Tools for Detecting Uniparental Disomy

Abstract

Genomic alterations are hallmarks of human cancer and complex diseases. Genomic alterations include point mutations, deletion, duplication/amplification, fusion genes, complex rearrangements and uniparental disomy. When both homologous chromosome pair is originated from the same parent called uniparental disomy. Uniparental disomy can occur as constitutive (germline) and as acquired UPD. Constitutive UPD is associated with developmental diseases and cancer, while acquired (somatic) UPD occur in human cancers. aUPD pinpoints homozygous regions for existing alterations such as loss‐of‐function, gain‐of‐function mutations, deletions, methylations or imprinting.

Key Concepts

  • aUPD is common alterations in cancers, and aUPD regions are associated with survival or risk factors of cancer.
  • UPD regions pinpoint homozygosity for existing alterations such as mutation, deletion, methylation or imprinting. Therefore it is important to detect aUPD.
  • Currently, multiple UPD detection tools are freely available.
  • Some of the tools are capable of detecting also ploidy and/or purity of tumour.
  • Some of the tools can detect UPD as low as in 10% tumour purity.

Keywords: uniparental disomy; constitutive; acquired; detection tools; cancer

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Tuna, Musaffe(Dec 2019) Tools for Detecting Uniparental Disomy. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022430.pub2]