Loh Segments

Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion.

Description

Loss of heterozygosity can be screened through minor-allele copy states along genomic segments.

Loss of heterozygosity can be screened through minor-allele copy states along genomic segments. Touching qualifying intervals can form one reported tract.

Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion.

When to use Loh Segments

Use this for the following task: Merge contiguous segments meeting a supplied minor-allele copy-number LOH criterion.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Loh Segments 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 segmentStarts, segmentEnds, minorCopyNumbers, maximumMinorCopies using the field table, then run the tool.
Read lohStarts, lohEnds, lohBases. 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
segmentStarts	Segment starts	list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0	Required
segmentEnds	Segment ends	list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0	Required
minorCopyNumbers	Nonnegative integer minor-allele copy states; no inference from read depth.	list of integer; minimum entries 1; maximum entries 100000; each entry: integer; minimum 0	Required
maximumMinorCopies	Maximum minor copies	number; minimum 0	Required

Supply ordered disjoint positive-length half-open intervals with aligned integer minor-copy states. Merge only exactly touching qualifying segments and sum tract lengths.^[1]

qualifies when minorCopyNumber ≤ maximumMinorCopies; tractBases = Σ(end−start)

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
lohStarts	Loh starts	list of integer
lohEnds	Loh ends	list of integer
lohBases	Loh bases	integer

json

{
  "input": {
    "segmentStarts": [
      0,
      10,
      20
    ],
    "segmentEnds": [
      10,
      20,
      30
    ],
    "minorCopyNumbers": [
      0,
      0,
      1
    ],
    "maximumMinorCopies": 0
  },
  "output": {
    "lohStarts": [
      0
    ],
    "lohEnds": [
      20
    ],
    "lohBases": 20
  }
}

Limitations and assumptions

No chromosome field is supplied, so use one coordinate space per request. LOH criteria are caller-defined and do not establish a clinical result.

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 Tumor Normal Copy Ratio for this operation: Interpret log2 tumor/normal ratios with an explicit normal-cell admixture and baseline ploidy model. For a complementary task, use Genomic Scar Composite for this operation: Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Loh Segments — tool.io

Similar or alternative tools

Tumor Normal Copy Ratio
Interpret log2 tumor/normal ratios with an explicit normal-cell admixture and baseline ploidy model.
Genomic Scar Composite
Combine supplied LOH, telomeric imbalance, and large-transition counts with explicit weights; not a clinical HRD test.