Figure 2. Technical performance of the Arc-well method.
(A) Comparison of overdispersion metrics for the genomic bin counts and (B) breadth of coverage metrics for six different scDNA-seq methods using cell line or frozen tissue data. Coverage was calculated from 80 randomly sampled cells per methods and using 500K reads per cell as input. The methods using cell lines included Arc-well (315A, diploid; MDA231, aneuploid), ACT (MDA231, aneuploid) and DLP+(GM18507, diploid), while the methods using frozen tissues included 10X CNA, DLP, DOP-PCR.
(C) Overdispersion and breadth of coverage (500K reads per cell) computed from non-fixed and formalin fixed diploid 315A cell line, aneuploid MDA231 cell line and from frozen and FFPE tissue from the same human IDC sample.
(D) Overdispersion of bin counts computed using Arc-well data from 22 breast cancer, 2 lung cancer and 2 prostate cancer samples.
(E) Correlations between FFPE block age and QC metrics for the mean overdispersion, the mean PCR duplicate rates, and correlations between DNA integrity number (DIN) and overdispersion metrics.
(F) Two examples of copy number profiles with ratio values (dots) and segmentation values (lines) of two different single cells from patient P6 (cell 1: ArcN759-ArcS519) and patient P10 (cell 2: ArcN741-ArcS541, table S6). BA: block age of FFPE samples.
(G) UMAP plot of single cell copy number profiles from FFPE tissue of P1, where each color represents a subclone.
(H) Clustered heatmap of single cell copy number profiles for P1 (top panel) and bottom panel shown the consensus integer CNA profiles of each subclone with selected breast cancer genes annotated below.