Abstract
Next-generation sequencing has greatly advanced genomics, enabling large-scale studies of population genetics and complex traits. Genomic DNA (gDNA) from white blood cells has traditionally been the main data source, but cell-free DNA (cfDNA), found in bodily fluids as fragmented DNA, is increasingly recognized as a valuable biomarker in clinical and genetic studies. However, a direct comparison between cfDNA and gDNA has not been fully explored. In this study, we analyzed cfDNA and gDNA from 186 healthy individuals, using the same sequencing platform. We compared sequencing quality, variant detection, allele frequencies (AF), genotype concordance, population structure, and genomic association results (genome-wide association study and expression quantitative trait locus). While cfDNA showed higher duplication rates and lower effective sequencing depth, both DNA types displayed similar quality metrics at the same depth. We also observed that significant depth differences between cfDNA and gDNA were mainly found in centromeric regions. While gDNA identified more variants with more uniform coverage, AF spectra, population structure, and genomic associations were largely consistent between the two DNA types. This study provides a detailed comparison of cfDNA and gDNA, highlighting the potential of cfDNA as an alternative to gDNA in genomic research. Our findings could serve as a reference for future studies on cfDNA and gDNA.