Home LiteratureArticle Details
PMID: 19267393 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Classifying MLH1 and MSH2 variants using bioinformatic prediction, splicing assays, segregation, and tumor characteristics.

Human mutation ·Vol. 30 ·No. 5 ·2009-05-00 ·Pages 757-70

Arnold S, Buchanan DD, Barker M, Jaskowski L, Walsh MD, Birney G, Woods MO, Hopper JL, Jenkins MA, Brown MA, Tavtigian SV, Goldgar DE, Young JP, Spurdle AB

Abstract

Reliable methods for predicting functional consequences of variants in disease genes would be beneficial in the clinical setting. This study was undertaken to predict, and confirm in vitro, splicing aberrations associated with mismatch repair (MMR) variants identified in familial colon cancer patients. Six programs were used to predict the effect of 13 MLH1 and 6 MSH2 gene variants on pre-mRNA splicing. mRNA from cycloheximide-treated lymphoblastoid cell lines of variant carriers was screened for splicing aberrations. Tumors of variant carriers were tested for microsatellite instability and MMR protein expression. Variant segregation in families was assessed using Bayes factor causality analysis. Amino acid alterations were examined for evolutionary conservation and physicochemical properties. Splicing aberrations were detected for 10 variants, including a frameshift as a minor cDNA product, and altered ratio of known alternate splice products. Loss of splice sites was well predicted by splice-site prediction programs SpliceSiteFinder (90%) and NNSPLICE (90%), but consequence of splice site loss was less accurately predicted. No aberrations correlated with ESE predictions for the nine exonic variants studied. Seven of eight missense variants had normal splicing (88%), but only one was a substitution considered neutral from evolutionary/physicochemical analysis. Combined with information from tumor and segregation analysis, and literature review, 16 of 19 variants were considered clinically relevant. Bioinformatic tools for prediction of splicing aberrations need improvement before use without supporting studies to assess variant pathogenicity. Classification of mismatch repair gene variants is assisted by a comprehensive approach that includes in vitro, tumor pathology, clinical, and evolutionary conservation data.

MeSH Terms
Adaptor Proteins, Signal Transducing/genetics Aged Biological Assay Chromosome Segregation/genetics Colonic Neoplasms/genetics Computational Biology DNA, Complementary/genetics Female Heterozygote Humans Male Middle Aged MutL Protein Homolog 1 MutS Homolog 2 Protein/genetics Mutation/genetics Nuclear Proteins/genetics Polymerase Chain Reaction RNA Splicing/genetics
Chemicals
Adaptor Proteins, Signal Transducing DNA, Complementary MLH1 protein, human Nuclear Proteins MSH2 protein, human MutL Protein Homolog 1 MutS Homolog 2 Protein
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Arnold Sven
Genetics and Population Health Division, Queensland Institute of Medical Research, Brisbane, Australia.
Buchanan Daniel D
Barker Melissa
Jaskowski Lesley
Walsh Michael D
Birney Genevieve
Woods Michael O
Hopper John L
Jenkins Mark A
Brown Melissa A
Tavtigian Sean V
Goldgar David E
Young Joanne P
Spurdle Amanda B
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Article Info
Journal
Human mutation
Abbr.
Hum Mutat
ISSN
1098-1004
DOI
10.1002/humu.20936
Published
2009-05-00
Pages
757-70
Language
English
Region
United States
NLM ID
9215429
PMCID
PMC2707453
Subset
IM
Grants
NCI NIH HHS · P50 CA116201 · United States
NCI NIH HHS · U01 CA097735 · United States
NCI NIH HHS · U01 CA097735-05 · United States
NCI NIH HHS · RFA CA-95-011 · United States
External Links
PubMed source DOI: 10.1002/humu.20936 PMC Full Text View journal details
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