The International Society for Gastrointestinal Hereditary Tumours and the Human Variome Project have had a long and fruitful collaboration. Finlay Macrae, InSiGHT's Secretary spoke at the 4th Biennial Meeting of the Human Variome Project Consortium to update delegates on the progress of the collaboration and to share some of the methods that InSiGHT has used to build their organisation and their database.

1. Gene/Disease Specific Databases
The InSiGHT-Human Variome Project
collaboration
Finlay Macrae
Secretary, International Society for Gastrointestinal Hereditary Tumours
Head, Colorectal Medicine and Genetics, The Royal Melbourne Hospital
Professor of Medicine, Departments of Medicine, Melbourne and Monash
Universities, Victoria, Australia
4th Bi-ennial Human Variome Project
Paris, June 2nd, 2012

2. Human Variome Project – InSiGHT
collaboration
Talk Summary
• What is Lynch Syndrome?
• What is InSiGHT?
• What is the Human Variome Project?
• Governance, Ethics, Data use policy
• Indemnity, Disclaimers
• The InSiGHT Mutation Interpretation Committee
• Interoperability:PathoKB, Clin Var, Mutadatabase
• Future Activities

3. What is Lynch Syndrome?

4. What is Lynch Syndrome?
• Hereditary non Polyposis Colon Cancer Syndrome –
HNPCC
• Caused by a germline (inheritable) mutation in a
mismatch repair gene
• hMLH1, hMSH2, hMSH6 or hPMS2
• LS is identified through various strategies….
• The Amsterdam criteria, Bethesda criteria, Melbourne
criteria, Ohio State University Criteria

5. What is Lynch Syndrome?
The Amsterdam criteria
3:2:1 rule
3 first degree relatives over
2 or more generations with
1 under 50 years of age
affected with
Colorectal, endometrial cancer,
Ovarian, small bowel, hepatobiliary, pancreatic,
pelvi-ureteric, stomach, brain cancers,
breast, prostate, kidney cancers

6. What is Lynch Syndrome?
The Ohio State University Criteria
Population screening:
• Test all cancers presenting routinely by MSI or
Immunohistochemistry for mismatch repair
protein loss
Note: Determines chemotherapy decisions in
Stage 2 and 3 cancers

7. What characterizes tumours within
Lynch Syndrome

8. What characterizes tumours within
Lynch Syndrome
• Microsatellite instability
• Loss of expression of MMR gene in the tumour
identified through immunohistochemistry:
– MLH1 and PMS2 loss = MLH1 germline (or sporadic
MSI due to methylation of MLH1 somatically)
– MSH2 and MSH6 loss = MSH2 (or MSH6)
– MSH6 loss = MSH6
– PMS2 loss = PMS2

9. What is Lynch Syndrome?
• Hereditary non Polyposis Colon Cancer Syndrome – HNPCC
• Caused by a germline (inheritable) mutation in a mismatch
repair gene
• hMLH1, hMSH2, hMSH6 or hPMS2
• LS is identified through various strategies….
• The Amsterdam criteria, Bethesda criteria, Melbourne
criteria, Ohio State University Criteria
• How are individuals and families worked up for diagnosis of
Lynch Syndrome?

10. How are patients worked up for
diagnosis of Lynch Syndrome?
• Suspect the diagnosis: Amsterdam, Bethesda,
(Melbourne or OHSU)
Amsterdam and Bethesda
• Identify youngest live family member affected with CRC
or other cancer
• Offer IHC or MSI testing
All strategies
• If loss of expression or positive MSI, proceed with
mutational analysis of relevant gene indicated by IHC
…sequencing and MLPA
• Cascade testing through the family pedigree

11. Surveillance in LS
• Colonoscopy annually (some say 2 to 3
yearly)
• ?Gastroscopy
• ?Annual pelvic ultrasound, endometrial
sampling
• ?annual urine cytology
• ?Capsule endoscopy
The Dutch criteria: Screen for site with >1 cancer in family

12. Colorectal surgery for Lynch Syndrome
The metachronous colorectal cancer rate after
40 years is 60%
• Colectomy with ileo-rectal anastomosis
• Proctocolectomy with restorative ileo-anal
pouch
• Segmental resection

13. What is InSiGHT?

14. What is InSiGHT
• The International Society for Gastrointestinal
Hereditary Tumours formed with the merger of the
Leeds Castle Polyposis Group and ICG HNPCC in 2005
• Followed a courtship when the two groups met in
Melbourne in 1999 under LCPG chairmanship
• Governed by elected Council; Non voting
administrative directors
• Maintains a database of MisMatch Repair (and other
genes responsible for GI cancer) DNA variants
through its website
www.insight-group.org

