Method quality statistics.

<p>(<b>a</b>) Based on cell and endpoint PCR imaging, wells can be categorized as true positive (TP), false positive (FP), false negative (FN), and true negative (TN). These counts allow us to calculate a false positive and false negative rate for each array to assess performance. (<b>b</b>) Images show two wells of the SD chip before (top) and after (bottom) PCR. A single OCI-AML3 cell was identified in the right well, and the well was PCR positive after thermalcycling. The scale bar is 100 μm. (<b>c</b>) For the 12 SD chip arrays used for genotyping single OCI-AML3 cells, colored bars represent the fraction of filled wells that fall into each category described in panel A. Wells with more than one cell (doublet+) are also reported. (<b>d</b>) False positive rates and false negative rates were calculated for each OCI-AML3 or KG1a single-cell genotyping SD chip array. The average rate between arrays is reported for arrays with KG1a cells (blue) and arrays with OCI-AML3 cells (yellow). Scale bar represents standard deviation (N = 12 arrays with OCI-AML3 cells, N = 4 arrays with KG1a cells). (<b>e</b>) The fraction of wells containing no cells, one cell, or more than one cell (doublet+) was quantified from images of cells in arrays of the SD chip. Using Poisson’s equation, we calculated a predicted number of wells (black circle) that would be expected to contain one cell or more than one cell using the number of wells containing zero cells. For arrays containing either KG1a cells (blue) or OCI-AML3 cells (yellow), the actual number of wells with one cell was below the predicted number while the number of multiple cell wells was higher.