Patton Simon J, Wallace Andrew J, Elles Rob
European Molecular Genetics Quality Network, National Genetics Reference Laboratory, St. Mary's Hospital, Manchester, United Kingdom.
Clin Chem. 2006 Apr;52(4):728-36. doi: 10.1373/clinchem.2005.061887. Epub 2006 Feb 2.
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.
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.
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.
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.
在过去15年中，临床检验科学因采用跨越传统检验学科界限的技术而发生了变革。然而，在此期间，质量问题并非始终得到充分关注。欧洲分子遗传学质量网络（EMQN）已开发出一种用于评估DNA测序的新型外部质量评估方案。我们报告了一项对来自21个国家的64个实验室的DNA测序质量的国际调查结果。
通过在线问卷确定DNA序列分析的当前实践。为参与实验室提供4个经过验证的基因型DNA样本。对结果的评估包括评估序列数据质量、变异基因型和突变命名法。为适应突变命名法的差异，对参与者指出的变异按照3种可接受的标记方案进行评分以确定其合规性。
共分析了346个基因型。其中，出现了19个（5%）基因分型错误。其中，10个（53%）为假阴性，9个（47%）为假阳性结果。在突变命名方面又出现了27个（8%）错误。对数据质量的3个指标进行了结果分析：PHRED质量分数、高质量读段长度和高质量读段重叠。根据这些指标判断，大多数实验室产生的结果具有可接受的诊断质量。这些结果被用于计算DNA测序的共识基准，各个实验室可据此对自身表现进行排名。
我们建议，该共识基准可作为一个基线，据此逐年跟踪DNA测序的总体和各个实验室标准。
