European external quality control study on the competence of laboratories to recognize rare sequence variants resulting in unusual genotyping results

János Márki-Zay, Christoph L. Klein, David Gancberg, Heinz G. Schimmel, L. Dux

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: Depending on the method used, rare sequence variants adjacent to the single nucleotide polymorphism (SNP) of interest may cause unusual or erroneous genotyping results. Because such rare variants are known for many genes commonly tested in diagnostic laboratories, we organized a proficiency study to assess their influence on the accuracy of reported laboratory results. methods: Four external quality control materials were processed and sent to 283 laboratories through 3 EQA organizers for analysis of the prothrombin 20210G>A mutation. Two of these quality control materials contained sequence variants introduced by site-directed mutagenesis. results: One hundred eighty-nine laboratories participated in the study. When samples gave a usual result with the method applied, the error rate was 5.1%. Detailed analysis showed that more than 70% of the failures were reported from only 9 laboratories. Allele-specific amplification-based PCR had a much higher error rate than other methods (18.3% vs 2.9%). The variants 20209C>T and [20175T>G; 20179-20180delAC] resulted in unusual genotyping results in 67 and 85 laboratories, respectively. Eighty-three (54.6%) of these unusual results were not recognized, 32 (21.1%) were attributed to technical issues, and only 37 (24.3%) were recognized as another sequence variant. conclusions: Our findings revealed that some of the participating laboratories were not able to recognize and correctly interpret unusual genotyping results caused by rare SNPs. Our study indicates that the majority of the failures could be avoided by improved training and careful selection and validation of the methods applied.

Original languageEnglish
Pages (from-to)739-747
Number of pages9
JournalClinical Chemistry
Volume55
Issue number4
DOIs
Publication statusPublished - Apr 1 2009

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Quality Control
Mental Competency
Quality control
Single Nucleotide Polymorphism
Mutagenesis
Prothrombin
Site-Directed Mutagenesis
Polymorphism
Amplification
Nucleotides
Genes
Alleles
Polymerase Chain Reaction
Mutation

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

European external quality control study on the competence of laboratories to recognize rare sequence variants resulting in unusual genotyping results. / Márki-Zay, János; Klein, Christoph L.; Gancberg, David; Schimmel, Heinz G.; Dux, L.

In: Clinical Chemistry, Vol. 55, No. 4, 01.04.2009, p. 739-747.

Research output: Contribution to journalArticle

Márki-Zay, János ; Klein, Christoph L. ; Gancberg, David ; Schimmel, Heinz G. ; Dux, L. / European external quality control study on the competence of laboratories to recognize rare sequence variants resulting in unusual genotyping results. In: Clinical Chemistry. 2009 ; Vol. 55, No. 4. pp. 739-747.
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