Genomic Scar Composite
Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.
Description
Genomic scar summaries can combine different structural event counts.
Genomic scar summaries can combine different structural event counts. The score depends on explicit component definitions and weights.
Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.
When to use Genomic Scar Composite
Use this for the following task: Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Genomic Scar Composite and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter lohEvents, telomericImbalances, largeTransitions, componentWeights, scoreThreshold using the field table, then run the tool.
- Read compositeScore, aboveThreshold. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| lohEvents | Loh events | integer; minimum 0 | Required |
| telomericImbalances | Telomeric imbalances | integer; minimum 0 | Required |
| largeTransitions | Large transitions | integer; minimum 0 | Required |
| componentWeights | Component weights | list of number; minimum entries 3; maximum entries 3; each entry: number; minimum 0 | Required |
| scoreThreshold | Score threshold | number; minimum 0 | Required |
Supply supported counts, exactly three aligned weights and a threshold. Sum weighted components and set aboveThreshold when score is at least the threshold.1
score = LOH×w0 + telomericImbalance×w1 + largeTransition×w2 This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| compositeScore | Composite score | number |
| aboveThreshold | Above threshold | boolean |
{
"input": {
"lohEvents": 3,
"telomericImbalances": 2,
"largeTransitions": 4,
"componentWeights": [
1,
2,
1
],
"scoreThreshold": 10
},
"output": {
"compositeScore": 11,
"aboveThreshold": true
}
}Limitations and assumptions
No events are detected or standardized here. This is not a clinical homologous-recombination-deficiency test.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Loh Segments for this operation: Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion. For a complementary task, use Copy Number Switches for this operation: Count copy-number state switches as an oscillation feature, not a chromothripsis diagnosis.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Genomic Scar Composite — tool.io
Similar or alternative tools
- Loh Segments
Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion.
- Copy Number Switches
Count copy-number state switches as an oscillation feature, not a chromothripsis diagnosis.