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The protein truncation test (PTT) is currently the fastest method in general use for detecting previously unidentified mutations in tumor suppressor genes. Greater than three kilobases of coding sequence can be screened by one PCR reaction, one coupled in vitro transcription/translation reaction, and one lane on an SDS-PAGE gel. The 16 kb of BRCA1/2 coding sequence can be screened with nine overlapping segments. Since 90% of BRCA1/2 mutations result in a truncated protein product, the theoretical false negative rate for a BRCA1/2 PTT screen should be 10%. In practice the false negative rate is much higher, especially when cDNA is used as template. However, the actual false negative rate for a given screen will depend on the details of how the test is performed. Design of the overlapping segments, gel parameters, and nonsense mediated mRNA decay can all influence the effectiveness of the screen. BRCA1/2 screening by PTT can be optimised by considering these variables. Furthermore, nonsense-mediated mRNA decay can be inhibited by blocking protein synthesis with cycloheximide.

A complete protein truncation test for BRCA1 and BRCA2