Sequence polymorphism can produce serious artefacts in real-time PCR assays: hard lessons from Pacific oysters

• Published in: BMC Genomics
• Main Authors: Camara Mark D, Lang Robert P, Taris Nicolas
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2008
• Subjects: Biotechnology; TP248.13-248.65; Genetics; QH426-470; Pacific; Crassostrea gigas
• Online Access: https://doi.org/10.1186/1471-2164-9-234; https://doaj.org/article/7fd337d1d8bd49daaf5e50eee00a1ff9

Abstract Background Since it was first described in the mid-1990s, quantitative real time PCR (Q-PCR) has been widely used in many fields of biomedical research and molecular diagnostics. This method is routinely used to validate whole transcriptome analyses such as DNA microarrays, suppressive subtractive hybridization (SSH) or differential display techniques such as cDNA-AFLP (Amplification Fragment Length Polymorphism). Despite efforts to optimize the methodology, misleading results are still possible, even when standard optimization approaches are followed. Results As part of a larger project aimed at elucidating transcriptome-level responses of Pacific oysters ( Crassostrea gigas ) to various environmental stressors, we used microarrays and cDNA-AFLP to identify Expressed Sequence Tag (EST) fragments that are differentially expressed in response to bacterial challenge in two heat shock tolerant and two heat shock sensitive full-sib oyster families. We then designed primers for these differentially expressed ESTs in order to validate the results using Q-PCR. For two of these ESTs we tested fourteen primer pairs each and using standard optimization methods (i.e. melt-curve analysis to ensure amplification of a single product), determined that of the fourteen primer pairs tested, six and nine pairs respectively amplified a single product and were thus acceptable for further testing. However, when we used these primers, we obtained different statistical outcomes among primer pairs, raising unexpected but serious questions about their reliability. We hypothesize that as a consequence of high levels of sequence polymorphism in Pacific oysters, Q-PCR amplification is sub-optimal in some individuals because sequence variants in priming sites results in poor primer binding and amplification in some individuals. This issue is similar to the high frequency of null alleles observed for microsatellite markers in Pacific oysters. Conclusion This study highlights potential difficulties for using Q-PCR as a validation tool ...