Detection of de novo copy number deletions from targeted sequencing of trios

Bioinformatics. 2019 Feb 15;35(4):571-578. doi: 10.1093/bioinformatics/bty677.


Motivation: De novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms.

Results: We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability.

Availability and implementation: MDTS is freely available as open source software from the Bioconductor repository.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Computational Biology
  • DNA Copy Number Variations*
  • Sequence Deletion*
  • Software*