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Fig. 2 | Genome Medicine

Fig. 2

From: Next-generation sequencing diagnostics of bacteremia in septic patients

Fig. 2

Rationale of the SIQ score and SIQ plot. a Outline for obtaining a SIQ score and SIQ plot. Total cfDNA is isolated from a patient’s plasma and sequenced. From sequencing results, human cfDNA are removed after mapping and only unmapped reads are further processed. From these unmapped reads, microbial species are classified and reads are normalized, counted, and sorted by their abundance. For each species obtained from a patient, results are compared with likewise processed samples of uninfected controls, exemplified for microbial species X, which is found in the patient’s sample as well as in most control samples and, therefore, represents a contaminant. However, species Y is found in high abundance only in the patient’s sample and in none of the controls and, therefore, receives a high significance and consequently a high SIQ score, indicated by the radius of its data point in the SIQ plot. b Distribution of normalized counts for each species found in the plasma sample of patient S9 at the onset of sepsis (T0). Only the most abundant species, Enterobacter cloacae, was labeled. c Distribution of the normalized counts for E. cloacae for all samples analyzed. Red, septic patients; blue, controls (elective surgery and healthy volunteers). Only sample S9 with the most abundant E. cloacae reads was labeled. d Distribution of the normalized counts of Propionibacterium acnes for all samples. Red, septic patients; blue, controls (elective surgery and healthy volunteers). e SIQ plot integrating abundance and significance of all species for patient S9 at the onset of sepsis (T0). Coordinates of the data points (species) are the relative abundance (log2) on the x-axis and the significance expressed as 1 − p value on the y-axis. The dashed line marks a p value of 0.05. Data points with log2 > 0 and p value <0.05 are labeled. The SIQ score of a species in the respective sample is integrated as the radius of the data point

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