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Genetics Technology: Next Generation Sequencing in Clinical Practice

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Presentation on theme: "Genetics Technology: Next Generation Sequencing in Clinical Practice"— Presentation transcript:

1 Genetics Technology: Next Generation Sequencing in Clinical Practice
Dr Yvonne Wallis FRCPath Principal Clinical Scientist Head of Familial Cancer Services/ Head of Research, Academic and Service Developments West Midlands Regional Genetics Laboratory Healthcare Science Making an Impact in the New NHS 9th November 2012

2 Next Generation Sequencing: a technology worth getting excited about
Estimated 100 trillion cells in human body

3 Next generation sequencing invented
Landmarks in Genetics Sanger sequencing first reported Draft sequence of human genome Cost: $2.7 bn Mendel publishes work on inheritance Cost of sequencing a human genome reduced to < $10,000 1866 1953 1977 1983 2001 2005 2012 The structure of DNA is described Kary Mullis invented Polymerase Chain Reaction Next generation sequencing invented 300,000th of the price

4 The importance of DNA sequencing
Sequencing decodes DNA to produce the precise order of four component bases A, C, G and T The order of these bases defines who and what we are now and in the future Changes to base sequence cause disease either inherited or acquired during our lifetime

5 Next Generation Sequencing-a game changer
Capillary 2005 60,000 bases 0.002% of genome 10 genes MiSeq 150,000,000 bases 2% of genome >20,000 genes At WMRGL Sequencing Facility HiSeq 6,000,000,000 bases 2 whole genomes joint initiative At WMRGL Sequencing Facility

6 How is NGS improving patient care?
Massively Parallel Sequencing Reduces cost per base >1000x Increases data throughput per run More genes More Patients Increasing diagnostic yield Reducing time to diagnosis

7 Challenges of NGS implementation
Technology is demanding, relatively new & evolving Few standard protocols/Limited agreed best practise All new NGS workflows require significant validation Fit for purpose Best possible quality Specialist equipment and data storage requirements Trained workforce: Bioinformatics skills required for data analysis Clinical interpretation of base changes

8 Developed NGS service panels
Paraganglioma and Phaeochromocytoma 9 genes Renal Cell Carcinoma 5 genes Colorectal Cancer 6 genes Neonatal liver disease

9 NGS service performance metrics
181 reports issued in 2012 using NGS technology Increasing number reported every month Genetic cause confirmed in 21 patients

10 Improved service for our users/patients
Phaeochromocytoma gene panel Previous strategy NGS strategy 5 genes analysed Cost = £1700 Time = 10 months 9 genes analysed Cost = £500 Time = 4 months

11 Case Study 1 Next generation sequencing screen:
RET SDHB SDHC SDHD VHL MAX* SDHA * SDHF2* TMEM127* DNA testing now available to appropriate family members Pathogenic mutation identified TMEM127* c.268G>A p.Val90Met 54 years Mesenteric paraganglioma No F/H 3 children

12 Case Study 2 Next generation sequencing screen
ABCB4 ABCB11 ATP8B1 NPC1 NPC2 SLC25A13 2 weeks Neonatal choleostasis 2 pathogenic mutations identified NPC1 c.2000C>T p.Ser667Phe c.3182T>C p.Ile1060Thr Diagnosis of Niemann Pick disease Appropriate treatment Prenatal testing available for future pregnancies

13 Diverse clinical applications of NGS in development
Inherited breast cancer gene panel 11 genes Diseases of sexual differentiation panel 20 genes Genomic profiling in acute myeloid leukaemia gene panel 59 genes Somatic cancer-stratified medicine gene panel 60 genes

14 NGS-driven landmarks in Genomic Medicine for Genetics Laboratories
Whole exome sequencing: Missing heritability Stratified medicine Gene panel screens: Across all areas of medicine 2012 300,000th of the price Deep sequencing for non- invasive testing: Prenatal diagnosis Circulating tumour markers Whole genome sequencing: “One-stop shop”

15 Partnership for NGS-driven Genomic Medicine
High Quality Patient Care Academic Commercial NHS

16 NGS: Changing Healthcare

17 Acknowledgements NGS Team Head of Cancer Programme Director of WMRGL
Eleanor Rattenberry Kim Reay Kirsten McKay Lindsey Vialard Anna Yeung Hayley Bair Head of Cancer Programme Jennie Bell, FRCPath Director of WMRGL Professor Mike Griffiths

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