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A quality assessment survey of SNP genotyping laboratories

Lahermo, P; Liljedahl, U; Alnaes, G; Axelsson, T; Brookes, AJ; Ellonen, P; Groop, PH; Halldén, Christer LU ; Holmberg, D and Holmberg, K, et al. (2006) In Human Mutation 27(7). p.711-714
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... (More)
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. (c) 2006 Wiley-Liss, Inc. (Less)
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type
Contribution to journal
publication status
published
subject
keywords
quality assessment, SNP, genotyping
in
Human Mutation
volume
27
issue
7
pages
711 - 714
publisher
John Wiley & Sons
external identifiers
  • pmid:16786507
  • wos:000238548500013
  • scopus:33745728341
ISSN
1059-7794
DOI
10.1002/humu.20346
language
English
LU publication?
yes
id
f56e2ec5-560e-4d33-88d6-fcb5b4f8daaf (old id 686480)
date added to LUP
2008-01-06 10:18:40
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2019-02-20 04:38:29
@article{f56e2ec5-560e-4d33-88d6-fcb5b4f8daaf,
  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. Hum Mutat 27(7), 711-714,2006. (c) 2006 Wiley-Liss, Inc.},
  author       = {Lahermo, P and Liljedahl, U and Alnaes, G and Axelsson, T and Brookes, AJ and Ellonen, P and Groop, PH and Halldén, Christer and Holmberg, D and Holmberg, K and Keinanen, M and Kepp, K and Kere, J and Kiviluoma, P and Kristensen, V and Lindgren, C and Odeberg, J and Osterman, P and Parkkonen, M and Saarela, J and Sterner, M and Stromqvist, L and Talas, U and Wessman, M and Palotie, A and Syvanen, AC},
  issn         = {1059-7794},
  keyword      = {quality assessment,SNP,genotyping},
  language     = {eng},
  number       = {7},
  pages        = {711--714},
  publisher    = {John Wiley & Sons},
  series       = {Human Mutation},
  title        = {A quality assessment survey of SNP genotyping laboratories},
  url          = {http://dx.doi.org/10.1002/humu.20346},
  volume       = {27},
  year         = {2006},
}