Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial.

AIMS: Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. METHODS: 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. RESULTS: Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p

A quality control program for mutation detection in KIT and PDGFRA in gastrointestinal stromal tumours.

BACKGROUND: Although most gastrointestinal stromal tumours (GIST) carry oncogenic mutations in KIT exons 9, 11, 13 and 17, or in platelet-derived growth factor receptor alpha (PDGFRA) exons 12, 14 and 18, around 10% of GIST are free of these mutations. Genotyping and accurate detection of KIT/PDGFRA mutations in GIST are becoming increasingly useful for clinicians in the management of the disease. METHOD: To evaluate and improve laboratory practice in GIST mutation detection, we developed a mutational screening quality control program. Eleven laboratories were enrolled in this program and 50 DNA samples were analysed, each of them by four different laboratories, giving 200 mutational reports. RESULTS: In total, eight mutations were not detected by at least one laboratory. One false positive result was reported in one sample. Thus, the mean global rate of error with clinical implication based on 200 reports was 4.5%. Concerning specific polymorphisms detection, the rate varied from 0 to 100%, depending on the laboratory. The way mutations were reported was very heterogeneous, and some errors were detected. CONCLUSION: This study demonstrated that such a program was necessary for laboratories to improve the quality of the analysis, because an error rate of 4.5% may have clinical consequences for the patient.

I/Q imbalance in two-way AF relaying: Performance analysis and detection mode switch

This paper studies the impact of in-phase and quadrature-phase imbalance (IQI) in two-way amplify-and-forward (AF) relaying systems. In particular, the effective signal-to-interference-plus-noise ratio (SINR) is derived for each source node, considering four different linear detection schemes, namely, uncompensated (Uncomp) scheme, maximal-ratio-combining (MRC), zero-forcing (ZF) and minimum mean-square error (MMSE) based schemes. For each proposed scheme, the outage probability (OP) is investigated over independent, non-identically distributed Nakagami-m fading channels, and exact closed-form expressions are derived for the first three schemes. Based on the closed-form OP expressions, an adaptive detection mode switching scheme is designed for minimizing the OP of both sources. An important observation is that, regardless of the channel conditions and transmit powers, the ZF-based scheme should always be selected if the target SINR is larger than 3 (4.77dB), while the MRC-based scheme should be avoided if the target SINR is larger than 0.38 (-4.20dB).