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Comparison of Techniques for the Successful Detection of BRCA1 Mutations in Fixed Paraffin-Embedded Tissue¹

Department of Community and Preventive Medicine, Mount Sinai School of Medicine, New York, New York 10029 [J. L. B., S. S. T.]; Department of Applied Medical Sciences, University of Southern Maine, Portland, Maine 04104 [W. D. T.]; Department of Cancer Biology, Cleveland Clinic Foundation, Cleveland, Ohio 44195 [G. C., S. V.]; Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263 [R. A. D.]; Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California 94305 [A. S. W.]; Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, California 90033 [A. T. D., S. X., R. W. H.]

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.

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