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RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy.

ABSTRACT: Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex. RAPIDR has been extensively tested with a large sample set as part of the RAPID project in the UK. The package contains quality control steps to make it robust for use in the clinical setting.RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html.kitty.lo@ucl.ac.ukSupplementary data are available at Bioinformatics online.

SUBMITTER: Lo KK 

PROVIDER: S-EPMC4184262 | biostudies-other | 2014 Oct

REPOSITORIES: biostudies-other

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RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy.

Lo Kitty K KK   Boustred Christopher C   Chitty Lyn S LS   Plagnol Vincent V  

Bioinformatics (Oxford, England) 20140701 20

<h4>Unlabelled</h4>Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex.  ...[more]