A quality assessment survey of SNP genotyping laboratories.
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.
Lahermo
Päivi
P
Finnish Genome Center, University of Helsinki, Helsinki, Finland.
Liljedahl
Ulrika
U
Alnaes
Grethe
G
Axelsson
Tomas
T
Brookes
Anthony J
AJ
Ellonen
Pekka
P
Groop
Per-Henrik
PH
Halldén
Christer
C
Holmberg
Dan
D
Holmberg
Kristina
K
Keinänen
Mauri
M
Kepp
Katrin
K
Kere
Juha
J
Kiviluoma
Päivi
P
Kristensen
Vessela
V
Lindgren
Cecilia
C
Odeberg
Jacob
J
Osterman
Pia
P
Parkkonen
Maija
M
Saarela
Janna
J
Sterner
Maria
M
Strömqvist
Linda
L
Talas
Ulvi
U
Wessman
Maija
M
Palotie
Aarno
A
Syvänen
Ann-Christine
AC
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