P3.iscn2024

ISCN 2024 counting

전체 counting policy 메인으로 돌아가기
Label

ISCN 6.5 / Table 7 sample-level counting

Basis

ISCN 2024 section 6.5 and Table 7

Scope

Whole sample

Clone handling

Repeated abnormalities across clones are deduplicated at the sample level.

Weighting

Single-chromosome derivatives retain distinct Table 7 component abnormalities; derivatives involving two or more chromosomes count as two, while related derivative abnormalities are not counted as additional.

When to use

Use for standards-oriented, disease-agnostic structural complexity review.

Summary

Counts sample-level distinct abnormalities using ISCN 2024 section 6.5, Table 7, and the worked examples in Table 8.

Algorithm

  1. Build a sample-level set of acquired abnormalities from all clones.
  2. Deduplicate repeated identical abnormalities across related or parallel clones.
  3. Apply ISCN Table 7 weights to each retained abnormality.
  4. Keep per-event decision records so the final total can be traced back to individual abnormalities.

Counted units

  • Whole-chromosome numerical gains and losses count as one abnormality each.
  • Balanced structural abnormalities such as t and inv count as one abnormality.
  • Derivative chromosomes involving two or more chromosomes count as two abnormalities.
  • Explicit marker/ring/hsr/dmin multiplicity is retained when the notation states a copy count.

Exclusions and collapse rules

  • The same abnormality is not counted more than once solely because it appears in multiple clones.
  • Related derivative events that are already represented by the same Table 7 abnormality are not counted as additional independent abnormalities.
  • Constitutional polymorphism-style events are excluded when they are marked as constitutional.

Examples

  • 46,XY,der(5)t(5;7)(q31;q22): the two-chromosome derivative contributes 2.
  • 47~49,XY,+1~3mar: marker chromosome multiplicity contributes 3.
  • 46,XX,t(9;22)(q34;q11.2): the balanced translocation contributes 1.

Notes

  • This is the default standards-oriented comparison policy in CytoMut.
  • It is disease-agnostic; disease-specific interpretation should be checked separately.

Source Documents

  • docs/counting_abnormalities/6.5 Counting Chromosome Abnormaliti.txt
  • paper/abnormality_counting_methods_and_policies.md