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A quality assessment survey of SNP genotyping laboratories
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
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2006 (English)In: Human Mutation, ISSN 1059-7794, E-ISSN 1098-1004, Vol. 27, no 7, 711-714 p.Article in journal (Other academic) Published
Abstract [en]

To survey the quality of SNP genotyping, a joint Nordic quality assessment (QA) round was organized between 11 laboratories in the Nordic and Baltic countries. The QA round involved blinded genotyping of 47 DNA samples for 18 or six randomly selected SNPs. The methods used by the participating laboratories included all major platforms for small- to medium-size SNP genotyping. The laboratories used their standard procedures for SNP assay design, genotyping, and quality control. Based on the joint results from all laboratories, a consensus genotype for each DNA sample and SNP was determined by the coordinator of the survey, and the results from each laboratory were compared to this genotype. The overall genotyping accuracy achieved in the survey was excellent. Six laboratories delivered genotype data that were in full agreement with the consensus genotype. The average accuracy per SNP varied from 99.1 to 100% between the laboratories, and it was frequently 100% for the majority of the assays for which SNP genotypes were reported. Lessons from the survey are that special attention should be given to the quality of the DNA samples prior to genotyping, and that a conservative approach for calling the genotypes should be used to achieve a high accuracy.

Place, publisher, year, edition, pages
2006. Vol. 27, no 7, 711-714 p.
Keyword [en]
Clinical Laboratory Techniques/*standards, Estonia, Finland, Genotype, Norway, Polymorphism; Single Nucleotide, Quality Control, Research Support; Non-U.S. Gov't, Sequence Analysis; DNA/*standards, Sweden
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-82133DOI: 10.1002/humu.20346PubMedID: 16786507OAI: oai:DiVA.org:uu-82133DiVA: diva2:110048
Available from: 2006-09-19 Created: 2006-09-19 Last updated: 2012-04-12Bibliographically approved

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Publisher's full textPubMedhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=16786507&dopt=Citation

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Syvänen, Ann-Christine
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