Clinical classification of BRCA1 and BRCA2 DNA sequence variants: the value of cytokeratin profiles and evolutionary analysis--a report from the kConFab Investigators.
OBJECTIVE
Rare missense substitutions and in-frame deletions of BRCA1 and BRCA2 genes present a challenge for genetic counseling of individuals carrying such unclassified variants. We assessed the value of tumor immunohistochemical markers in conjunction with genetic and evolutionary approaches for investigating the clinical significance of unclassified variants.


METHODS
We studied 10 BRCA1 and 12 BRCA2 variants identified in Australian families with breast cancer. Analyses assumed a prior probability based on revised cross-species sequence alignment methods assessing amino acid evolutionary conservation and position, combined with likelihoods from data on co-occurrence with pathogenic mutations in the same gene, segregation analysis, and immunohistochemistry. We specifically explored the value of estrogen receptor, cytokeratin 5/6, and cytokeratin 14 as tumor markers of BRCA1 mutation status.


RESULTS
Posterior probabilities classified 72% of variants. BRCA1 variants IVS18+1 G>T (del exon 18) and 5632 T >A (V1838E) were classified as pathogenic, with >99% posterior probability of being deleterious, and tumor histopathology was particularly important for their classification. BRCA2 variant classification was improved over previous studies, largely by incorporating the prior probability of pathogenicity based on amino acid cross-species sequence alignments.


CONCLUSIONS
Variant classification was considerably improved by analysis of estrogen receptor, cytokeratin 5/6, and cytokeratin 14 tumor expression, and use of updated methods estimating the clinical relevance of amino acid evolutionary conservation and position. These methodologies may assist genetic counseling of individuals with unclassified sequence variants.
Spurdle
Amanda B
AB
Queensland Institute of Medical Research, c/o Royal Brisbane Hospital Post Office, Herston, Queensland 4029, Australia. Amanda.Spurdle@qimr.edu.au
Lakhani
Sunil R
SR
Healey
Sue
S
Parry
Suzanne
S
Da Silva
Leonard M
LM
Brinkworth
Ross
R
Hopper
John L
JL
Brown
Melissa A
MA
Babikyan
Davit
D
Chenevix-Trench
Georgia
G
Tavtigian
Sean V
SV
Goldgar
David E
DE
D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D014408:Biomarkers, Tumor / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics*; D002851:Chromatography, High Pressure Liquid; D004252:DNA Mutational Analysis; D005260:Female; D019398:Genes, BRCA1; D024522:Genes, BRCA2; D014644:Genetic Variation; D006801:Humans; D007150:Immunohistochemistry; D007633:Keratins / Q000378:metabolism*; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D009154:Mutation; D010375:Pedigree; D011960:Receptors, Estrogen / Q000096:biosynthesis; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D014408:Biomarkers, Tumor; D011960:Receptors, Estrogen; D007633:Keratins