthcare providerPayerPersonalized healthcare has potentially far-reaching benefits for all members of the healthcare system.For patients, quality of care can be improved by selecting the treatment most likely to be effective and minimizing their exposure to adverse effects.For healthcare professionals, the insight provided through diagnostic tests enables more informed treatment decisions to be made. With personalized healthcare, treatment can be administered with more confidence, ‘trial and error’ prescribing is reduced, and the risk of causing adverse effects is minimized.Personalized healthcare also has the potential to benefit payers by supporting efficient utilization of healthcare budgets and resources. Cost savings may be made by using expensive therapies for targeted patient groups, minimizing costly adverse events, and potentially reducing long-term expenditure on treating progressive disease.Improved benefit to risk ratioInformed treatment decisionsEfficient use of healthcare budgets46
47 Near to mid-term genomics and oncology portfolio Platform consolidation; Pharma driven focus on oncologyRMD is committed to expanding the oncology menu in order to remain competitive in the oncology IVD market.
48 Current Cobas® Oncology Portfolio Clinically validated biomarker tests on one platform DiseaseTherapeutic ClassDrug(s)cobas® BRAF Mutation TestMetastatic MelanomaBRAF InhibitorsRG7204 (PLX 4032), Zelborafcobas® KRAS Mutation TestColorectal CancerAnti-EGFR MonoclonalAntibodies (mAb)Anti-EGFR mAbTherapies, cetuximab, panitumumabcobas® EGFR Mutation TestNon-Small Cell Lung Cancer (NSCLC)Anti-EGFR Tyrosine Kinase InhibitorsErlotinib, GefitinibSpeaker NotesRoche has a growing pipeline of oncology assays in development that are being developed on the cobas 4800 system.The most advanced of these programs are the BRAF, KRAS and EGFR mutation detection tests.BRAF V600 mutation assay is being developed in conjunction with the RG7204 (vemurafenib) BRAF inhibitor in metastatic melanoma.KRAS mutations are associated with lack of response to anti-EGFR mAb therapies.EGFR mutations are associated with better response to Tyrosine Kinase Inhibitors (TKIs), Tarceva (Roche) and Iressa (AstraZeneca).PIK3CA mutation assay is being developed in conjunction with the Genentech PI3K inhibitor that is currently in phase 1.The P53 resequencing assay is an Amplichip test being developed on the Affymetrix platform.
49 cobas® 4800 Oncology Tests Workflow Overview cobas® 4800 BRAF V600 Mutation Test:The need for macrodissection must be determined prior to deparaffinization. For each specimen, a pathologist will perform a microscopic assessment of an H&E stained slide and will document the percent tumor cell content. The middle section from a series of slides should be used for the H&E staining. If the percent tumor content is greater than 25%, macrodissection is not required. If the percent tumor content is less than 25%, the section used for DNA Isolation should be macrodissected beforehand.H&E stain, HE stain or hematoxylin and eosin stain, is a popular staining method in histology. It is the most widely used stain in medical diagnosis; for example when a pathologist looks at a biopsy of a suspected cancer, the histological section is likely to be stained with H&E and termed H&E section, H+E section, or HE section.The staining method involves application of hemalum, which is a complex formed from aluminium ions and oxidized haematoxylin. This colors nuclei of cells (and a few other objects, such as keratohyalin granules) blue. The nuclear staining is followed by counterstaining with an aqueous or alcoholic solution of eosin Y, which colors eosinophilic other structures in various shades of red, pink and orange.
