Reproducibility and reliability of SNP analysis using human cellular DNA at or near nanogram levels

BMC Research Notes

Chih-Lin Hsieh³  Michael R Lieber¹  David J Van Den Berg²  Cindy Y Okitsu³ 

[1] Department of Pathology, Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA;Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90033, USA;Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA

关键词: SNP array;    Reduced DNA quantity;    Reproducibility of SNP array analysis;    Chromosome deletion;   

Others  :  1140542
DOI  :  10.1186/1756-0500-6-515

 received in 2013-09-20, accepted in 2013-12-02,  发布年份 2013

【 摘 要 】

Background

Illumina SNP arrays have been routinely used for genome-wide association studies to identify potential biomarkers for various diseases. The recommended 200 ng of DNA for high-quality results is a roadblock to utilizing this assay when such quantities of DNA are not available. The goal of this study is to determine the reproducibility and reliability of the assay when reduced amounts of DNA are used for the SNP arrays.

Findings

A serial 3-fold reduction of DNA from 200 ng to 0.8 ng was used for an Illumina SNP array in duplicates (200 ng, 66.7 ng, 22,2 ng, and 7.4 ng) or triplicates (2.47 ng and 0.8 ng). The reproducibility of the assay was determined by comparing allele calls (genotypes) at each locus within the duplicates or triplicates. The reliability of samples of reduced quantity was determined by comparing allele calls from samples of different quantities. As expected, the reproducibility and reliability both decrease with decreasing amounts of DNA used for the arrays. However, results of comparable quality to the 200 ng DNA recommended by Illumina can be obtained with much reduced amounts of DNA.

Conclusion

Reasonably reproducible and reliable results can be obtained with quantities of DNA, as low as 0.8 ng (equivalent to 133 human cells), well below the manufacturer’s recommendation. Results of nearly equal quality to that of using 200 ng DNA can be obtained with 22.2 ng of DNA reliably, and clearly acceptable data can be obtained using 7.4 ng of DNA for Illumina SNP arrays.

【 授权许可】

   
2013 Okitsu et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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