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 H Beaty; Robert B Scharpf; Ingo Ruczinski

doi:10.1093/bioinformatics/bty677

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

Journal article

Open access

Peer reviewed

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 H Beaty, Robert B Scharpf and Ingo Ruczinski

Bioinformatics (Oxford, England), Vol.35(4), pp.571-578

02/15/2019

DOI: 10.1093/bioinformatics/bty677

PMCID: PMC6378941

PMID: 30084993

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Abstract

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. 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. MDTS is freely available as open source software from the Bioconductor repository. Supplementary data are available at Bioinformatics online.

Algorithms

Computational Biology

DNA Copy Number Variations

Sequence Deletion

Software

Details

Title: Subtitle: Detection of de novo copy number deletions from targeted sequencing of trios
Creators: Jack M Fu - Johns Hopkins University
Elizabeth J Leslie - Emory University
Alan F Scott - Johns Hopkins Medicine
Jeffrey C Murray - University of Iowa
Mary L Marazita - University of Pittsburgh
Terri H Beaty - Johns Hopkins University
Robert B Scharpf - Johns Hopkins Medicine
Ingo Ruczinski - Johns Hopkins University
Resource Type: Journal article
Publication Details: Bioinformatics (Oxford, England), Vol.35(4), pp.571-578
DOI: 10.1093/bioinformatics/bty677
PMID: 30084993
PMCID: PMC6378941
NLM abbreviation: Bioinformatics
ISSN: 1367-4803
eISSN: 1367-4811
Grant note: R01 DE016148 / NIDCR NIH HHS R37 DE008559 / NIDCR NIH HHS R00 DE025060 / NIDCR NIH HHS R03 DE025279 / NIDCR NIH HHS U01 HG005925 / NHGRI NIH HHS U01 DE024425 / NIDCR NIH HHS R01 DE009886 / NIDCR NIH HHS
Language: English
Date published: 02/15/2019
Academic Unit: Anatomy and Cell Biology; Stead Family Department of Pediatrics; Epidemiology; Pediatric Dentistry; Craniofacial Anomalies Research Center; Dental Research
Record Identifier: 9985034990002771

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