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Comparative Analysis of DNA Extraction Methods on Quality Control and Data Quality in Genomic Studies

This study investigates the impact of DNA extraction methods (Roche vs. Qiagen) on the quality control (QC) values, SNP call rates, and LRR variance using samples from genomic analyses. The assessment involved 22 pairs of samples for QC qPCR, 10 for SNP call rates, and 13 for LRR variance. Results showed no consistent superiority of either method in QC assessments. Notably, Qiagen yielded better SNP call rates and lower LRR variance in several samples, enhancing the detection of copy number alterations. Statistical analysis revealed insignificant associations between extraction method and performance.

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Comparative Analysis of DNA Extraction Methods on Quality Control and Data Quality in Genomic Studies

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  1. A B C Supplementary Figure 5 - Effect of DNA extraction method on QC values, SNP call rates and LRR Variance Roche and Qiagen DNA extraction methods were compared to determine whether the method affected i) the suitability of DNA for restoration and Infinium analysis and ii) data quality. (A) QC qPCR (22 pairs of samples extracted using both methods): neither method consistently outperformed the other in QC qPCR assessment. (B) SNP call rates (10 pairs) and (C) LRR variance (13 pairs): most samples performed equally well in the Infinium assay whether extracted with Roche or Qiagen methods, however, Qiagen outperformed Roche in several samples leading to improved SNP call rates and reduced LRR variance, and consequently improved detection of copy number alterations (see Supplementary Figure 2 and 3). For each comparison, there was no significant association between performance and extraction method (Wlicoxon non-parametric paired t-test; P= not significant).

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