Fast and efficient method for parallel construction of targeted exome and methylome single-stranded DNA sequencing libraries

Based on single-stranded DNA library method, we established an efficient workflow to parallelly construct targeted genomic and epigenomic sequencing libraries from a small amount of DNA. We applied the protocol to nine pediatric brain cancer DNA samples containing various extents of damage from formalin fixation and/or DNA oxidation. Compared to our previous study, the new exome protocol showed superior uniformity of coverage. Many artifactual mutation calls introduced by DNA damages were eliminated by bioinformatics filtering tools. After filtration, 89.4-97.0% of somatic single nucleotide variant (SNV) calls generated by double-stranded DNA library were reproduced in formalin-fixed paraffin-embedded (FFPE) samples, which was achieved with substantially reduced DNA input amounts (26.7-50ng). In methylome analysis, we obtained methylation calls for 78-92% of target CpGs with at least 10x coverage when using 100ng of FFPE DNA, which is comparable to those obtained from fresh frozen samples. We also obtained SNV calls from methylome data, recovering 39-76% of filtered SNVs from exome data in nine brain cancer samples. In conclusion, we present a simple protocol for parallel construction of targeted exome and methylome sequencing libraries, which was successfully applied to damaged brain cancer DNA samples from FFPE tissues stored for prolonged periods.