title: Comparison of techniques for the successful detection of BRCA1 mutations in fixed paraffin-embedded tissue.
abstract: Genomic DNA isolated from archived paraffin-embedded tissues (PETs) has important applicability in genetic epidemiological studies. To determine the accuracy of the sequence data, using DNA derived from PET among patients with known mutations characterized from blood, we conducted a blinded factorial experiment to simultaneously examine the influence of mutation type, age of the PET, PCR product type, and Taq DNA polymerase on BRCA1 gene mutation detection. The probability of detecting sequencing artifacts was also investigated. We found that: (a) gene detection was most accurate for newer PET; (b) high fidelity Taq with shorter PCR amplicon length yielded the highest mutation detection success rate and lowest artifact rate; and (c) base substitutions were more often correctly identified than frameshift mutations or wild-type sequences. We concluded that DNA derived from PET that archived for less than 18 years can be used successfully for detecting BRCA1 gene mutations if quality control is strictly maintained.
authors.affiliation: Department of Community and Preventive Medicine, Mount Sinai School of Medicine, New York, New York 10029, USA. jonine.bernstein@mssn.edu
authors.forename: Jonine L
authors.initials: JL
authors.lastname: Bernstein
authors.forename: W Douglas
authors.initials: WD
authors.lastname: Thompson
authors.forename: Graham
authors.initials: G
authors.lastname: Casey
authors.forename: Richard A
authors.initials: RA
authors.lastname: DiCioccio
authors.forename: Alice S
authors.initials: AS
authors.lastname: Whittemore
authors.forename: Anh T
authors.initials: AT
authors.lastname: Diep
authors.forename: Seema S
authors.initials: SS
authors.lastname: Thakore
authors.forename: Susan
authors.initials: S
authors.lastname: Vaziri
authors.forename: Shanyan
authors.initials: S
authors.lastname: Xue
authors.forename: Robert W
authors.initials: RW
authors.lastname: Haile
mesh_terms: D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000032:analysis / Q000235:genetics*; D005260:Female; D019398:Genes, BRCA1; D005819:Genetic Markers; D006801:Humans; D016612:Paraffin Embedding; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm; D005819:Genetic Markers