Qualitative analysis of the gDNA samples
Considering the high volume of blood samples processed in this study, we undertook a small-scale comparison to identify the most time-cost efficient DNA extraction method that would provide optimal DNA quality. Ten blood samples were randomly selected, and genomic DNA was extracted using a bead-based method (MagMAX™CORE Nucleic Acid Purification Kit) and a classical phenol-chloroform extraction method. Sample quality (i.e. concentration and purity) was assessed by spectrophotometry.
Analysis of the gDNA samples extracted with the phenol-chloroform method determined a mean DNA concentration of 215.3 ng/μl (SD = 35.2, range = 156 – 286), a A260/A230 ratio of 1.7 (SD = 0.098, range = 1.49 – 1.80) and a A260/A280 ratio of 1.45 (SD = 0.02, range = 1.42 – 1.48). On the other hand, the mean DNA concentration obtained with the MagMAX™CORE extraction kit was lower (p = 0.0007) (mean 80.4 ng/μl, SD = 81.2, range = 28 – 283), although, these samples presented similar (p = 0.4) A260/A230 ratio (mean 1.7, SD = 0.04, range = 1.64 – 1.76) but a higher (p <0.0001) A260/A280 ratio with a mean of 1.9 (SD = 0.08, range = 1.77 – 2.00). Therefore, the DNA purity with MagMAX extraction method was deemed more consistent and superior when compared to the phenol-chloroform method. Subsequently, MagMAX™CORE was used to extract genomic DNA from all the 243 blood samples included in this study.