A quality assessment survey of SNP genotyping laboratories

Päivi Lahermo, Ulrika Liljedahl, Grethe Alnaes, Tomas Axelsson, Anthony J. Brookes, Pekka Ellonen, Per-Henrik Groop, Christer Halldén, Dan Holmberg, Kristina Holmberg, Mauri Keinänen, Katrin Kepp, Juha Kere, Päivi Kiviluoma, Vessela Kristensen, Cecilia Lindgren, Jacob Odeberg, Pia Osterman, Maija Parkkonen, Janna SaarelaMaria Sterner, Linda Strömqvist, Ulvi Talas, Maija Wessman, Aarno Palotie, Ann-Christine Syvänen

Forskningsoutput: TidskriftsbidragArtikelPeer review

Sammanfattning

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.

OriginalspråkEngelska
Sidor (från-till)711-714
Antal sidor3
TidskriftHuman Mutation
Volym27
Utgåva7
DOI
StatusPublicerad - 2006
Externt publiceradJa

Nationell ämneskategori

  • Biologi (106)

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