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.Availability and implementation: RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html.Contact: kitty.lo@ucl.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Since the first demonstration of the use of cell-free DNA to detect aneuploidy (Chiu et al, 2008; Fan et al, 2008), many groups around the world have reported large studies showing high sensitivities and specificities for the detection of trisomies 13, 18 and 21 (Jiang et al, 2012; Palomaki et al, 2011; Sehnert et al, 2011)
To perform non-invasive prenatal testing (NIPT), cell-free DNA (cfDNA) is extracted from maternal plasma and sequenced using short reads and high-throughput DNA sequencing
RAPIDR combines several analytical techniques that have been proposed for NIPT analysis and has been tested with a large sample set from the RAPID project (NIHR funded project to evaluate the use of NIPT)
Summary
Since the first demonstration of the use of cell-free DNA (cfDNA) to detect aneuploidy (Chiu et al, 2008; Fan et al, 2008), many groups around the world have reported large studies showing high sensitivities and specificities for the detection of trisomies 13, 18 and 21 (Jiang et al, 2012; Palomaki et al, 2011; Sehnert et al, 2011). In contrast to invasive methods such as amniocentesis, non-invasive prenatal testing (NIPT) uses cfDNA in maternal plasma and does not present a risk of miscarriage. To perform NIPT, cfDNA is extracted from maternal plasma and sequenced using short reads and high-throughput DNA sequencing. Previous studies have shown that an acceptable level of test sensitivity can be reached with relatively short read lengths (36–52 bp) and modest coverage (2–10 million reads per sample) (Liang et al, 2013; Sehnert et al, 2011). RAPIDR combines several analytical techniques that have been proposed for NIPT analysis and has been tested with a large sample set from the RAPID project (NIHR funded project to evaluate the use of NIPT). RAPID validation results can be found in the Supplementary Material (Supplementary Figs S1–S4, Supplementary Text S1 and Supplementary Tables S1 and S2)
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