Development of rules for the
interpretation of mismatch repair
gene variants based on the 5-tiered
IARC classification sys...
Human Mutation (2008) 29:1282–1291.
InSiGHT Mutation Database:
data cleaning, nomenclature standardization and systematic data review
12,645 MMR gene submissi...
Criteria development process
• Used modified Delphi approach
– http://en.wikipedia.org/wiki/Delphi_method
• Evolution of c...
Current Multifactorial
Likelihood Model
Quantitative
classification
MMR
Sequence
Variant
+ =
Thompson et al Hum Mutat, 201...
QUALITATIVE RULES:
POINTS OF EVIDENCE
a. Co-segregation
b. Tumor molecular characteristics: MSI, IHC (BRAF)
c. Population ...
Qualitative points of evidence
5’…TCT CAA AAA TTT ACG…3’
S Q K F T
5’…TCT CAA TAA TTT ACG…3’
S Q *
Sequence-based
Segregat...
• Major issue in
classification process
was conflicting data from
functional assays
• Functional assay
subcommittee formed...
Class 5
Pathogenic:
Class 4 Likely
pathogenic:
Class 3
Uncertain:
Class 2 Likely
not pathogenic:
4 points of evidence:
Abr...
Nature Genetics 46, 107–115 (2014)
Rationale underlying Class 5
criteria
Class 5: evidence from tumor
molecular pathology
Criterion
• > 2 tumors with MSI-H
and/or appropriate IHC loss
Rationale
•...
Transparent presentation of summary
data for classifications
www.insight-group.org/classifications
Future Perspectives
• Rule revision (ie, de novo mutations)
• Revise classifications
• Gene-specific rules
• Intermediate ...
InSiGHT Variant Interpretation Committee (VIC)
Bryony A. Thompson
Amanda B. Spurdle
Marc Greenblatt
John-Paul Plazzer
Kiwa...
Development of rules for the interpretation of mismatch repair gene variants based on the 5-tiered IARC classification sys...
Development of rules for the interpretation of mismatch repair gene variants based on the 5-tiered IARC classification sys...
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Development of rules for the interpretation of mismatch repair gene variants based on the 5-tiered IARC classification system - Maurizio Genuardi

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The International Society for Gastrointestinal Hereditary Tumors (InSIGHT) has established a committee (Variant Interpretation Committee; VIC) for the interpretation of sequence variants in the mismatch repair (MMR) genes associated with Lynch syndrome (LS). One of the major steps involved in this process has been the establishment of qualitative specific classification rules for the MMR genes, with the aim to improve the clinical utility of MMR gene testing. The 5-class variant classification system proposed by the International Agency for Research on Cancer (IARC) was used to this purpose, since it links all classes to specific clinical recommendations. Multiple lines of evidence were required for class assignment and in order to classify a variant as pathogenic or likely pathogenic, (Classes 5 and 4, respectively), or as not pathogenic or likely not pathogenic (Classes 1 and 2, respectively), concordant evidence derived from both clinical and functional datasets had to be available. Variants with discordant information or with lack of either clinical or functional information, were considered of uncertain significance (Class 3). The following specific points of evidence were considered: 1. Type of sequence variation; 2) functional protein assays; 3) mRNA assays; 4) phenotype associated in compound heterozygotes for the variant under scrutiny and a clearly pathogenic variant in the same gene; 5) presence of the variant on different haplotypes across LS families; 6) co-segregation data and clinical phenotype; 7) tumor molecular characteristics; 8) population frequency; 9) risk estimated from case-control studies. Since interpretation of functional assays proved to be difficult and variable across committee members, specific supporting information and flowcharts were developed. In addition, whenever available, quantitative multifactorial analysis2 was used and the outcome compared to that of qualitative assessment. The classification scheme was modified by consensus to accommodate new data and inconsistencies over multiple classification teleconferences and face-to-face meetings. Overall, the rules were successfully applied to classify 2,360 variants lodged onto the InSiGHT database. These criteria provide a baseline for standardized clinical classification of MMR gene sequence variation that may be linked to patient and family management in the genetic counseling arena according to published guidelines.

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Development of rules for the interpretation of mismatch repair gene variants based on the 5-tiered IARC classification system - Maurizio Genuardi

