Genetics: Direct Comparison of Detection Systems Used for the Development of Single-Cell Genetic Tests in Preimplantation Genetic Diagnosis

Purpose: Single-cell polymerase chain reaction (PCR) requires efficient amplification and accurate detection. We compare the accuracy of heteroduplex, fluorescent-fragment, and fluorescent single-strand conformation polymorphism (F-SSCP) analysis as detection systems for analysis of a PCR assay developed for preimplantation genetic diagnosis.Methods: A single-cell, fluorescent multiplex PCR assay was developed for the cystic fibrosis F508 mutation and the short tandem repeat, D21S11. Detection systems were compared by analyzing blinded PCR products.Results: Amplification rates for cystic fibrosis were 89% by heteroduplex and 91% by fragment analysis, while it was 72% for D21S11 by fragment analysis. No difference in allele dropout was detected for cystic fibrosis by any method (2%). Overall accuracy was high, >97%, although SSCP was the least accurate.Conclusions: Heteroduplex and fragment analysis proved equal in the diagnosis of a single amplified locus. We determined that fragment analysis allows maximal accuracy of detection and permits analysis of a second loci, controlling for DNA contamination and allelic dropout.