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Uniparental disomy

The Genomics England WGS pipeline can detect uniparental disomies (UPDs) in individuals for whom both parents have been sequenced, or for parent-child duos when the undertransmitting parent has been sequenced.

Predicted uniparental disomies (UPDs) are flagged in the CIP-API and the Interpretation Portal using a label with the format pddddddddddd-[mat|pat]UPDnn-[i|h|m][c|p].

  • pddddddddddd is the participant ID of the person in whom the UPD was detected
  • mat|pat indicates whether the parent who contributed two chromosomes was the mother (mat) or the father (pat)
  • nn indicates the chromosome where two homologues were inherited from one parent
  • i|h|m indicates whether the UPD event involves isodisomy (i), heterodisomy (h) or both (m for mixed)
  • c|p indicates whether the UPD event involves an entire chromosome (c for complete) or part of a chromosome (p for partial)

For example, p99999999999-matUPD14-ic denotes that complete maternal isodisomy of chromosome 14 was detected in participant p99999999999.

Note

Uniparental disomies will be flagged irrespective of their segregation with disease and the penetrance setting used.

Note

Variants showing the appropriate segregation pattern can be tiered under the UniparentalIsodisomy segregation filter and this is independent of flagging.

If approximate coordinates of the predicted regions of isodisomy and/or heterodisomy detected are required, please contact the Genomics England Service Desk.