15. What is the Human Variome Project?

16. The Human Variome Project
Human Variome Project International Ltd in Consultative
Partnership with
the United Nations Educational, Scientific and Cultural
Organisation (UNESCO) as an NGO
Initiated 20-23 June 2006 in Melbourne, Australia and co-
sponsored by WHO
Scientific Director:
Professor Richard Cotton
Nat Genet, 2007. 39(4): p. 433-6

17. Human Variome Project:
Goals
• Global inclusive initiative
• Ensure the translation of genetic variation
data into direct patient benefits
• Facilitate the establishment and maintenance
of standards, systems and infrastructure for
sharing the worldwide collection of genetic
variations effecting human disease
• Sharing data – reducing disease

18. InSiGHT and the
Human Variome Project
Consensus
InSiGHT meeting Yokohama,
March 2007

19. InSiGHT/HVP:
Databases and curation April 2007
• DNA Variant Curators and Governance: M Woods, P
Peltomaki, R Sijmons, H Vasen, J den Dunnen, F Macrae
• Phenotype: F Macrae, (Chair) , R Scott, S Clarke, C Burke,
T Weber, P Watson, A Lindblom, P Rozen, G Moeslein, I
Bernstein, A Spigelman
• Virtual Histology: H Morreau, E Brazowski
• Missense And Functional Assays: R Sijmons (Chair), R
Hofstra, M Nystrom, N Winds, (Lene Jule Rasmussen)
• Mutation Interpretation Committee: M Genuardi (Chair),
J Utsunomiya, R Ramesar, J Burn, M Greenblatt, P
Peltomaki, R Hofstra, R Sijmons, R Scott, M Corish, D
Golgar, M Woods, B Bapat, S Tavtigian, A Spurdle, S
Lipkin, M Dunlop, I Frayling, E Holinski Feder, A
Lindblom, T Weber, J Wijnen, F Macrae

20. MMR mutation
Identified
(DNA Lab)
InSiGHT Flow IHC &/or MSI data added
Plan B (Histopathology)
(commencing Interpretation of
Virtual pathology added
(Histopathology)
genotype
with genotype) (Clinicians & Lab) Functional data added
(Research Labs)
Clinical phenotype
added
(Clinicians)
Identified dataset stored De-identified data stored with InSiGHT
locally Interpretation
(Family Cancer Clinic) (InSiGHT)
Data from other
DbGaP (NCBI) centres can be
UCSC submitted to update
EBI information

21. InSiGHT LSDB Governance Committee
Terms of Reference
• Appointed by Council, with reference to expertise in
databasing, and to an extent, geographic representation.
• Consists of 6 InSiGHT members with the capacity to appoint
scientists with special expertise ad hoc .
• Oversees the functions the database and its supporting
committees including interpretation, functional assays,
phenotype, virtual pathology.
• Monitors database security, back up, access and
confidentiality
• Reports to InSiGHT Council before Council meetings.
• Ensures compliance with the LOVD Database and Usage Policy
• Endorses a disclaimer on the website relating to the InSiGHT
database, in line with the LOVD policy.

22. LSDB Governance Committee
• Determines the Gastrointestinal Cancer genes to be
included in the InSiGHT database
• Approves the reference sequence for each gene
• Definition of data fields that will be included
• Disclosure policies per field
– Fields with uninhibited exposure through public access
– limited access fields
– further data available through curator fields
• Appoints the curator: Allocates available resources for
curation
• Appoints Ethics Committee

23. COMPANIES ACT 2006
COMPANY LIMITED BY GUARANTEE
NOT HAVING A SHARE CAPITAL
ARTICLES OF ASSOCIATION
- of -
THE INTERNATIONAL SOCIETY FOR GASTROINTESTINAL
HEREDITARY TUMOURS
As instructed to Bircham, Dyson & Bell,
50 Broadway, London, SW1H 1OL,UK
Shortlisted as Charity Advisor of the Year by CityWealth Magic Circle Awards, 2010
Registered Charity in
UK

24. Incorporation and
Charity Registration
means
• Pathogenicity can be assigned with substantial
medico-legal protection
• InSiGHT can enter contractual arrangements
with organizations, government and DNA
diagnostic and research labs where needed
• InSiGHT can attract funds as a
tax deductible charity world-wide
• Director/Office bearer roles clarified

