Figure 5: Coverage comparison of PrimPol-mediated MDA of single cells to random primed MDA.
From: TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol
Comparison of genome coverage of NA HEK293 cell DNA and single human HEK293 cells amplified by either TruePrime, a generic RP-MDA, a commercial RP-MDA kit (REPLI-g single cell kit, Qiagen) or MALBAC. (a) Circos plot showing genome coverage using exactly 12 million read pairs as input. From outward to inward: NA-sample (grey), TruePrime (blue), commercial RP-MDA kit (orange), MALBAC (red) and generic RP-MDA protocol (yellow). Plot was generated using bin sizes of 50 kb. TruePrime shows a more even coverage distribution compared with the other methods. (b) Sliding window coverage comparison of chromosome 4 between NA (grey), TruePrime (blue), commercial RP-MDA kit (orange), MALBAC (red) and generic RP-MDA protocol (yellow). TruePrime shows a highly similar coverage pattern compared with NA. The commercial RP-MDA kit, MALBAC and generic RP-MDA display a higher jitter. The y axis is cut at a read depth of 50. For a detailed close-up, see Supplementary Fig. 4. (c) Comparison of coverage depth frequency distribution between NA sample and amplified samples (logarithmic y axis). The similarity of the TruePrime to the NA curves is noteworthy. (d) Coverage breadth saturation of human genome (fraction covered=y axis) at a minimum coverage of 1 × with increasing number of matched reads (x axis) (upper panel) and resulting deviation from expected coverage using a Poisson distribution model (middle panel). The lower panel shows the saturation curve for a minimal coverage depth of 10 × . The TruePrime-amplified sample shows the highest similarity in all analyses to the NA material. (e) Coverage over different chromosomes (% chromosome covered) for NA (grey), TruePrime (blue), commercial RP-MDA kit (orange) and MALBAC (red). Coverage of NA, TruePrime and commercial RP-MDA kit are relatively similar, whereas MALBAC shows some differences and an overall lower coverage for some of the chromosomes. (f) Comparison of GC-content dependency of read frequency between NA (grey), TruePrime (blue), the commercial RP-MDA kit (orange) and MALBAC (red). Again, the behaviour between NA, TruePrime and commercial RP-MDA kit is very similar. MALBAC shows a right shift.
