Sanger sequencing in molecular pathology and genetics

Transcription

1 Thermo Fisher Scientific: Corporate Satellite Meetings Room Ballerup, Sunday, May 28, 11:15 12:45 hrs Sanger sequencing in molecular pathology and genetics Dr Luca Quagliata - Senior Director Contract R&D and Strategic Partnership Unit Institute For Medical Genetics and Pathology University Hospital of Basel

2 LQ Disclosure The data presented here represent a solely property of the author and his institution. The idea and concepts proposed are based on his experience and are not influenced by any means by Thermo Fisher Scientific. Thermo has agreed to cover travel and accommodation expenses to LQ. LQ has received no honorarium for this presentations.

3 Our Working Frame Why do we need high tech instruments to support our work Thermo Fisher Scientific: Corporate Satellite Meetings Room Ballerup, Sunday, May 28, 11:15 12:45 hrs

4 Living in the Personalized Medicine Era The concept in nutshell Non Molecular Diagnostic Lars Grimm, MD, MHS December 22, 2015, Medscape DNA/RNA extraction Defining the landscape mutations Targeted therapy Sample collection Matching clinical information Tissue or Blood Molecular Profiling Diagnosis or/and Choice of therapy

5 Living In The Personalized Medicine Era The concept in nutshell DRUG TARGET MANUFACTURER Imaging suspect Lars Grimm, MD, MHS December 22, 2015, Medscape Tumor Biopsy Traditional histology based classification DNA/RNA extraction Molecular Tumor Profiling Defining the landscape tumor mutations Erlotinib (Tarceva) EGFR Roche Dacomitinib/PF EGFR Pfizer Gefitinib (Iressa) EGFR AstraZeneca Afatinib (Gilotrif) EGFR Boehringer Ingelheim Rociletinib/CO-1686 EGFR T790M Clovis Targeted therapy AZD9291 EGFR T790M AstraZeneca Icotinib EGFR Beta Pharma, Inc Necitumumab/IMC-11F8 EGFR (Mab) Lilly Trastuzumab (Herceptin) ERBB2 Roche T-DM1 (Kadcyla) ERBB2 Roche MM-121 ERBB3 Merrimack Crizotinib (Xalkori) ALK, ROS Pfizer LDK378/ceritinib (Zykadia) ALK Novartis Matching clinical information Alectinib/RO / ALK Roche, Chugai PF ALK, ROS Pfizer RXDX-101 ALK, ROS, NTRK1 Ignyta Cabozantinib/XL184 MET, RET Exelixis INC280 MET Novartis, Incyte Choice of targeted therapy Vandetanib/ZD6474 RET AstraZeneca

6 Our Ultimate Aim: Focusing in the Oncology Space Where do we want to go eventually Tumour Heterogeneity Lung cancer: Bevacizumab (Avastin ) Crizotinib (Xalkori ) Erlotinib (Tarceva ) Gefitinib (Iressa ) Afatinib dimaleate (Gilotrif ) Ceritinib (LDK378/Zykadia ) Ramucirumab (Cyramza ) Nivolumab (Opdivo ) Pembrolizumab (Keytruda ) Osimertinib (Tagrisso ) Necitumumab (Portrazza ) Alectinib (Alecensa ) Atezolizumab (Tecentriq ) Limited Number of Target

7 Increasing demand of molecular testing Simple and affordable, sequencing for all Thermo Fisher Scientific: Corporate Satellite Meetings Room Ballerup, Sunday, May 28, 11:15 12:45 hrs

8 Approaching a new era in Capillary Electrophoresis technology Satisfying our needs in term of flexibility, performances and Sanger Sequencing is evolving to catch up with the evolving and demanding needs of nowadays genetics laboratories: SeqStudio Genetic Analyzer for Sequencing and Fragment Analysis

9 First impressions, at glance An versatile instrument that does not scare the users On-instrument capillaries, buffer & polymer All that in a single cartridge for 500 samples ONE cartridge. ALL IN SOLUTION. (capillaries, buffer, polymer, and pump incorporated) A simple 4-capillary system with 4-months on-instrument cartridge stability 4 minutes hands-on time, reduced from hours to minutes.

