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A. B. C. Supplementary Figure 5 - Effect of DNA extraction method on QC values, SNP call rates and LRR Variance

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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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