A Multifactorial Likelihood Model for MMR Gene Variant Classification Incorporating Probabilities Based on Sequence Bioinformatics and Tumor Characteristics: A Report from the Colon Cancer Family Registry

Bryony A. Thompson, David E. Goldgar, Carol Paterson, Mark Clendenning, Rhiannon Walters, Sven Arnold, Michael T. Parsons, Walsh D. Michael, Steven Gallinger, Robert W. Haile, John L. Hopper, Mark A. Jenkins, Loic Lemarchand, Noralane Morey Lindor, Polly A. Newcomb, Stephen N Thibodeau, Joanne P. Young, Daniel D. Buchanan, Sean V. Tavtigian, Amanda B. Spurdle

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

Mismatch repair (MMR) gene sequence variants of uncertain clinical significance are often identified in suspected Lynch syndrome families, and this constitutes a challenge for both researchers and clinicians. Multifactorial likelihood model approaches provide a quantitative measure of MMR variant pathogenicity, but first require input of likelihood ratios (LRs) for different MMR variation-associated characteristics from appropriate, well-characterized reference datasets. Microsatellite instability (MSI) and somatic BRAF tumor data for unselected colorectal cancer probands of known pathogenic variant status were used to derive LRs for tumor characteristics using the Colon Cancer Family Registry (CFR) resource. These tumor LRs were combined with variant segregation within families, and estimates of prior probability of pathogenicity based on sequence conservation and position, to analyze 44 unclassified variants identified initially in Australasian Colon CFR families. In addition, in vitro splicing analyses were conducted on the subset of variants based on bioinformatic splicing predictions. The LR in favor of pathogenicity was estimated to be ∼12-fold for a colorectal tumor with a BRAF mutation-negative MSI-H phenotype. For 31 of the 44 variants, the posterior probabilities of pathogenicity were such that altered clinical management would be indicated. Our findings provide a working multifactorial likelihood model for classification that carefully considers mode of ascertainment for gene testing.

Original languageEnglish (US)
Pages (from-to)200-209
Number of pages10
JournalHuman Mutation
Volume34
Issue number1
DOIs
StatePublished - Jan 2013

Fingerprint

DNA Mismatch Repair
Computational Biology
Colonic Neoplasms
Virulence
Registries
Microsatellite Instability
Genes
Colorectal Neoplasms
Neoplasms
Hereditary Nonpolyposis Colorectal Neoplasms
Research Personnel
Phenotype
Mutation

Keywords

  • BRAF
  • Mismatch repair
  • MSI
  • Multifactorial likelihood model
  • Unclassified variants

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

A Multifactorial Likelihood Model for MMR Gene Variant Classification Incorporating Probabilities Based on Sequence Bioinformatics and Tumor Characteristics : A Report from the Colon Cancer Family Registry. / Thompson, Bryony A.; Goldgar, David E.; Paterson, Carol; Clendenning, Mark; Walters, Rhiannon; Arnold, Sven; Parsons, Michael T.; Michael, Walsh D.; Gallinger, Steven; Haile, Robert W.; Hopper, John L.; Jenkins, Mark A.; Lemarchand, Loic; Lindor, Noralane Morey; Newcomb, Polly A.; Thibodeau, Stephen N; Young, Joanne P.; Buchanan, Daniel D.; Tavtigian, Sean V.; Spurdle, Amanda B.

In: Human Mutation, Vol. 34, No. 1, 01.2013, p. 200-209.

Research output: Contribution to journalArticle

Thompson, BA, Goldgar, DE, Paterson, C, Clendenning, M, Walters, R, Arnold, S, Parsons, MT, Michael, WD, Gallinger, S, Haile, RW, Hopper, JL, Jenkins, MA, Lemarchand, L, Lindor, NM, Newcomb, PA, Thibodeau, SN, Young, JP, Buchanan, DD, Tavtigian, SV & Spurdle, AB 2013, 'A Multifactorial Likelihood Model for MMR Gene Variant Classification Incorporating Probabilities Based on Sequence Bioinformatics and Tumor Characteristics: A Report from the Colon Cancer Family Registry', Human Mutation, vol. 34, no. 1, pp. 200-209. https://doi.org/10.1002/humu.22213
Thompson, Bryony A. ; Goldgar, David E. ; Paterson, Carol ; Clendenning, Mark ; Walters, Rhiannon ; Arnold, Sven ; Parsons, Michael T. ; Michael, Walsh D. ; Gallinger, Steven ; Haile, Robert W. ; Hopper, John L. ; Jenkins, Mark A. ; Lemarchand, Loic ; Lindor, Noralane Morey ; Newcomb, Polly A. ; Thibodeau, Stephen N ; Young, Joanne P. ; Buchanan, Daniel D. ; Tavtigian, Sean V. ; Spurdle, Amanda B. / A Multifactorial Likelihood Model for MMR Gene Variant Classification Incorporating Probabilities Based on Sequence Bioinformatics and Tumor Characteristics : A Report from the Colon Cancer Family Registry. In: Human Mutation. 2013 ; Vol. 34, No. 1. pp. 200-209.
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abstract = "Mismatch repair (MMR) gene sequence variants of uncertain clinical significance are often identified in suspected Lynch syndrome families, and this constitutes a challenge for both researchers and clinicians. Multifactorial likelihood model approaches provide a quantitative measure of MMR variant pathogenicity, but first require input of likelihood ratios (LRs) for different MMR variation-associated characteristics from appropriate, well-characterized reference datasets. Microsatellite instability (MSI) and somatic BRAF tumor data for unselected colorectal cancer probands of known pathogenic variant status were used to derive LRs for tumor characteristics using the Colon Cancer Family Registry (CFR) resource. These tumor LRs were combined with variant segregation within families, and estimates of prior probability of pathogenicity based on sequence conservation and position, to analyze 44 unclassified variants identified initially in Australasian Colon CFR families. In addition, in vitro splicing analyses were conducted on the subset of variants based on bioinformatic splicing predictions. The LR in favor of pathogenicity was estimated to be ∼12-fold for a colorectal tumor with a BRAF mutation-negative MSI-H phenotype. For 31 of the 44 variants, the posterior probabilities of pathogenicity were such that altered clinical management would be indicated. Our findings provide a working multifactorial likelihood model for classification that carefully considers mode of ascertainment for gene testing.",
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AU - Gallinger, Steven

AU - Haile, Robert W.

AU - Hopper, John L.

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