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Genomics Inform > Volume 7(1); 2009 > Article
Choosing Optimal STR Markers for Quality Assurance of Distributed Biomaterials in Biobanking.
Tae Hoon Chung, Heejung Lee, Mihee Lee, Jae Pil Jeon, Kisang Kim, Bok Ghee Han
Korea Biobank, Center for Genome Science, Korean National Institute of Health, Korea Center for Disease Control and Prevention, Seoul, Korea.
The quality assurance (QA) is of utmost importance in biobanks when archived biomaterials are distributed to biomedical researchers. For sample authentication and cross-contamination detection, the two fundamental elements of QA, STR genotyping is usually utilized. However, the incorporated number of STR markers is highly redundant for biobanking purposes, resulting in time and cost inefficiency. An index to measure the cross-contamination detection capability of an STR marker, the mixture probability (MP), was developed. MP as well as other forensic parameters for STR markers was validated using STR genotyping data on 2328 normal Koreans with the commercial AmpFlSTR kit. For Koreans, 7 STR marker (D2S1338, FGA, D18S51, D8S1179, D13S317, D21S11, vWA) set was sufficient to provide discrimination power of ~10(-10) and cross-contamination detection probability of ~1. Interestingly, similar marker sets were obtained from African Americans, Caucasian Americans, and Hispanic Americans under the same level of discrimination power. Only a small subset of commonly used STR markers is sufficient for QA purposes in biobanks. A procedure for selecting optimal STR markers is outlined using STR genotyping results from normal Korean population.
Keywords: Biobank; cross-contamination detection; quality assurance; sample authentication; short tandem repeat
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