P9.event_collapsed

Event-collapsed counting

전체 counting policy 메인으로 돌아가기
Label

CytoMut event-collapsed imbalance counting

Basis

CytoMut custom policy built on Table 7 weights plus biological-equivalence collapse rules

Scope

Whole sample

Clone handling

Repeated abnormalities across clones are deduplicated at the sample level.

Weighting

Unsigned replacement derivatives keep their Table 7 weight while compensatory whole-chromosome gains are not counted separately.

When to use

Use when equivalent encodings such as +1,der(1;7) and +der(1;7),-7 should yield the same total.

Summary

Starts from ISCN Table 7 sample-level weighting, then absorbs compensatory whole-chromosome gains into accompanying unsigned replacement derivatives.

Algorithm

  1. Start from the ISCN 2024 sample-level event set and Table 7-style weights.
  2. Find whole-chromosome gains or losses that only compensate an accompanying replacement derivative.
  3. Collapse those compensatory numerical events into the derivative event instead of counting them separately.
  4. Keep the derivative abnormality as the representative event for the collapsed group.

Counted units

  • Unbalanced replacement derivatives retain their Table 7-derived contribution.
  • Numerical gains and losses still count when they are independent events.
  • Marker/ring/hsr/dmin multiplicity remains explicit and is not collapsed into unrelated events.

Exclusions and collapse rules

  • A gain is not counted separately when it only restores a source chromosome already represented by the derivative.
  • A loss is not counted separately when it only balances a chromosome source already represented by the derivative.
  • Balanced rearrangements are not collapsed because they are not compensatory copy-number events.

Examples

  • +1,der(1;7)(q10;q10) and +der(1;7)(q10;q10),-7 converge to the same event-collapsed total.
  • 46,XY,+8 remains a numerical gain because no replacement derivative explains it.

Notes

  • This is a CytoMut harmonization policy, not a named external scoring system.
  • Use it when alternate encodings of the same biological imbalance should compare equally.

Source Documents

  • paper/abnormality_counting_methods_and_policies.md