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

Jack M. Fu, Elizabeth J. Leslie, Alan F Scott, Jeffrey C. Murray, Mary L. Marazita, Terri L Beaty, Robert B Scharpf, Ingo Ruczinski

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)571-578
Number of pages8
JournalBioinformatics
Volume35
Issue number4
DOIs
StatePublished - Feb 15 2019

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Formal methods
Deletion
Sequencing
Scalability
Minimum Distance
Formal Methods
Voids
False Positive

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Detection of de novo copy number deletions from targeted sequencing of trios. / Fu, Jack M.; Leslie, Elizabeth J.; Scott, Alan F; Murray, Jeffrey C.; Marazita, Mary L.; Beaty, Terri L; Scharpf, Robert B; Ruczinski, Ingo.

In: Bioinformatics, Vol. 35, No. 4, 15.02.2019, p. 571-578.

Research output: Contribution to journalArticle

Fu, Jack M. ; Leslie, Elizabeth J. ; Scott, Alan F ; Murray, Jeffrey C. ; Marazita, Mary L. ; Beaty, Terri L ; Scharpf, Robert B ; Ruczinski, Ingo. / Detection of de novo copy number deletions from targeted sequencing of trios. In: Bioinformatics. 2019 ; Vol. 35, No. 4. pp. 571-578.
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