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

Lennart F Johansson; Hendrik A de Weerd; Eddy N de Boer; Freerk van Dijk; Gerard J Te Meerman; Rolf H Sijmons; Birgit Sikkema-Raddatz; Morris A Swertz

doi:10.1186/s12859-018-2557-8

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

Lennart F Johansson^*, Hendrik A de Weerd, Eddy N de Boer, Freerk van Dijk, Gerard J Te Meerman, Rolf H Sijmons, Birgit Sikkema-Raddatz, Morris A Swertz

^*Corresponding author for this work

Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI)

Research output: Contribution to journal › Article › Academic › peer-review

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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.

Original language	English
Article number	531
Number of pages	5
Journal	Bmc Bioinformatics
Volume	19
Issue number	1
DOIs	https://doi.org/10.1186/s12859-018-2557-8
Publication status	Published - 17-Dec-2018

Keywords

DNA

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10.1186/s12859-018-2557-8Licence: CC BY

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Additional file 5: of NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing
Johansson, L. (Contributor), Weerd, H. (Contributor), de Boer, E. (Contributor), van Dijk, F. (Contributor), te Meerman, G. (Contributor), Sijmons, R. (Contributor), Raddatz, B. (Contributor) & Swertz, M. (Contributor), University of Groningen, 17-Dec-2018
DOI: 10.6084/m9.figshare.7479080.v1
Dataset
Additional file 3: of NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing
Johansson, L. (Contributor), Weerd, H. (Contributor), de Boer, E. (Contributor), van Dijk, F. (Contributor), te Meerman, G. (Contributor), Sijmons, R. (Contributor), Raddatz, B. (Contributor) & Swertz, M. (Contributor), University of Groningen, 17-Dec-2018
DOI: 10.6084/m9.figshare.7479071.v1
Dataset
Additional file 4: of NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing
Johansson, L. (Contributor), Weerd ,de, H. (Contributor), de Boer, E. (Contributor), van Dijk, F. (Contributor), te Meerman, G. (Contributor), Sijmons, R. (Contributor), Raddatz, B. (Contributor) & Swertz, M. (Contributor), University of Groningen, 17-Dec-2018
DOI: 10.6084/m9.figshare.7479074.v1
Dataset

Cite this

@article{9d9dd9e811c94ceca3bfe7b7d0fab963,

title = "NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing",

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 = "DNA",

author = "Johansson, {Lennart F} and {de Weerd}, {Hendrik A} and {de Boer}, {Eddy N} and {van Dijk}, Freerk and {Te Meerman}, {Gerard J} and Sijmons, {Rolf H} and Birgit Sikkema-Raddatz and Swertz, {Morris A}",

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doi = "10.1186/s12859-018-2557-8",

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T2 - an R package for fast and accurate trisomy prediction in non-invasive prenatal testing

AU - Johansson, Lennart F

AU - de Weerd, Hendrik A

AU - de Boer, Eddy N

AU - van Dijk, Freerk

AU - Te Meerman, Gerard J

AU - Sijmons, Rolf H

AU - Sikkema-Raddatz, Birgit

AU - Swertz, Morris A

PY - 2018/12/17

Y1 - 2018/12/17

N2 - 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.

AB - 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.

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DO - 10.1186/s12859-018-2557-8

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JO - Bmc Bioinformatics

JF - Bmc Bioinformatics

IS - 1

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ER -

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

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Additional file 5: of NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing

Additional file 3: of NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing

Additional file 4: of NIPTeR: an R package for fast and accurate trisomy prediction in non-invasive prenatal testing

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