Bioinformatics

⚠️ This page highlights exploratory tools, algorithmic approaches, and visualisations currently under development by our team. These methods may be experimental, in active refinement, or used internally to support research and assay development. Unless otherwise specified, content in this section does not reflect validated components of any clinical product or service.

Melaseq Liquid Biopsy: Interactive Diagnostic Plots

1. PCA vs MEL38+ Diagnostic Score (3D)

This interactive 3D plot visualizes each sample’s microRNA signature using Principal Component Analysis (PC1 and PC2), with the MEL38+ diagnostic score plotted on the vertical axis. It enables visual clustering of diagnostic groups and helps identify patterns in the data.

  • Color: Samples are color-coded by diagnostic group — benign (shades of blue), melanoma (shades of red), and unknown (yellow).
  • Shape: Circles represent non-melanoma (Dx = 0), squares represent melanoma (Dx = 1), and diamonds are samples with unknown diagnosis (Dx = NA).
  • Threshold Surface: A grey horizontal plane marks the classification decision boundary (MEL38+ score = 5.5).

2. PC1 vs Probability vs MEL38+ Score (3D)

This alternative 3D plot replaces PC2 with the predicted probability of invasive melanoma (Platt-scaled), providing an integrated view of unsupervised expression patterns, diagnostic confidence, and score distribution.

  • X-axis: Principal Component 1 (unsupervised)
  • Y-axis: Probability of being Class B (melanoma)
  • Z-axis: MEL38+ diagnostic score (supervised)

It is especially useful for identifying borderline classifications and interpreting the confidence behind each result.


3. Individual Sample View (Dx = NA)

For each sample with unknown diagnosis (Dx = NA), an individual 3D plot is generated to highlight its position relative to the validated diagnostic database. These standalone plots provide an intuitive way to interpret the result in context.

  • Highlighted Sample: The tested sample is shown in bright yellow with a larger diamond marker.
  • Background: All known samples from the validation cohort are shown for reference — benign (circles, blue tones) and melanoma (squares, red tones).
  • Hover Panel: Each plot includes an embedded information panel summarizing the sample ID, diagnostic score, and probability of melanoma.
  • Use: These plots are ideal for inclusion in diagnostic reports or detailed clinical review of individual patient results.


4. Melaseq microRNA expression heatmap

This view of our database is a gene expression “heatmap”, a color-coded visualization of microRNA abundances derived from over 500 samples from individuals with clinically confirmed melanoma status. These data contribute to the validation the Melaseq assay.

Each row (horizontal) corresponds to a specific microRNA measured in the test. Each column (vertical) represents the average microRNA profile for a specific clinical diagnosis or melanoma stage. Colors indicate relative microRNA levels: red signifies higher abundance, while blue indicates lower abundance.

By examining these heatmap patterns, Melaseq detects changes in microRNA expression—both increases and decreases—across clinical diagnoses and melanoma stages. These directional changes are used to compute a personalized melanoma genomic score, identifying microRNA signatures linked to melanoma presence and progression.