Extended Data Fig. 6: Sensitivity analysis.
From: ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin
a, Total sizes (in nucleosomes) of TSS (Left) and Enhancer (Right) signatures of various cell types. b, Estimates of specific capture rate and of SNR (specific capture / non-specific capture) over 88 healthy samples, assuming 1000 genomes/ml and 2 ml input. Box limits: 25% –75% quantiles, middle: median, upper (lower) whisker to the largest (smallest) value no further than 1.5 * inter-quartile range from the hinge. c, Signal level is linear with input. Plasma of a healthy donor was spiked in with different amounts of yeast nucleosomes (x-axis). The number of counts observed (y-axis) for signatures of different sizes. Error bars show 20-80% range over 100 different sampled signatures of the given size. d, Genome browser of chrY male-specific promoters (left) and a representative autosomal region (right) in the male/female titration experiment. e, Test of sensitivity using male spike-in. Plasma of healthy female and male donors were titrated at different ratios. Detection of male-specific promoters as a function of percent of chrY genomes in the sample (x-axis). Shown are the number of counts (y-axis) and significance (circle radius) of signal above background distribution (Methods). f, Simulation study of the effect of capture probability on detection. The blue marks denote the concentrations used in the male-female titration experiment which had capture probabilities ~0.1% and SNRs of ~500-800. g, Simulation study of the effect of SNR levels on detection probability.
