http://www.clinchem.org/cgi/content/abstract/52/4/728

(Clinical Chemistry. 2006;52:728-736.)

Laboratory Management

Benchmark for Evaluating the Quality of DNA Sequencing: Proposal from an International External Quality Assessment Scheme

Simon J. Patton^a, Andrew J. Wallace and Rob Elles

European Molecular Genetics Quality Network, National Genetics Reference Laboratory, St. Mary’s Hospital, Manchester, United Kingdom.

^aAddress correspondence to this author at: European Molecular Genetics Quality Network (EMQN), c/o National Genetics Reference Laboratory, St. Mary’s Hospital, Hathersage Road, Manchester M13 0JH, United Kingdom. Fax 44-161-276-6606; e-mail simon.patton@... .

Background: In the past 15 years, clinical laboratory science has been transformed by the use of technologies that 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 evaluation of DNA sequencing. We report the results of an international survey of the quality of DNA sequencing among 64 laboratories from 21 countries.

Methods: Current practice for DNA sequence analysis was established by use of an online questionnaire. Participating laboratories were provided with 4 DNA samples of validated genotype. Evaluation of the results included assessing the quality of sequence data, variant genotypes, and mutation nomenclature. To accommodate variations in mutation nomenclature, variants indicated by participants were scored for compliance with 3 acceptable marking schemes.

Results: A total of 346 genotypes were analyzed. 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 analyzed for 3 indicators of data quality: PHRED quality scores, Quality Read Length, and Quality Read Overlap. Most laboratories produced results of acceptable diagnostic quality as judged by these indicators. The results were used to calculate a consensus benchmark for DNA sequencing against which individual laboratories could rank their performance.

Conclusions: We propose that the consensus benchmark can be used as a baseline against which the aggregate and individual laboratory standard of DNA sequencing may be tracked from year to year.