10 First impressions, at glance An versatile instrument that does not scare the users Integrated Polymer & Syringes Single polymer for both sequencing and fragment analysis No cleaning required 4 months on-instrument life Integrated Capillaries & Detection Window One-step click installation with automatic calibration Covers for window and arrays Integrated Buffer A few things that we really like of it: No dilutions or refills required No need to manually install Septa 125 injections/500 reactions; Universal Polymer products (for performing sequencing and fragment analysis); No need to change polymers for different applications; 4 months after opening (every project can have its own!); Monitor usage on consumable during, before and after runs from anywhere; It is intuitive and easy to use; interactive touch screen with graphical user interface.

11 First impression, at glance An versatile instrument that does not scare the users

12 First impression, at glance An versatile instrument that does not scare the users Primer designer PCR Sequencing and clean-up Capillary Electrophoresis Data Analysis 96-well plate with M13-tailed primers BigDye Direct Cycle Sequencing + BigDye XTerminator SeqStudio

13 Approaching a new era in Capillary Electrophoresis technology Our run stats We tested the Early Access SeqStudio instrument for 8 weeks We performed 346 runs, sequenced 1384 samples, including 768 samples from the RAS project We obtained 84% of good quality data Data are consistant between existing CE existing sequencing platform (3130 XL) and the new SeqStudio instrument

14 SeqStudio Stress Test Putting the instrument under pressure Thermo Fisher Scientific: Corporate Satellite Meetings Room Ballerup, Sunday, May 28, 11:15 12:45 hrs

15 Extended RAS Research Assay A useful tool, simple, quick and reliable Targets 8 (actionable) hot-spot regions of and NRAS genes: Low DNA input (down to 1 ng/reaction) from FFPE samples Low-level minor variant detection (down to 5%) You don t need much to run it: just 4 components: A SeqStudio instrument; 96-well preloaded primer plate (most reagents are already on the plate); Applied Biosystems - BigDye Direct Cycle Sequencing Kit - BigDye XTerminator Purification Kit; Minor Variant Finder software (free and usable on the cloud);

16 A snapshot about the Workflow 5 main step to get you to the results Days Extended RAS Research Assay PCR plate BDD BDX PCR Pre-loaded 96-well plate with M13-tailed primers Sequencing and clean-up BigDye Direct Cycle Sequencing + BigDye XTerminator Capillary Electrophoresis SeqStudio or Data Analysis Minor Variant Finder software Note: it is virtually impossible to mix-up or contaminate samples

17 Extended RAS Research Assay 96-well dried down primer plate for 5 samples + 1 control C A useful tool, simple, quick and reliable Gene Chr Exon Hot spot codon NRAS NRAS NRAS NRAS am ple C Cont rol * T T arget or ard ev erse am ple C Cont rol * T T arget or ard ev erse * The CEPH control DNA supplied in the BigDye Direct Cycle Sequencing kit can be used as the control for reference sequence Minor Variant Finder Representative electrophoregrams NRAS codon 146 at 5%

18 Extended RAS Research Assay A useful tool, simple, quick and reliable, more example

19 Extended RAS Research Assay A useful tool, simple, quick and reliable, example of variant candidate table

20 Extended RAS Research Assay VAF Comparison: NGS vs Sanger, 22 FFPE samples G12C Minor Variant 5.25% Q61H L19F Q61K NRAS G12C Q61L NRAS G12V G13C G13D G12V G13D G12A G12V G12D G12A G13D Variant 91.1% G12D G13D G12V G12C G12C Q61K NRAS NGS % Sanger % 0.37ng 0.63ng 0.71ng 0.67ng Very low DNA input 0.90ng 0.094ng 6 samples below 1 ng / reaction input amount

21 Extended RAS Research Assay SeqStudio Fragment analysis data example: MLPA data Courtesy of Jan Schouten, MRC Holland, Amsterdam

22 Extended RAS Research Assay Conclusions Easiness to use and to setup Fast to setup Consistency of results across all the CE platforms No change in sample prep/seq reaction Seq reaction workflow improved using the BigDye direct chemistry

23 Acknowledgments Institute of Medical Genetics and Pathology Molecular Team: A Foster T Diteche S Tschumi V Perrina A Fluchi C Burthscher B Till S Bertschin N Bosch L Schwezer Research Unit: Dr C Ruiz Dr I Bratic Hech Dr Charlotte NG Molecular Pathologists: Prof L Terracciano Dr S Piscuoglio Dr M Matter Dr M Bihl Dr S Holler Contact: luca.quagliata@usb.ch