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

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.

SUBMITTER: Fu JM 

PROVIDER: S-EPMC6378941 | biostudies-literature |

REPOSITORIES: biostudies-literature