Whole Genome Sequencing From Low Input Control Circulating Cell-Free DNA

Cell-free DNA circulates in plasma at low levels as a normal byproduct of cellular apoptosis. Multiple clinical pathologies, as well as environmental stressors can accentuate circulating cell-free DNA (ccfDNA) levels. Plasma DNA studies employ targeted amplicon deep sequencing platforms due to limited concentrations (ng/mL) of ccfDNA in the blood. Here we report whole genome sequencing (WGS) and read distribution across chromosomes of ccfDNA extracted from two normal, human, plasma samples. Amplification worked well with ~90% of the reference genome (GRCh38.p2) exhibiting 10X coverage. Chromosome read coverage was uniform and directly proportional to the number of reads for each chromosome across both samples. Almost 99% of the identified genomic sequence variants were known annotated dbSNP variants in the hg38 reference genome. The remaining 1% consisted of single nucleotide polymorphisms (SNPs) and indels. In summary, we demonstrate isolation and amplification procedures from low input ccfDNA samples that will detect sequence variants across the whole genome from amplified plasma ccfDNA for clinical and environmental health science studies with the potential to translate to the toxicology discipline.