title: A quality assessment survey of SNP genotyping laboratories.
abstract: 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.
authors.affiliation: Finnish Genome Center, University of Helsinki, Helsinki, Finland.
authors.forename: Päivi
authors.initials: P
authors.lastname: Lahermo
authors.forename: Ulrika
authors.initials: U
authors.lastname: Liljedahl
authors.forename: Grethe
authors.initials: G
authors.lastname: Alnaes
authors.forename: Tomas
authors.initials: T
authors.lastname: Axelsson
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Brookes
authors.forename: Pekka
authors.initials: P
authors.lastname: Ellonen
authors.forename: Per-Henrik
authors.initials: PH
authors.lastname: Groop
authors.forename: Christer
authors.initials: C
authors.lastname: Halldén
authors.forename: Dan
authors.initials: D
authors.lastname: Holmberg
authors.forename: Kristina
authors.initials: K
authors.lastname: Holmberg
authors.forename: Mauri
authors.initials: M
authors.lastname: Keinänen
authors.forename: Katrin
authors.initials: K
authors.lastname: Kepp
authors.forename: Juha
authors.initials: J
authors.lastname: Kere
authors.forename: Päivi
authors.initials: P
authors.lastname: Kiviluoma
authors.forename: Vessela
authors.initials: V
authors.lastname: Kristensen
authors.forename: Cecilia
authors.initials: C
authors.lastname: Lindgren
authors.forename: Jacob
authors.initials: J
authors.lastname: Odeberg
authors.forename: Pia
authors.initials: P
authors.lastname: Osterman
authors.forename: Maija
authors.initials: M
authors.lastname: Parkkonen
authors.forename: Janna
authors.initials: J
authors.lastname: Saarela
authors.forename: Maria
authors.initials: M
authors.lastname: Sterner
authors.forename: Linda
authors.initials: L
authors.lastname: Strömqvist
authors.forename: Ulvi
authors.initials: U
authors.lastname: Talas
authors.forename: Maija
authors.initials: M
authors.lastname: Wessman
authors.forename: Aarno
authors.initials: A
authors.lastname: Palotie
authors.forename: Ann-Christine
authors.initials: AC
authors.lastname: Syvänen
mesh_terms: D019411:Clinical Laboratory Techniques / Q000592:standards*; D004957:Estonia; D005387:Finland; D005838:Genotype; D009664:Norway; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000592:standards*; D013548:Sweden