Format

Send to

Choose Destination
BMC Bioinformatics. 2018 Dec 17;19(1):531. doi: 10.1186/s12859-018-2557-8.

NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing.

Author information

1
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. l.johansson@umcg.nl.
2
Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands. l.johansson@umcg.nl.
3
Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
4
Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
5
School of Bioscience, Systems biology research center, University of Skövde, Skövde, Sweden.

Abstract

BACKGROUND:

Various algorithms have been developed to predict fetal trisomies using cell-free DNA in non-invasive prenatal testing (NIPT). As basis for prediction, a control group of non-trisomy samples is needed. Prediction accuracy is dependent on the characteristics of this group and can be improved by reducing variability between samples and by ensuring the control group is representative for the sample analyzed.

RESULTS:

NIPTeR is an open-source R Package that enables fast NIPT analysis and simple but flexible workflow creation, including variation reduction, trisomy prediction algorithms and quality control. This broad range of functions allows users to account for variability in NIPT data, calculate control group statistics and predict the presence of trisomies.

CONCLUSION:

NIPTeR supports laboratories processing next-generation sequencing data for NIPT in assessing data quality and determining whether a fetal trisomy is present. NIPTeR is available under the GNU LGPL v3 license and can be freely downloaded from https://github.com/molgenis/NIPTeR or CRAN.

KEYWORDS:

NIPT; Next-generation sequencing; Trisomy prediction

PMID:
30558531
PMCID:
PMC6296037
DOI:
10.1186/s12859-018-2557-8
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center