UK STRATIFIED MEDICINE PROGRAMME: NGS ANALYSIS AND CHALLENGES OF REPORTING. Dr. Alessandro Rettino West Midlands Regional Genetics Laboratory

Transcription

1 UK STRATIFIED MEDICINE PROGRAMME: NGS ANALYSIS AND CHALLENGES OF REPORTING Dr. Alessandro Rettino West Midlands Regional Genetics Laboratory

2 Overview CRUK Stratified Medicine Programme phase 1 and 2 CRUK Stratified Medicine Programme 2 (SMP2) NGS panel and data analysis Reporting for SMP2

3 Next Generation Sequencing (NGS) Progress Limited access due to costs Informatics bottleneck Informative reporting SMP1 SMP2

4 The CRUK Stratified Medicine Programme was designed to demonstrate how cancer gene testing can be done on a large scale Central data repository (ECRiC) Research infrastructure Service delivery component

5 The Programme Network : 3 technology hubs, 8 clinical hubs and 26 feeder hospitals Stratified Medicine Programme Cardiff Birmingham RMH Cardiff Manchester Glasgow Birmingham Edinburgh Cambridge RMH Leeds University Hospital of Wales The Christie Royal Infirmary University Hospital Western General Addenbrooke's Marsden St. James's Morriston Wythenshawe Western Infirmary City Royal Infirmary Papworth Royal Brompton General Infirmary Singleton Royal Gwent Velindre Salford Royal Pennine Acute Southern General Golden Jubilee Gartnavel Victoria Infirmary Infrastructure versus population density Technology Hubs Clinical Hubs Feeder Hospitals Stobhill Hospital

6 SMP2 : the NGS panel CR-UK NGS Panel 2 Nextera hybridisation 28 genes Developed and validated in partnership with Illumina A technology transfer to the TH ensures consistency between the laboratories Panel linked to Matrix Trial AKT1 ALK BRAF CCND1 CCND2 CCND3 CCNE1 CDK2 Validated test sensitivity set at 10% for SNVs and indel CDK4 CDKN2A EGFR FGFR2 FGFR3 Her2* HRAS KRAS MET NF1 NRAS NTRK1 The use of matched blood sample eliminates germline variants. PIK3CA PTEN RB1 RET ROS1 STK11 TSC1 TSC2

7 SMP2 : the NGS analysis CR-UK NGS Panel 2 Bioinformatics CR-UK NGS Panel 2 Variant Classification Streamlined bespoke bioinformatic pipeline List of molecular aberrations by pharmaceutical partners Detects SNVs, insertions/deletions, CNV, translocations Split into 3 tiers to help variant prioritization Use of commercially available (Illumina Variant Studio) and Open source tools (Manta) Tier 1= trial eligible Tier 2= trial eligible Tier 3= not trial eligible

8 Wild type confidence score For trial eligibility the wild type status of a gene is critical A scoring system has been developed to allow us to be confident that in a given tumour sample no variants above a 10% frequency have been missed. This considers; Sequencing coverage across the region of interest Tumour % of sample

9 Read depth 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/ % 1% 1/ % 2% 1/ % 4% 1/ % 5% 1/ % 10% 1/ Relationship between tumour content and coverage Tumour % information critical for analysis Really important to define this to the nearest 10%. Gene is passed or failed based on criteria below Relationship between tumour %, test sensitivity and NGS read depth Tumour %

10 Sample analysis summary

11 XML Report

12 Summary The programme is a robust National effort across the entire CRUK ECMC network and beyond NGS analysis process is constantly being optimised to deliver informative reporting to the clinicians SMP2 takes us another step along the pathway to true precision medicine

13 THANK YOU CRUK SMP2 Technology Hubs Birmingham- Mike Griffiths, Jennie Bell, Pauline Rehal, Alessandro Rettino, Matt Smith, Sam Clokie Cardiff- Rachel Butler, Ian Williams, Michelle Wood, Helen Roberts RMH- David Gonzalez de Castro, Keeda Dover, Brian Walker Illumina David McBride and Mark Ross