25. InSiGHT Database:
A lead LSDB for the HVP
• Merge of MMR (Mike Woods), functional assay (R Sijmons) with
InSiGHT databases – 2008
• German HNPCC consortium data uploaded
• Hicks Foundation InSiGHT curator appointed - 2010 in Melb
• National submissions of diagnostic lab DNA variants (n=25,000
including 3500 unique variants)
• Calibration of functional assay of missense variants R Hofstra
• in silico analyses S Tavtigian
• Quantitative phenotype dataset drafted
• Interpretation processes implemented

26. InSiGHT LSDB database
Page hits/month and
unique IP addresses through LOVD
•
2011
2011

27. InSiGHT/HVP database
Work in progress
• Data submission..France, Sweden, Denmark, Poland, Australia, US CFR,
Quest Diags
• MoU with MuDB: UK NHS diagnostic labs - A Devereau (UK)
• InSiGHT Mutation Interpretation Committee for VUS met in San Antonio, March
2011: modus operandi established: 4 teleconferences completed (Chair: M Genuardi,
Italy)
• Endorsement of SNPs as clearly pathogenic or benign polymorphism as calibration
tools for functional assays and Bayesian algorithm: NCI R01
• Phenotype agreement, and commissioning on database: Germany
• Preparation of paper describing InSiGHT pathway: F Macrae (Australia)
• International Mismatch Repair Consortium: NCI R01
• Microattribution: Myles Axton, ORCID, , George Patrinos (Greece)
• Clin Var: NCBI Justin Paschall, Donna Maglott USA
• Mutadatabase : Patrick Willems, Heidi Rehms (Belgium and USA)
• Gen2Phen and PathoKB: Tony Brookes (UK)

28. The InSiGHT
Hicks Foundation Curator
• Check integrity of submissions
Nomenclature, duplicate entries,
• Promote submissions internationally
• Liaison role: Travel
• Assist in development of annotations
• Present data on unclassified variants to
Interpretation Committee: Display outcomes
• Located in Melbourne
JohnPaul@variome.org

29. LSDB Minimal Data Requirements (Variant) Present Derivable from other fields
Source: Gen2Phen - D3.4 Scope and Range Requirements of Specialized Domain Models; O = Obligatory, R = Recommended
Field Name D3.4 InSiGHT LOVD Example
gene Symbol O MLH1
Exon R 1
DNA_genomic O g.445345
DNA_coding R c.125delC>T
RNA O r.125c>u
Protein O p.pro41arg
DBID O 12
Reference O Chan et al., 1999
DNA_published R 125 C -> T
Detection/Template O DNA
Detection/Technique O Sequencing
DNA_remark R Free text comment
Frequency R 1/1012 controls
Origin R germline
Allele R 1
Pathogenicity R Pathogenic

30. LSDB Minimal Data Requirements (Patient Information)
Source: Gen2Phen - D3.4 Scope and Range Requirements of Specialized Domain Models; O = Obligatory, R = Recommended
Field Name D3.4 InSiGHT LOVD Example
Patient_ID O 12345
Disease O CRC
Remarks R Free Text
Geographic R Australia
Ethnic R Caucasian
Gender R Male
Submitter_ID O 5

31. LSDB Minimal Data Requirements (Patient
Phenotype)
Source: Gen2Phen - D3.4 Scope and Range Requirements of Specialized Domain Models
• Age, Gender, Age of Diagnosis, Signs and
Symptoms
• Family history and pedigree:
• Use of Controlled Vocabulary for Signs and
Symptoms (e.g. Human Phenotype Ontology,
ICD10; SNOMED)
• Therapy information is optional – however,
currently no ontology exists.

32. Summary Family History Statistic
• Provides probability assessment based on
density of phenotype across the family
• Is non-identifiable, protecting privacy
• Can be added in to a Bayesian Likelihood Ratio
to assist in quantitation of VUSs
• Requires full pedigree to derive the data, but
only at source/submitter
• SISA: simplified analytic technique (P Moller)

36. China establish MMR database on
LOVD database platform 2010
• 2006 Dr Ming Qi engages with the Human
Variome Project
• 2007 Dr Ming Qi joins InSiGHT
• 2010 Dr Ming Qi establishes Chinese MMR
database on LOVD platform
• 2011 Dr Ming Qi invited to join InSiGHT Council as
ad hoc Councillor
• 2011 HVP China Meeting Beijing
• 2012 Chinese MMR data merging with InSiGHT
database

