Generic EQA/PT: experience from the European DNA sequencing scheme
In the past 15 years clinical laboratory science has been transformed by the use of generic technologies which cross the traditional boundaries between laboratory disciplines. However, during this period issues of quality have not always been given adequate attention. The European Molecular Genetics Quality Network (EMQN) has developed a novel external quality assessment scheme for the evaluation of one of the common generic technologies, DNA sequencing. This presentation reports the results of an international survey of the quality of DNA sequencing amongst 64 laboratories from 21 countries. Current practice for DNA sequence analysis was established using an online questionnaire. Participating laboratories were provided with four DNA samples of validated genotype. Evaluation of the results included assessment of the quality of sequence data, variant genotypes and mutation nomenclature. To accommodate variation in mutation nomenclature, variants indicated by participants were scored for compliance with three acceptable marking schemes. Three hundred and forty six genotypes were analysed. Of these, 19 (5%) genotyping errors were made. Of these 10 (53%) were false negative and 9 (47%) were false positive results. A further 27 (8%) errors were made in naming mutations. Results were analysed for three indicators of data quality (PHRED quality scores, Quality Read Length and Quality Read Overlap) - the majority of laboratories produced data which met these indicators and was of acceptable diagnostic quality. The results were used to calculate a consensus benchmark for DNA sequencing against which individual laboratories could rank their performance. We propose that this could establish a baseline against which the aggregate and individual laboratory standard of DNA sequencing may be tracked from year to year. We will discuss the role of this and similar published technical schemes in the provision of EQA for diagnostic molecular genetics.