Data from: An immunosignature test distinguishes Trypanosoma cruzi, hepatitis B, hepatitis C and West Nile Virus seropositivity among asymptomatic blood donors

Background: The complexity of the eukaryotic parasite Trypanosoma (T.) cruzi manifests in its highly dynamic genome, multi-host life cycle, progressive morphologies and immune-evasion mechanisms. Accurate determination of infection or Chagas’ disease activity and prognosis continues to challenge researchers. We hypothesized that a diagnostic platform with higher ligand complexity than previously employed may hold value. Methodology: We applied the ImmunoSignature Technology (IST) for the detection of T. cruzi-specific antibodies among healthy blood donors. IST is based on capturing the information in an individual’s antibody repertoire by exposing their peripheral blood to a library of >100,000 position-addressable, chemically-diverse peptides. Principal findings: Initially, samples from two Chagas cohorts declared positive or negative by bank testing were studied. With the first cohort, library-peptides displaying differential binding signals between T. cruzi sero-states were used to train an algorithm. A classifier was fixed and tested against the training-independent second cohort to determine assay performance. Next, samples from a mixed cohort of donors declared positive for Chagas, hepatitis B, hepatitis C or West Nile virus were assayed on the same library. Signals were used to train a single algorithm that distinguished all four disease states. As a binary test, the accuracy of predicting T. cruzi seropositivity by IST was similar, perhaps modestly reduced, relative to conventional ELISAs. However, the results indicate that information beyond determination of seropositivity may have been captured. These include the identification of cohort subclasses, the simultaneous detection and discerning of other diseases, and the discovery of putative new antigens. Conclusions & significance: The central outcome of this study established IST as a reliable approach for specific determination of T. cruzi seropositivity versus disease-free individuals or those with other diseases. Its potential contribution for monitoring and controlling Chagas lies in IST’s delivery of higher resolution immune-state readouts than obtained with currently-used technologies. Despite the complexity of the ligand presentation and large quantitative readouts, performing an IST test is simple, scalable and reproducible

A set of library peptides reproducibly displayed antibody-binding signals that were significantly different between Chagas seropositive and seronegative donors.

<p>A volcano plot is used to assess this discrimination as the joint distribution of t-test <i>p</i>-values versus the ratio of geometric mean intensities for Chagas positive donors relative to Chagas negative. The density of peptides at each plotted position is indicated by the color scale. The 356 peptides above the dashed white line discriminate between positive and negative Chagas sero-status by IST with 95% confidence after applying a Bonferroni adjustment for multiplicity. The colored circles indicate individual peptides with intensities that were significantly correlated to the <i>T</i>. <i>cruzi</i> ELISA-derived S/CO value either by a Bonferroni threshold of <i>p</i> < 4e-7 (green) or the less stringent false discovery rate (FDR) of <10% (blue).</p

Immune assay confusion matrix.

<p>Cross tabulation of the IST classifications and ELISA results of Chagas positivity for the 2016 test cohort.</p

Alignment score frequencies displayed for the library peptides.

<p>A histogram of alignment scores from the top 370 informative peptides against all <i>T</i>. <i>cruzi</i> proteins are depicted in the blue bars. The mapping algorithm was repeated with equivalent alignments of 370 randomly chosen library peptides ten times. These yielded histograms that are shown as rainbow-colored line plots overlaid upon the blue bars.</p

Signal intensity patterns displayed by donors’ Chagas sero-status informing peptides versus their S/CO value.

<p>A heatmap orders the ranges of signal intensities displayed by the 370 library peptides that inform a sample’s Chagas positivity status; the side-bar graph relates these to each donor’s ELISA S/CO value.</p

Binary Classification Disease Biomarker Data

This data set consists of 903 rows and 126018 columns in a tab delimited text file. The first 9 columns correspond to the sample meta data. The first column, sample, corresponds to a given donor. The second column, analysis_set, identifies the cohort as testing or training. The third column, process_lock,is an indicator of what process was used to create this particular set of arrays. The fourth column, Ab2, is the secondary antibody either Anti-IgA or Anti-IgG. The fifth column is diagnostic class either healthy or chagas. The sixth column,med_SCO, is the median ELISA S/CO values. The seventh column is the donors' age. The eigth column the donors' Gender listed as F (Female), M (Male), or U (Unknown). The 9th column, Ethnicity, provides any ethnicity information associated with the donor. The remaining 126009 correspond to the raw intensities associated with the peptide sequence that defines that column name

Precision studies based on signal intensities of Chagas-informative peptides.

<p>Precision studies based on signal intensities of Chagas-informative peptides.</p

Confusion matrix and performance estimates of the multiclass prediction model.

<p>Confusion matrix and performance estimates of the multiclass prediction model.</p

Binding of monoclonal antibody standards to cognate-epitope control features.

<p>Four well-characterized mAbs (4C1, p53Ab1, p53Ab8 and LnkB2) were separately applied to arrays at 2.0 nM with competitor, in triplicate, and then detected with an anti-mouse secondary reagent. For each binding assay the mean log₁₀ relative fluorescent intensity (RFI) of the epitope control features were used to calculate a Z-score. The results corresponding to each epitope were plotted as separate bar graphs, with the mAb recognition sequences shown above the graphs. The mAb clones are indicated as bars along the x axes within each graph. Error bars represent the standard deviation of the individual control feature Z-scores. Cognate controls were saturated, leaving a standard deviation of zero on the Z scores for these feature replicates.</p