Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?
BACKGROUND
Many of the DNA sequence variants identified in the breast cancer susceptibility gene BRCA1 remain unclassified in terms of their potential pathogenicity. Both multifactorial likelihood analysis and functional approaches have been proposed as a means to elucidate likely clinical significance of such variants, but analysis of the comparative value of these methods for classifying all sequence variants has been limited.


METHODS
We have compared the results from multifactorial likelihood analysis with those from several functional analyses for the four BRCA1 sequence variants A1708E, G1738R, R1699Q, and A1708V.


RESULTS
Our results show that multifactorial likelihood analysis, which incorporates sequence conservation, co-inheritance, segregation, and tumour immunohistochemical analysis, may improve classification of variants. For A1708E, previously shown to be functionally compromised, analysis of oestrogen receptor, cytokeratin 5/6, and cytokeratin 14 tumour expression data significantly strengthened the prediction of pathogenicity, giving a posterior probability of pathogenicity of 99%. For G1738R, shown to be functionally defective in this study, immunohistochemistry analysis confirmed previous findings of inconsistent 'BRCA1-like' phenotypes for the two tumours studied, and the posterior probability for this variant was 96%. The posterior probabilities of R1699Q and A1708V were 54% and 69%, respectively, only moderately suggestive of increased risk. Interestingly, results from functional analyses suggest that both of these variants have only partial functional activity. R1699Q was defective in foci formation in response to DNA damage and displayed intermediate transcriptional transactivation activity but showed no evidence for centrosome amplification. In contrast, A1708V displayed an intermediate transcriptional transactivation activity and a normal foci formation response in response to DNA damage but induced centrosome amplification.


CONCLUSIONS
These data highlight the need for a range of functional studies to be performed in order to identify variants with partially compromised function. The results also raise the possibility that A1708V and R1699Q may be associated with a low or moderate risk of cancer. While data pooling strategies may provide more information for multifactorial analysis to improve the interpretation of the clinical significance of these variants, it is likely that the development of current multifactorial likelihood approaches and the consideration of alternative statistical approaches will be needed to determine whether these individually rare variants do confer a low or moderate risk of breast cancer.
Lovelock
Paul K
PK
Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Herston Road, Queensland 4029, Australia.
Spurdle
Amanda B
AB
Mok
Myth T S
MT
Farrugia
Daniel J
DJ
Lakhani
Sunil R
SR
Healey
Sue
S
Arnold
Stephen
S
Buchanan
Daniel
D
Couch
Fergus J
FJ
Henderson
Beric R
BR
Goldgar
David E
DE
Tavtigian
Sean V
SV
Chenevix-Trench
Georgia
G
Brown
Melissa A
MA
D000409:Alanine; D001120:Arginine; D014408:Biomarkers, Tumor / Q000032:analysis*; D001943:Breast Neoplasms / Q000737:chemistry* / Q000235:genetics* / Q000473:pathology; D018385:Centrosome; D018076:DNA, Complementary; D005163:Factor Analysis, Statistical; D005260:Female; D019398:Genes, BRCA1; D020022:Genetic Predisposition to Disease; D018698:Glutamic Acid; D005973:Glutamine; D005998:Glycine; D006801:Humans; D007150:Immunohistochemistry; D007633:Keratins / Q000032:analysis; D020125:Mutation, Missense; D021141:Nucleic Acid Amplification Techniques; D010957:Plasmids; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D011960:Receptors, Estrogen / Q000032:analysis; D018570:Risk Assessment; D012307:Risk Factors; D017422:Sequence Analysis, DNA; D014633:Valine
D014408:Biomarkers, Tumor; D018076:DNA, Complementary; D011960:Receptors, Estrogen; D005973:Glutamine; D018698:Glutamic Acid; D007633:Keratins; D001120:Arginine; D014633:Valine; D000409:Alanine; D005998:Glycine