37. The International
Mismatch Repair Gene Consortium
• The C-CFR is keen to promote utilization of its resource (40,000
individuals)
• InSiGHT and the C-CFR met at InSiGHT meeting in Dusseldorf (June
2009)and agreed to collaborate with a number of projects targeted
• InSiGHT is strong on clinical collaborations and access to families with
MMR mutations, and unique clinical science
• C-CFR is strong on epidemiology, molecular epidemiology, molecular
biology and epigenetics
• C-CFR has excellent grantsmanship skills, and is well funded
• Agreement in Washington April 2010 to form an InSiGHT C-CFR MMR
consortium as vehicle to attract further funds from NCI, EU and Australia
• 90 investigators from 45 countries representing 15000 variants
• Two R01 applications on penetrance submitted in Feb 2011: not funded
• Re-application planning in progress
All countries are warmly invited to join the consortium..through InSiGHT!
Contact: Finlay.Macrae@mh.org.au

38. InSiGHT Interpretation Committee
Modus operandi
• Chair appointed by Council: Maurizio Genuardi (Italy)
• Invitations for core and extended committee memberships
• Qualitative approach to classification discussed, circulated, and agreed
• Initial set of missense variants with discordant interpretations and 3 lines of
evidence classified according to approach agreed across the committee
• Variant list for discussion is circulated to extended committee – any additional
available data canvassed
• All data is then assembled by curator for Core Committee plus rolling other
membership to classify at international teleconferences (sponsored)
• One line entry to be included on InSiGHT database describing outcomes
• Later, preliminary approach to all InSiGHT members to seek all available
information of variants under consideration at each meeting
• InSiGHT members encouraged to submit data at each contact, and signal
variants of particular clinical concern for Committee consensus
•

39. Interoperability
• Annotation on InSiGHT databases website
• ClinVar (NCBI)
• Mutadatabase
• Gen2Phen
• DMuDB
• Patho KB (data model)

40. InSiGHT Interpretation Committee Mar 2012
• R Ramesar (South Africa)
• M Genuardi (Italy, Chair) • M Qi (China)
• JP Plazzer (Curator) • R Hofstra (Netherlands)
• F Macrae (Sec, InSiGHT) • M Vihinen (Finland)
• A Spurdle (Australia) • M Nystrom (Finland)
• T Weber (USA)
• B Thompson (Australia)
• S Tavtigian (USA)
• M Woods (Canada) • D Goldgar (USA)
• R Sijmons (Netherlands) • C Heinen (USA)
• P Peltomaki (Finland) • S Lipkin (USA)
• M Greenblatt (USA) • A Lindblom (Sweden)
• K Akagi (Japan)
• I Frayling (UK)
• F Al-Mulla (Kuwait)
• J Burn (UK) • L Rasmussen (Denmark)
• M Dunlop (UK) • I Bernstein (Denmark)
• S Farrington (UK) • F Wikman (Denmark)
• B Royer Pokora (Germany) • T Frebourg (France)
• S. Olschwang (France)
• E Holinski Feder (Germany)
• A Fabre (France)
• G Moeslein (Germany) • M Tosi (France)
• I Blanco (Spain) • S Leung (Hong Kong)
• G Capella (Spain) • T Liu (Sweden)
• M Pineda (Spain) • P Moller (Norway)
• B Bapat (Canada)
• D Du Sart (Australia)
• M Farrell (Ireland)
• M Kohonen Corish (Australia) • C Tops (Holland)
• R Scott (Australia) • D-W Kim (Korea)
• B Talseth (Australia) • J Wijnen (Netherlands)
• Kristina Lagerstedt-Robinson (Sweden)

41. HVP members are welcome to join InSiGHT and
contribute to our program
• Join InSiGHT
• Submit variant data to InSiGHT MMR and other
databases
• Consider membership of the InSiGHT Mutation
Interpretation Committee for VUSs
• Join the International Mismatch Repair Consortium
• Exchange scientific personnel in training (PhDs, MDs
etc)
• Assist in funding the InSiGHT Mismatch Repair LSDB
curator

42. CAIRNS CONVENTION CENTRE - AUSTRALIA
InSiGHT
Bi-Ennial Meeting
August 29- 31st. 2013
Join us..it will be a great meeting!
Serious Business in Australia’s Most

44. CAIRNS CONVENTION CENTRE - AUSTRALIA
InSiGHT
Bi-Ennial Meeting
August 29- 31st. 2013
Join us..it will be a great meeting!
Serious Business in Australia’s Most