Translating genomics to the clinic: from rare disease diagnosis to precision oncology
Dr. Mark Cowley
Wednesday, December 7, 2016
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Chapters
Introduction
Overview
The diverse impact of genomic variation
Clinical Genomics throughout the whole of life healthcare
The Kinghorn Centre for Clinical Genomics
From test request, to clinical report
Research vs Clinical?
Why Clinical WGS? Why not exomes? panels?
Purpose-built for population-scale human genome sequencing
Why WGS as a first line diagnostic test?
WGS driving improved diagnostic rates
Coverage of WGS is more uniform than Targeted Sequencing
Disease Gene Discovery rates continue to rise
Why not WGS?
How to remain agile in a clinically regulated environment?
Sabretooth - genomic analysis pipeline
quality software modular, testable pipelines
Clinical change management: Verify that data is fit for purpose
Analytical Performance of Clinical WGS
Precision FDA
Diagnostic Rates from WGS
Autosomal Dominant Polycystic Kidney Disease
WGS aligns reads well to PKD1
ADPKD - Diagnostic Rate of 86% from WGS
PCR-Free Library Preparation
Hereditary Spastic Paraplegia (HSP)
ROHmer: Homozygosity mapping from WGS
Using WGS to detect mitochondrial heteroplasmy
8Kb deletion detected in patient with Kearns-Sayre syndrome read depth: 8/2474 (VAF=0.323%)
ending a 5-year diagnostic odyssey
a new era in Genomic Medicine
Summary so far
Rapid turn around precision genomic medicine
FromcfDNA to answers about cancer
Rapid turn around precision genomic medicine
Tumour Evolution in response to therapy CMML exceptional responder case
“Overall, our study revealed potentially actionable findings in tumor or germline in 42 patients (46%)
Case history
Cancer Genomics WGS pipeline
Diagram
TSC1 + Temsirolimus
Patient Timeline
Journey of a child
WGS revealing substantial differences in SV profiles in childhood cancers
Molecular Screening and Therapeutics study - 1000 patients
Take Home Messages
Acknowledgements pt 1
Acknowledgements pt 2
Acknowledgements pt 3
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