50 197,000 people worldwide are diagnosed with melanoma each year Melanoma ProgressionMelanoma is the most aggressive form of skin cancer originating in the melanocytes.197,000 people worldwide are diagnosed with melanoma each year
51 BRAF Mutation Test Designed to identify metastatic melanoma patients who may benefit from BRAF inhibitorsThe cobas®4800 BRAF V600 Mutation TestIs designed to determine mutation status of the BRAF geneIs the companion diagnostic used in the clinical trials for RG7204 (also known as PLX4032), an oral inhibitor of mutated BRAF co-developed by Roche Pharmaceuticals and Plexxikon. BRIM2 +3 clinical trials (>2,000 patients)~ Roche kit is the ONLY clinically validated kit.RG7204 has shown strong clinical activity in metastatic melanomas harboring the BRAF V600E mutation; clinical data suggests that patients with wild-type BRAF do not respond or respond adversely.Not all patients with metastatic melanoma respond to BRAF inhibitors.1The cobas® 4800 BRAF V600 Mutation Test* is designed to determine the BRAF mutation status of patients. Used in conjunction with other clinical data, this information can help physicians select the best treatment options for an individual patient.1. Flaherty KT, Puzanov I, Kim KB, et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med 2010; 363:* Product in development51
53 Colorectal Cancer Progression Incidence in the UK: ~70 cases per 100,000>95% of colorectal cancers arise from the glandular epithelium that lines the gut (adenocarcinomas)
54 cobas® KRAS Mutation Test Designed to help identify colorectal patients who are unlikely to benefit from anti-EGFR mAb therapiescobas® KRAS Mutation Test:Is designed to determine mutation status of the KRAS oncogeneColorectal cancer tumors with KRAS mutations are unresponsive to anti-EGFR therapies1When combined with other clinical data, this information will help physicians identify colorectal cancer patients who may not benefit from anti-EGFR mAb therapies1. Amado et al. J Clin Oncol 2009;26:16261634
55 cobas® KRAS Mutation Test Designed to help identify colorectal patients who are unlikely to benefit from anti-EGFR mAb therapiescobas® KRAS Mutation Test:Is designed to determine mutation status of the KRAS oncogeneColorectal cancer tumors with KRAS mutations are unresponsive to anti-EGFR therapies1When combined with other clinical data, this information will help physicians identify colorectal cancer patients who may not benefit from anti-EGFR mAb therapies1. Amado et al. J Clin Oncol 2009;26:16261634
56 Non-small cell lung cancer Overview Lung cancer is the most frequently diagnosed cancer and the leading cause of cancer-related deaths worldwide: ~106,000 new cases of advanced lung cancer per year in the UK, France, Spain, Italy and Germany combined.NSCLC is the most prevalent and accounts for approximately 85% of all cases.Prognosis for patients with NSCLC is poor with a 5-year survival rate of only 15%.
57 Non-small Cell Lung Cancer Therapy Options - Overview Treatment of cancer is guided by disease stage:early stages: primary treatment is surgical resectionlocally advanced or metastatic disease:platinum-based chemotherapytargeted therapyanti-EGFR (cetuximab, panitumumab)tyrosine kinase inhibitors: erlotinib (Roche Tarceva® and gefitinib (AstraZenaca Iressa®)anti-VEGF (Roche Avastin®)
58 Non-small Cell Lung Cancer Role of EGFR EGFR is a receptor tyrosine kinase located on the cell surface of epithelial cells.EGFR is linked to several signaling pathways including the RAS/MAPK pathway and the PI3K/Akt pathway.In normal cells, these pathways are tightly regulated and are activated only when a specific ligand (such EGF) binds to the receptor.In cancer cells, EGFR gene mutations activate the kinase in the absence of a ligand leading to abnormal cell proliferation and tumor formation.
59 cobas® EGFR Mutation Test Designed to help identify NSCLC patients who may benefit from anti-EGFR TKI therapycobas® EGFR Mutation Test:Is designed to detect mutations in the EGFR gene in NSCLC tumor tissueTest results will help physicians identify NSCLC patients who may benefit from anti- EGFR tyrosine kinase inhibitor therapy
60 Next Generation Sequencing High throughput, low cost (?) sequencing technologyHuman Genome Project started in 1990 and took 13 years to completeIt was an international collaboration which cost $3 billion and used traditional Sanger sequencingToday you could sequencing the human genome in ~month using NGSTarget is the $1000 genome
61 Next Generation Sequencing Many NGS techniques, chemistries and instruments now availablePersonal genome machines (PGMs) are affordable bench-top instruments e.g. Ion TorrentNGS allows you to look at many genes or regions of the genome, from many patients, simultaneouslyNGS has multiple applications and will replace many of the molecular tests currently available in the lab
64 Ion Torrent Personal Genome Machine Bench-top NGS instrument from Life Technologies.Purchase the Comprehensive Cancer Panel from Life Technologies which targets exons within 409 oncogenes and tumour suppressor genes.Requires 10ng of input DNA from FFPE tissue.Produces amplicons of between bp and has 16,000 primers in 4 tubes.From DNA extraction to results is less than 24 hours, and the laboratory process is almost fully automated
65 The future: bigger and better What is bigger and better?Bigger is looking at more genes, better is improving the patients diagnosis and treatment in doing soHow do we do bigger and better?By sequencing the entire exome, every single base of each coding exon in the genomeIn the future it will be cheaper and easier to sequence the whole exome for every patient