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A quality assessment survey of SNP genotyping laboratories
Author(s) -
Lahermo Päivi,
Liljedahl Ulrika,
Alnaes Grethe,
Axelsson Tomas,
Brookes Anthony J.,
Ellonen Pekka,
Groop PerHenrik,
Halldén Christer,
Holmberg Dan,
Holmberg Kristina,
Keinänen Mauri,
Kepp Katrin,
Kere Juha,
Kiviluoma Päivi,
Kristensen Vessela,
Lindgren Cecilia,
Odeberg Jacob,
Osterman Pia,
Parkkonen Maija,
Saarela Janna,
Sterner Maria,
Strömqvist Linda,
Talas Ulvi,
Wessman Maija,
Palotie Aarno,
Syvänen AnnChristine
Publication year - 2006
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.20346
Subject(s) - biology , genotyping , snp , snp genotyping , external quality assessment , computational biology , genetics , single nucleotide polymorphism , genotype , gene , engineering , operations management
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. Hum Mutat 27(7), 711–714, 2006. © 2006 Wiley‐Liss, Inc.