1. Standardisation of Somatic Variant Analysis using an AMP based Framework
Kirsty Russell
Trainee Clinical Scientist (Bioinformatics – Genomics)
Bristol Genetics Laboratory

2. Overview Somatic Variant Classification AMP guidelines
Development of AMP Based framework
Somatic Variant Analysis at BGL
Case Study
Future Developments

3. Somatic NGS & Variant Analysis
Increase in diagnostic somatic NGS
Test directory requires Cancer NGS Panels
Analysis of 100k genome results
Discrepancies between labs in how variants are classified and reported
Majority use 5 Class system (ACMG)
Not suitable for somatic variants
Li et al (2017)

4. AMP guidelines

5. AMP Tiered Variants
Variants are assessed based on the clinical significance / actionability
A variant is actionable if it has a known therapy or has prognostic or diagnostic relevance.
Variants can be therapeutic or prognostic/diagnostic
Assessment based on specific tumour type

6. Framework Development

7. Framework Development

8. Rule Set Development Defines the combinations which
lead to different tier classifications.
Example: 1xSPS + 1xSPM + 0xSBS/SBM = Tier IID
Developed and optimised using
10 solid tumour variants from
several cancer types

9. Duplication/ insertion
Framework Validation
Final framework validated through analysis of 62 unique variants identified using Solid Tumour NGS panel
- Further refinement of rules
Sent to several labs for feedback
Gene
No of Variants
BRAF 5
EGFR 18
KRAS 10
NRAS 4
KIT 14
PDGFRA 6
PIK3CA
Variant Type
No of Variants
SNVs 67
Deletion 30
Duplication/ insertion 12
Delins 10

10. Somatic Variant Analysis at BGL
Using this AMP framework for all somatic NGS analysis
Solid Tumour panel
100k genome return of results
More in future
In House Somatic Pipeline
Database Evidence
Somatic UV Form Completion
Evidence Gathering
Functional analysis
Literature Search

11. Evidence Therapeutic Databases Somatic Variant Databases
Cancer Genome Interpreter (Somatic Variant Report), My Cancer Genome, ClinicalTrials.gov, UK Clinical Trials Gateway
Somatic Variant Databases
COSMIC, CIViC, DOCM, IARC TP53
Population Databases
gnoMAD
Germline Databases
HGMD, ClinVar, InSiGHT, CaVaDa
Functional Analysis
In silico & literature
Literature Searching

12. KRAS:c.35G>T p.(Gly12Val) Lung
Case Study
KRAS:c.35G>T p.(Gly12Val) Lung

13. Case Study: Database Evidence

14. Case Study: Therapeutic Evidence
Some evidence shows lack of response to first line EGFR tyrosine kinase inhibitors
Some evidence shows association with a poor prognosis
Serves as inclusion in phase 2/3 trials
Known to confer decreased sensitivity to anti EGFR antibodies in Colorectal

15. Case Study: Functional Evidence
Highly Conserved Nucleotide & Amino Acid
Align GVGD, SIFT and Polyphen – Deleterious
Mutation type activating in an oncogene
Variant in a cancer pathway associated with tumour type
Predicted driver (OncoDriveMut)

16. Case Study: Result
KRAS:c.35G>T p.(Gly12Val) AMP Tier: IIC Variant of potential clinical significance for which there is some evidence towards therapeutic/prognostic status and serves as inclusion in Phase 2/3 clinical trials.
3 x SPS + 3 x SPM + 2 x SPP
= Tier IIC

17. However… Case Study: Result
KRAS:c.35G>T p.(Gly12Val) AMP Tier: IIC Variant of potential clinical significance for which there is some evidence towards therapeutic/prognostic status and serves as inclusion in Phase 2/3 clinical trials.
However…
3 x SPS + 3 x SPM + 2 x SPP
= Tier IIC

19. Case Study: Result
KRAS:c.35G>T p.(Gly12Val) AMP Tier: IB Variant of clinical significance listed in professional guidelines regarding its therapeutic and prognostic significance and serves as inclusion in Phase 2/3 clinical trials.
1x SPSV + 3 x SPS + 3 x SPM + 2 x SPP = Tier IB

20. Future Development
Working group started to work on standardisation across laboratories
First teleconference was 22nd June 2018
Capture what different laboratories are doing
Questionnaire to be sent around labs
Sharing of SOPs
Set of variants to be sent round labs for classification
Refinement of framework for haematological malignancy
First working group meeting Autumn ‘18

21. Everyone who has joined the Somatic Variant Analysis Working Group!
Acknowledgements
Bristol Genetics Laboratory Oncology Team
Chris Wragg
Claire Faulkner
Paula Waits
Helen Williamson
Kenneth Smith
Manchester Centre for Genomic Medicine
George Burghel
Everyone who has joined the Somatic Variant Analysis Working Group!
West Midlands Regional Genetics Laboratory
Paula Page
Joanne Mason
David Hill
Kim Reay