OCI-AML3 single and sparse cell analysis. OCI-AML SC-sequencing

The literature on single cell genomic analysis on the DNA level is conflicting regarding requirements of cell quality, amplification success rates and allelic dropouts, generally lacking comprehensive comparison from multiple cell input down to the single cell. To address these issues we analyzed a leukemic cell line (OCI-AML3) with a known set of genetic aberrations. By analyzing single and multiple cell replicates (2 to 50 cells) purified by micromanipulation and serial dilution, we have been able to systematically assess the signal-to-noise ratio (SNR), objectively, from single and few cells based on a multiple displacement amplification method and whole exome sequencing. In this setting, known OCI-AML3 mutations could be identified as well as copy number changes. In contrast, at the level of 1–2 cells, we observed that 40–50% of all alleles were not present in the replicate samples, and this allelelic discrepancy displayed a clear exponential function of cell input. Thus, it shows that even under highly optimized conditions, single cell WGA and interpretation must be taken with considerable caution, given that allele dropout is frequent and displays low SNR, with allelic noise rapidly alleviated with increased cell input, and coefficient of variation doubling from 2 to 50 cell assays. In conclusion, we suggest that data on single cell genomic analysis should be accompanied by cell dilution for relative qualitative assessment of individual procedures and inherent SNR, quantitatively.