Tumor Purity Proxy

Compute a caller-supplied marker-based tumor purity proxy, not a clinical ESTIMATE score.

Description

A marker-score purity proxy is the tumor score's share of tumor, stromal and immune scores.

A marker-score purity proxy is the tumor score's share of tumor, stromal and immune scores. That arithmetic share need not represent a calibrated tumor-cell fraction.^[1]

Compute a caller-supplied marker-based tumor purity proxy, not a clinical ESTIMATE score.

When to use Tumor Purity Proxy

Use this tool to compute a caller-supplied marker-based tumor purity proxy, not a clinical ESTIMATE score.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Tumor Purity Proxy and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter tumorMarkerScore, stromalMarkerScore, immuneMarkerScore, minimumPurity using the field table and calculation rules, then run the tool.
Read purityProxy, passes. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
tumorMarkerScore	Tumor marker score	number	Required
stromalMarkerScore	Stromal marker score	number	Required
immuneMarkerScore	Immune marker score	number	Required
minimumPurity	Minimum purity	number	Required

Supply nonnegative component scores with a positive total and a finite minimum criterion. Return the proxy and an inclusive proxy≥minimum flag. A zero tumor score gives zero proxy when other components are positive.

purityProxy=tumorScore/(tumorScore+stromalScore+immuneScore)

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
purityProxy	Purity proxy	number
passes	Passes	boolean

json

{
  "input": {
    "tumorMarkerScore": 8,
    "stromalMarkerScore": 2,
    "immuneMarkerScore": 2,
    "minimumPurity": 0.6
  },
  "output": {
    "purityProxy": 0.6666666666666666,
    "passes": true
  }
}

Limitations and assumptions

The threshold is not restricted to 0–1 by the calculation. No marker estimation, ESTIMATE model, clinical validation or pathology measurement is performed.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use Immune Signature Score: Score immune-cell signature enrichment from standardized gene expression. For a complementary task, use Cell Fraction Constraint: Check deconvolved cell fractions sum to one within tolerance.

References

Tumor Purity Proxy — tool.io

Similar or alternative tools

Immune Signature Score
Score immune-cell signature enrichment from standardized gene expression.
Cell Fraction Constraint
Check deconvolved cell fractions sum to one within tolerance.