Molecular pathology and single cell analysis: New technologies coming to practise Workshop

Basics of single cell sequencing

Lecture Time
16:00 - 16:30
Speakers
  • Florent Ginhoux, Singapore, Singapore, A*STAR - Singapore Immunology Network (SIgN)
Location
Abbey room, Queen Elizabeth II Centre, London, United Kingdom
Date
07.11.2019
Time
14:00 - 17:00
Molecular pathology and single cell analysis: New technologies coming to practise Workshop

Mass cytometry: Principles and applications

Lecture Time
15:00 - 15:30
Speakers
  • Sandra Tietscher, Zurich, Switzerland, UZH - University of Zurich - Irchel Campus
Location
Abbey room, Queen Elizabeth II Centre, London, United Kingdom
Date
07.11.2019
Time
14:00 - 17:00
Molecular pathology and single cell analysis: New technologies coming to practise Workshop

Digital pathology: Emerging technologies in the field

Lecture Time
14:00 - 14:30
Speakers
  • Julien Adam, Villejuif, France, Institut Gustave Roussy
Location
Abbey room, Queen Elizabeth II Centre, London, United Kingdom
Date
07.11.2019
Time
14:00 - 17:00
Molecular pathology and single cell analysis: New technologies coming to practise Workshop

Bioinformatics and mathematics to analyse single cell data

Lecture Time
16:30 - 17:00
Speakers
  • Charlotte K. Ng, Bern, Switzerland, University of Bern
Location
Abbey room, Queen Elizabeth II Centre, London, United Kingdom
Date
07.11.2019
Time
14:00 - 17:00
Molecular pathology and single cell analysis: New technologies coming to practise Workshop

Coffee break

Lecture Time
15:30 - 16:00
Location
Abbey room, Queen Elizabeth II Centre, London, United Kingdom
Date
07.11.2019
Time
14:00 - 17:00
Molecular pathology and single cell analysis: New technologies coming to practise Workshop

How to analyse data from digital pathology

Lecture Time
14:30 - 15:00
Speakers
  • Trevor Graham, London, United Kingdom, Barts Cancer Institute-Queen Mary University of London
Location
Abbey room, Queen Elizabeth II Centre, London, United Kingdom
Date
07.11.2019
Time
14:00 - 17:00
Welcome from the Chairs Welcome session

Welcome to MAP 2019

Lecture Time
08:40 - 08:50
Speakers
  • Charles Swanton, London, United Kingdom, The Francis Crick Institute
Location
Fleming room, Queen Elizabeth II Centre, London, United Kingdom
Date
08.11.2019
Time
08:40 - 08:50
Molecular target/Disease orientation Education session

Glioblastomas

Lecture Time
09:10 - 09:30
Speakers
  • Roel G. Verhaak, Farmington, United States of America, Jackson Laboratory for Genomic Medicine
Location
Fleming room, Queen Elizabeth II Centre, London, United Kingdom
Date
08.11.2019
Time
08:50 - 10:30
Molecular target/Disease orientation Education session

Biliary tract cancer

Lecture Time
09:30 - 09:50
Speakers
  • Lipika Goyal, Boston, United States of America, Massachusetts General Hospital, Harvard Medical School
Location
Fleming room, Queen Elizabeth II Centre, London, United Kingdom
Date
08.11.2019
Time
08:50 - 10:30
Molecular target/Disease orientation Education session

Pancreatic cancer

Lecture Time
08:50 - 09:10
Speakers
  • Andrew Biankin, Bearsden, United Kingdom, University of Glasgow - Wolfson Wohl Cancer Research Centre - Institute of Cancer Sciences
Location
Fleming room, Queen Elizabeth II Centre, London, United Kingdom
Date
08.11.2019
Time
08:50 - 10:30
Molecular target/Disease orientation Education session

Sarcoma

Lecture Time
09:50 - 10:10
Speakers
  • Jean-Yves Blay, Lyon, CEDEX, France, Centre Léon Bérard
Location
Fleming room, Queen Elizabeth II Centre, London, United Kingdom
Date
08.11.2019
Time
08:50 - 10:30
Molecular target/Disease orientation Education session

1O - 100,000 genomes project: Integrating whole genome sequencing (WGS) data into clinical practice

Lecture Time
10:10 - 10:20
Speakers
  • Alona Sosinsky, London, United Kingdom, QMUL
Location
Fleming room, Queen Elizabeth II Centre, London, United Kingdom
Date
08.11.2019
Time
08:50 - 10:30

Abstract

Background

The 100,000 Genomes Project aims to improve cancer care for NHS patients in the UK through personalised medicine. Our target is to return WGS results to clinicians in a clinically meaningful timescale to facilitate diagnosis and treatment choices for patients, and in parallel to provide a research platform of genomic data linked to longitudinal clinical data.

Methods

We present here an overview of clinical utility for reported outcomes. To date, bioinformatics reports for WGS, with links to potentially relevant therapies and UK clinical trials, have been produced for more than 14,000 cancer patients in the UK Currently our bioinformatics analysis of WGS includes clinical interpretation of somatic small variants, somatic structural and copy number variants (SV/CNV), germline pertinent findings, mutational burden and signatures. To iteratively develop a high-quality bioinformatics pipeline and to monitor clinical utility of returned results, we are collecting feedback via the 100,000 Genomes Project Interpretation Portal from NHS Molecular Tumour Boards. These data suggest that WGS has the potential to affect patient management. Future applications will include the utilisation of pan-genomic markers to better stratify patients within the context of a clinical study.

Results

WGS has the ability to replace multiple standard of care tests as it has the potential to detect all types of variants (SV/CNV/SNV/indels) as well as emerging pan-genome biomarkers in a single test. In this study we use samples submitted as part of the 100,000 Genomes Project to investigate the feasibility of WGS as an alternative to conventional testing. Overall comparison of WGS with the results of NGS panels (96 patients, 156 clinically-relevant SNVs), high-depth exome sequencing (10 patients, 3150 SNVs, 140 indels), cytogenetic FISH tests (70 patients, 259 SVs, 100 CNVs), immunohistochemistry tests for Mismatch Repair Deficiency (265 patients) and HER2 status (154 patients) demonstrated Positive Percentage Agreement > 90% and False Positive Rate < 5%.

Conclusions

Further work is required to validate fully all aspects of the WGS analysis pipeline but these results indicate that WGS can reliably detect clinically relevant biomarkers in the genomes of cancer patients.

Legal entity responsible for the study

Genomics England.

Funding

Genomics England.

Disclosure

All authors have declared no conflicts of interest.

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