  1. 1. Development of rules for the interpretation of mismatch repair gene variants based on the 5-tiered IARC classification system On behalf of the InSiGHT Variant Interpretation Committee 5° Biennial Human Variome Project Meeting Paris, 22-05-2014 INTERNATIONAL SOCIETYINTERNATIONAL SOCIETY FOR GASTROINTESTINALFOR GASTROINTESTINAL HEREDITARY TUMOURSHEREDITARY TUMOURS DEPT. MEDICAL GENETICSDEPT. MEDICAL GENETICS CATHOLIC UNIVERSITYCATHOLIC UNIVERSITY ROMEROME
  2. 2. Human Mutation (2008) 29:1282–1291.
  3. 3. InSiGHT Mutation Database: data cleaning, nomenclature standardization and systematic data review 12,645 MMR gene submissions 10 Source unknown / non- existant 3,468 nomenclature alterations (12 not resolvable) Duplicate entries resolved 230 Somatic 7 EPCAM 132 Synthetic 2,360 unique constitutional MMR gene variants (MSH2, MLH1, MSH6, PMS2)
  4. 4. Criteria development process • Used modified Delphi approach – http://en.wikipedia.org/wiki/Delphi_method • Evolution of criteria – Started with the 117 most commonly cited variants with discordant interpretation – Iterative amendments & clarifications over 12 meetings • Quantitative (multifactorial) or qualitative evidence considered • Work towards fully quantitative (Bayesian), recognising limits – Calibration of in silico algorithms
  5. 5. Current Multifactorial Likelihood Model Quantitative classification MMR Sequence Variant + = Thompson et al Hum Mutat, 2013. 34(1): p.200-09. Require ≥2 data points to promote robust classification
  6. 6. QUALITATIVE RULES: POINTS OF EVIDENCE a. Co-segregation b. Tumor molecular characteristics: MSI, IHC (BRAF) c. Population frequency d. Risk estimated from case-control studies e. Presence of the variant on different haplotypes across LS families f. Type of sequence variation g. Functional protein assays h. mRNA assays i. Co-occurrence of the variant with a clearly pathogenic variant in the same gene and CMMRD phenotype
  7. 7. Qualitative points of evidence 5’…TCT CAA AAA TTT ACG…3’ S Q K F T 5’…TCT CAA TAA TTT ACG…3’ S Q * Sequence-based Segregation data Tumour data Frequency data Co-occurrence in trans In vitro data Presence/absence of haematological malignancies, childhood cancers – CMMR-D phenotype Clinical/molecular Functional
  8. 8. • Major issue in classification process was conflicting data from functional assays • Functional assay subcommittee formed to tackle the issue • Flowchart developed to assist assay interpretation Functional assay interpretation
  9. 9. Class 5 Pathogenic: Class 4 Likely pathogenic: Class 3 Uncertain: Class 2 Likely not pathogenic: 4 points of evidence: Abrogated function or CMMRD or different background haplotypes Co-segregation with disease (~LR 10:1) ≥2 tumors with LS molecular phenotype Absence in 1000 genomes PP >0.99 or Nonsense/frameshi ft Full inactivation of variant allele by splicing aberration Large deletion Large duplication confirmed to encode a frameshift leading to NMD or or or or 2 points of evidence: PP 0.95-0.99 Canonical splice site, untested for splicing Co-segregation with disease (~LR 5:1) Or ≥2 tumors with LS molecular phenotype Abrogated function or CMMRD or different background haplotypes or or Synonymous or intronic variant with no mRNA aberration AF ≥1% in specific ethnic group 2 points of evidence if proficient function, otherwise 3 points of evidence required: Proficient function or co-occurrence with no CMMRD AF 0.01-1% No co-segregation with disease (~LR 0.01:1) ≥3 MSS CRC or inconsistent IHC tumors Odds Ratio with upper 95% CI <5 in case-control studies PP 0.001-0.049 or or or Class 1 Not pathogenic: 3 points of evidence if proficient function, otherwise 4 points of evidence required: AF ≥1% in control reference groups Proficient function or co-occurrence with no CMMRD AF 0.01-1% No co-segregation with disease (~LR 0.01:1) ≥3 MSS CRC or inconsistent IHC tumors Odds Ratio with upper 95% CI <4 in case-control studies PP <0.001 or or Insufficient evidence to classify PP 0.05-0.949 or
  10. 10. Nature Genetics 46, 107–115 (2014) Rationale underlying Class 5 criteria
  11. 11. Class 5: evidence from tumor molecular pathology Criterion • > 2 tumors with MSI-H and/or appropriate IHC loss Rationale • Provides evidence that the variant is associated with the clinical phenotype. Assumed conservative LR > 5:1 for tumor data
  12. 12. Transparent presentation of summary data for classifications www.insight-group.org/classifications
  13. 13. Future Perspectives • Rule revision (ie, de novo mutations) • Revise classifications • Gene-specific rules • Intermediate penetrance variants • Further genes (APC, MUTYH,…)
  14. 14. InSiGHT Variant Interpretation Committee (VIC) Bryony A. Thompson Amanda B. Spurdle Marc Greenblatt John-Paul Plazzer Kiwamu Akagi Fahd Al-Mulla Bharati Bapat Inge Bernstein Gabriel Capella Johan T den Dunnen Desiree du Sart Mark Farrell Susan Farrington Ian Frayling Established Yokohama, 2007 Ming Qi Rajkumar Ramesar Brigitte Royer-Pokora Rodney Scott Rolf Sijmons Carli Tops Thomas Weber Juul Wijnen Michael Woods Lene Rasmussen David Goldgar Sean Tavtigian Finlay Macrae Maurizio Genuardi Thierry Frebourg Chris Heinen Elke Holinski-Feder Maija Kohonen-Corish Suet Yi Leung Annika Lindblom Kristina Lagerstedt Alexandra Martins Pal Moller Monika Morak Minna Nystrom Aurelie Fabre Paivi Peltomaki Marta Pineda

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