Rare, evolutionarily unlikely missense substitutions in CHEK2 contribute to breast cancer susceptibility: results from a breast cancer family registry (CFR) case-control mutation screening study

Florence Le Calvez-Kelm , Fabienne Lesueur , Francesca Damiola , Maxime Vallee , Catherine Voegele , Davit Babikyan , Geoffroy Durand , Nathalie Forey , Sandrine McKay-Chopin , Nivonirina Robinot , Tu Nguyen-Dumont , Alun Thomas , Graham B Byrnes , The Breast Cancer Family Registry , John L Hopper , Melissa C Southey , Irene L Andrulis , Esther M John and Sean V Tavtigian

Breast Cancer Research 2011, 13:R6doi:10.1186/bcr2810

Published:	18 January 2011

Abstract (provisional)

Introduction

Both protein truncating variants and some missense substitutions in CHEK2 confer increased risk of breast cancer. However, no large-scale study has used full open reading frame mutation screening to assess the contribution of rare missense substitutions in CHEK2 to breast cancer risk. This absence has been due in part to a lack of validated statistical methods for summarizing risk attributable to large numbers of individually rare missense substitutions.

Methods

Previously, we adapted an in silico assessment of missense substitutions used for analysis of unclassified missense substitutions in BRCA1 and BRCA2 to the problem of assessing candidate genes using rare missense substitution data observed in case-control mutation screening studies. The method involves stratifying rare missense substitutions observed in cases and/ or controls into a series of grades a priori ordered from least to most likely to be evolutionarily deleterious, followed by a logistic regression test for trend to compare the frequency distributions of the graded missense substitutions in cases versus controls. Here we used this approach to analyze CHEK2 mutation screening data from a population based series of 1303 female breast cancer cases and 1109 unaffected female controls.

Results

We found evidence of risk associated with rare, evolutionarily unlikely CHEK2 missense substitutions. Additional findings were: (1) the risk estimate for the most severe grade of CHEK2 missense substitutions (denoted C65) is approximately equivalent to that of CHEK2 protein truncating variants; (2) the population attributable fraction and familial relative risk explained by the pool of rare missense substitutions were similar to those explained by the pool of protein truncating variants; and (3) post-hoc power calculations implied that scaling case-control mutation screening up to examine entire biochemical pathways would require roughly 2,000 cases and controls to achieve acceptable statistical power.

Conclusions

This study shows that CHEK2 harbors many rare sequence variants that confer increased risk of breast cancer, and a substantial proportion of these are missense substitutions. The study validates our analytic approach to rare missense substitutions and provides a method to combine data from protein truncating variants and rare missense substitutions into a one degree of freedom per gene test.

Source : http://breast-cancer-research.com/content/13/1/R6