Libraries were generated from single PBMC using the QIAseq FX Single Cell DNA Library Kit or kits from two other suppliers and sequenced at low depth using an MiSeq. Data analyzed according to Zhang, CZ, et al. (2015) Nat. Commun. 6, 6822. Computed maximum achievable coverage by unlimited sequencing capacity are plotted.
Libraries were generated from either bulk gDNA using the QIAseq FX DNA Library Kit or from single peripheral blood mononuclear cells (PBMC) using the QIAseq FX Single Cell DNA Library Kit or kits from two other suppliers.
Methods and specifics (chromosome, size of CNV). Single cell libaries from PBMCs and Jurkat cell were prepared using QIAseq FX Single Cell DNA Library Kit and sequenced at Depth 0.1x. Reads were mapped using BWA mem to human genome (GRCh38) and copy number variation of Jurkat vs PBMCs (control diploid cells) was assessed using the script published in: Chao Xie, Martti T Tammi, “CNV-seq, a new method to detect copy number variation using high-throughput sequencing”, BMC Bioinformatics, 2009,10:80, DOI:10.1186/1471-2105-10-80. Plotted is the Log2 ratio(Jurkat/PBMC) of coverage using a window size of 500Kb for chromosome 2 from a cell with an approximately 2.5 Mbp deletion.
Single cell libraries were prepared from isolated PBMCs using QIAseq FX Single Cell DNA Library Kit or kits from two other suppliers and sequenced with an Illumina MiSeq. Reads were mapped to the human genome (hg19) and sequence mismatches between NGS data and the reference were computed. All analysis was performed with CLC Genomic workbench 8.5.1. Data plotted are the mean proportion of sequence differences +/- standard deviation for 3 individual libraries prepared with each kit.