Genetic diagnosis of familial breast cancer using clonal sequencing.
Using conventional Sanger sequencing as a reference standard, we compared the sensitivity, specificity, and capacity of the Illumina GA II platform for the detection of TP53, BRCA1, and BRCA2 mutations in established tumor cell lines and DNA from patients with germline mutations. A total of 656 coding variants were identified in four cell lines and 65 patient DNAs. All of the known pathogenic mutations (including point mutations and insertions/deletions of up to 16 nucleotides) were identified, using a combination of the Illumina data analysis pipeline with custom and commercial sequence alignment software. In our configuration, clonal sequencing outperforms current diagnostic methods, providing a reduction in analysis times and in reagent costs compared with conventional sequencing. These improvements open the possibility of BRCA1/2 testing for a wider spectrum of at-risk women, and will allow the genetic classification of tumors prior to the use of novel PARP inhibitors to treat BRCA-deficient breast cancers.
Morgan
Joanne E
JE
University of Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, St. James's University Hospital, Beckett Street, Leeds, United Kingdom.
Carr
Ian M
IM
Sheridan
Eamonn
E
Chu
Carol E
CE
Hayward
Bruce
B
Camm
Nick
N
Lindsay
Helen A
HA
Mattocks
Chris J
CJ
Markham
Alexander F
AF
Bonthron
David T
DT
Taylor
Graham R
GR
D019313:BRCA1 Protein / Q000235:genetics; D024682:BRCA2 Protein / Q000235:genetics; D001483:Base Sequence; D001943:Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D002999:Clone Cells / Q000378:metabolism / Q000473:pathology; D021901:DNA, Intergenic / Q000235:genetics; D005260:Female; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
D019313:BRCA1 Protein; D024682:BRCA2 Protein; D021901:DNA, Intergenic