essay 1 plan Flashcards
Plan
Current genetic testing for diagnosis and management of lung cancer what changes in the next 5 years
• Poor prognosis (median survival = 1 year)
• Standard chemo only adds 2 months to survival, better to sub-group patients according to who will respond better to treatment
• Last decade a great advance is concept of personalised medicine in lung cancer – where therapeutic decisions are made on basis of histological and genetic characterisitics of tumour content
• Two types of lung cancer – small cell and non-small cell (NSCLC)(majority of patients (85%) have NSCLC)
• Genetic testing informs diagnosis, prognosis, and treatment options
• MG testing focuses on identifying patients where TKIs would be effective – TKI treatment slows or stops cancer growth by blocking chemical messengers that promote cell growth and division
• NICE recommends that 1st and 2nd generation EGFR TKIs for NSCLC patients with EGFR sensitising mutations, 3rd generation EGFR TKIs for locally advanced or metastatic NSCLC patients with an EGFR T790M mutations
• NSCLC patients are often also tested for ALK or POS1 rearrangements – if they have it then can be treated with targeted inhibitor crizotinib
• Currently offer MG testing to identify genetic base to stratify patients according to what will be most effective treatment for their condition (i.e. clinical trial for novel drug, antibody therapy, chemo or small molecular therapy)
• EGFR mutations and ALK rearrangements are effective targets for EGFR TKIs or ALK inhibitors
• Testing currently look for EGFR positive (response to antibody therapy), ALK positive (response to small molecular therapy)
• EGFR pathway
o Overexpressed or mutated in multiple lung tumours
o Have developed monoclonal antibodies that bind to extracellular portion of the EGFR receptor to block activation
o Treatment is expensive and has side effects
o Also have TKIs for this pathway
o EGRF signals through RAS/BRF pathway which causes proliferation and inhibits apoptosis
o 65% of all lung cancers express EGFR
• 35% of cases have up regulation of EGFR (so more WT receptors on surface, antibody treatment good here)
• 15% of cases have EGFR activating mutations in the TK domain of the receptor (so TKIs can block these, and patients then live longer)
• 20% have KRAS mutations (downstream of EGFR signalling)
• 65% have PTEN mutationa
• Technical considerations
o Germline or somatic testing
o Access to suitable tumour tissue – invasive, and often can’t get repeat
o Quality of RNA/DNA (cancer cells often poorer quality)
• Fresh or fixed? Histo often want fixed to look at intact cells, but this interferes with MG testing – longer tissue in fix more crosslinking and therefore more DNA damage
o Tumour enrichment
o Sensitivity of assay (% of tumour cells needed to be detected – critical point!)
o Scope of assay (single or multiple mutations or genes detected?)
o Reliability of assay
o Access to relevant equipment or staff
Due to high background of germline sequence, you need to enrich sample for tumour cells (either through selecting these from solid tumour, or use COLD-PCR o PCR cloning o increase mutant levels)
Wales currently do NSCLC multi gene NGS panel for all solid tumour samples from NSCLC patients – targets ‘hot spot’ regions within 9 genes – EGFR (exons 18 -21), BRAF, CDKN2A, ERBB2, KRAS, NRAS, PIK3CA, PTEN, RET. Then do FISH to look for ALK and ROS1 rearrangents
Bristol test EGFR, ALK, BRAF, KRAS, PIK3CA and ERBB2 mutation analysis for NSCLC patients. They do solid tumouor NGS panel hotspots of EGFR, BRAF, PIK3CA, KRAS, ERBB2. Detects min 5% AF, on background of WT. Then also do ALK FISH – breakapart probe to detect rearranegements of 2p23 (ALK). Accept paraffin embedded tumour tissue. 14 days TAT.
o EGFR – 10% have mutation for TKI
o ALK – found in 5% - get TKIs, IHC for expression and then FISH is used to confirm/clarify positive results
o BRAF – found in 4%, p.(Val600Glu) (V600E) is most common – and these ccould get BFRAK and MEK inhibitors
o KRAS – 15-25% of NSCLC patients, poorer prognosis, don’t overlap wth EGFR, ALK or ROS1
o PIK3CA – 1%, this is an inclusion criteria for some trials
o ERBB2 (HER2) – up to 4%, most common is insertion in exon 20 – clinical trials for anti-HER2 drug with this insertion of ERBB2 mutation
Future plans
o Heading more towards tumour burden of mutations
o Evidence to suggest that simply knowing how many mutations a tumour carries is the best guide to how well it will respond to immunotherapy
o Also expect larger panels to be tested as more drugs targets/gene associations come to light
o Panels will increase up to a point, and then there will be a tipping point when WGS becomes more economical and fully validated
o Defining causal drivers from benign passengers is critical, as well as identifying global patterns of mutations ‘signatures’ that provide information to clinicians
o Fast track cancer samples – to get high quality seq including mutational signatures and mutational burden
o Return a report that includes SNV, SV and CNV analysis, with actional results which give patients access to clinical trials
https://medicine.exeter.ac.uk/media/universityofexeter/medicalschool/cpdevents/exeterexpertseries-gastroenterologygenomics/Personalising_cancer_therapy_using_genome_sequencing_Yvonne_Wallis.pdf
