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

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

Author information

1
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
2
Department of Human Genetics, Emory University, Atlanta, GA, USA.
3
Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
4
Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
5
Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA.
6
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
7
Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.

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.

AVAILABILITY AND IMPLEMENTATION:

MDTS is freely available as open source software from the Bioconductor repository.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

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