UPD Segment Screen

Screen B-allele frequencies for a UPD-like segment.

Description

Consecutive B-allele-frequency deviations can identify a segment for review, without uniquely indicating uniparental disomy.

Consecutive B-allele-frequency deviations can identify a segment for review, without uniquely indicating uniparental disomy.^[1]

Screen B-allele frequencies for a UPD-like segment.

When to use UPD Segment Screen

Use this tool to screen B-allele frequencies for a UPD-like segment.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use UPD Segment Screen and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter bAlleleFrequencies, minimumDeviation, minimumRun using the field table and calculation rules, then run the tool.
Read longestRun, updFlag. 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
bAlleleFrequencies	B-allele frequencies	list of number	Required
minimumDeviation	Minimum deviation	number; minimum: 0; maximum: 0.5	Required
minimumRun	Minimum marker run	integer; minimum: 1	Required

Enter nonempty BAF 0–1, deviation 0–0.5 and positive integer run minimum. Find the longest consecutive qualifying run and compare inclusively.

deviant=abs(BAF−0.5)≥minimumDeviation

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

Output field	Meaning	Value type
longestRun	Longest deviant run	integer; minimum: 0
updFlag	UPD segment flag	boolean

json

{
  "input": {
    "bAlleleFrequencies": [
      0.1,
      0.15,
      0.2,
      0.5
    ],
    "minimumDeviation": 0.25,
    "minimumRun": 3
  },
  "output": {
    "longestRun": 3,
    "updFlag": true
  }
}

Limitations and assumptions

List order defines adjacency; no coordinates, copy number or parent of origin are analyzed.

Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. 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 Allele–Methylation Coupling: Detect allele-specific methylation from phased read counts. For a complementary task, use XY Intensity Classifier: Classify X/Y intensity contrast without inferring an individual’s gender.

References

UPD Segment Screen — tool.io

Similar or alternative tools

Allele–Methylation Coupling
Detect allele-specific methylation from phased read counts.
XY Intensity Classifier
Classify X/Y intensity contrast without inferring an individual’s gender.