For example, the sum of differences squared in linear scale could overemphasize the difference over the large scales, whereas the sum of differences squared after log transforming the data amplifies the differences at the smaller values of the predictions.
Because the YH cell line was derived from normal lymphocytes with few CNVs (≥1 Mb), we only observed few large CNVs at the single-cell level (Additional file 18: Figure S9) in most of the SCRS data amplified with DOP-PCR, MALBAC or MDA.
Using the further deep-sequenced whole genome sequencing (WGS) data amplified by the chosen kits, we further investigated the amplification bias and variations detection ability.
We then calculated the ADO ratio and FP ratio of SCRS data amplified by MDA-2, founding that the mean ADO ratio was 12.47 % (0.78 %, 3.23 % and 33.40 %, respectively), and the mean FP ratio was 5.31 × 10−5 (SD 0.007 %) which was comparable with ~4 × 10−5 of the FP ratio of MALBAC in previous report [ 18].
King, unpublished data) amplified and sequenced the cytochrome oxidase I region of mitochondrial DNA and the ITS-1 region of nuclear DNA in Novisuccinea chittenangoensis and Succinea sp. B. The results (sequence divergence of 10 15 percent) suggest large differences between the two species.
To further investigate the power of CNVs detection using real SCRS data amplified by MALBAC and MDA-2, we amplified 10 additional cells from a human gastric adenocarcinoma cell line (BGC823) using MALBAC (5 cells) and MDA-2 (5 cells) respectively, and sequenced them on Lifetech Ion Proton sequencer.
However, the identifier represents the configuration of stereogenic elements, as it is captured from source structural data amplified with either 2-D or 3-D coordinates.
In summary, SCRS data amplified by MDA or MALBAC had a lower duplication ratio, a higher mapping ratio, and a higher genome recovery than that from DOP-PCR.
To further explore the genome coverage bias introduced by WGA, we compared deep-sequenced data (~30×) amplified by DOP-1, MDA-2, MDA-3 or MALBAC respectively (Table 1), because LWGS data amplified by these four WGA kits had better genome recovery sensitivity or sequence evenness than other kits.
We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2).
