Optimizing DNA Extraction from Dried Blood Spots for Biological Age Measurements
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While the chronological age is the time that has passed since birth, the biological age is determined by physiological signs of aging. Methylation at CpG sites has proven to be a promising biomarker of biological age, and epigenetic clocks have been developed to measure the biological age from methylation patterns. Age Labs is a molecular diagnostics company working on an epigenetic clock to predict risk of disease and all-cause mortality. Dried blood spots (DBS), capillary blood spotted on filter paper, is the preferred sample material as the patient can prepare the samples themselves, while the samples are stable at room temperature and can be sent by regular mail. The small volumes of blood typically spotted on the filter paper combined with the adhesion of DNA to the filter paper and the DNA input requirements for methylation assay makes it challenging to extract the DNA quantity needed. The aim of the study was to optimize an automatable and high throughput protocol for DNA extraction from DBS that yields DNA of sufficient quantity and quality for biological age measurements by methylation analysis. For the optimization process, DBS were prepared by an equal volume of EDTA blood. DNA extraction was optimized by first using spin columns to establish a baseline for the DNA extraction procedure. The potential of automating a high throughput method was then investigated by DNA purification on MagNA Pure 96 and with the Invitrogen PureLink® Pro 96 Genomic DNA Kit. The resulting optimized Invitrogen protocol was validated by biological age measurements with three different epigenetic clocks: DNAm age, DNAm GrimAge and Skin & blood clock, and the results were compared with those of a “gold standard” DNA extraction method. In this study, no statistically significant difference was found between the biological ages in DNA from capillary blood (DBS) extracted with the optimized Invitrogen protocol and DNA from venous blood extracted with a “gold standard” DNA extraction method. The results from the biological age measurements show that the DNA extracted from DBS with the optimized Invitrogen protocol yields DNA of sufficient quantity and quality for methylation analysis with the Infinium MethylationEPIC BeadChip. Furthermore, the optimized Invitrogen protocol is a high throughput DNA extraction method for DBS that can be fully or partially automated to decrease hands-on time.