Cargando…

Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening

Non-invasive prenatal screening (NIPS) is a DNA sequencing-based screening test for fetal aneuploidies and possibly other pathogenic genomic abnormalities, such as large deletions and duplications. Validation and quality assurance (QA) of this clinical test using plasmas with and without targeted ch...

Descripción completa

Detalles Bibliográficos
Autores principales: Qi, Zhongxia, Yu, Jingwei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9886268/
https://www.ncbi.nlm.nih.gov/pubmed/36726805
http://dx.doi.org/10.3389/fgene.2023.971087
_version_ 1784880098817605632
author Qi, Zhongxia
Yu, Jingwei
author_facet Qi, Zhongxia
Yu, Jingwei
author_sort Qi, Zhongxia
collection PubMed
description Non-invasive prenatal screening (NIPS) is a DNA sequencing-based screening test for fetal aneuploidies and possibly other pathogenic genomic abnormalities, such as large deletions and duplications. Validation and quality assurance (QA) of this clinical test using plasmas with and without targeted chromosomal abnormalities from pregnant women as negative and positive controls are required. However, the positive plasma controls may not be available for many laboratories that are planning to establish NIPS. Limited synthetic positive plasmas are commercially available, but the types of abnormalities and the number/quantity of synthetic plasmas for each abnormality are insufficient to meet the minimal requirements for the initial validation. We report here a method of making synthetic positive plasmas by adding cell-free DNA (cfDNA) isolated from culture media of prenatal cells with chromosomal abnormalities to the plasmas from non-pregnant women. Thirty-eight positive plasmas with various chromosomal abnormalities, including autosomal and sex chromosomal aneuploidies, large deletions and duplications, were synthesized. The synthetic plasmas were characterized side-by-side with real positive plasmas from pregnant women and commercially available synthetic positive plasmas using the Illumina VeriSeq NIPT v2 system. All chromosomal abnormalities in the synthetic plasmas were correctly identified with the same testing sensitivity and specificity as in the real and commercial synthetic plasmas. The findings demonstrate that the synthetic positive plasmas are excellent alternatives of real positive plasmas for validation and QA of NIPS. The method described here is simple and straightforward, and can be readily used in clinical genetics laboratories with accessibility to prenatal cultures.
format Online
Article
Text
id pubmed-9886268
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-98862682023-01-31 Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening Qi, Zhongxia Yu, Jingwei Front Genet Genetics Non-invasive prenatal screening (NIPS) is a DNA sequencing-based screening test for fetal aneuploidies and possibly other pathogenic genomic abnormalities, such as large deletions and duplications. Validation and quality assurance (QA) of this clinical test using plasmas with and without targeted chromosomal abnormalities from pregnant women as negative and positive controls are required. However, the positive plasma controls may not be available for many laboratories that are planning to establish NIPS. Limited synthetic positive plasmas are commercially available, but the types of abnormalities and the number/quantity of synthetic plasmas for each abnormality are insufficient to meet the minimal requirements for the initial validation. We report here a method of making synthetic positive plasmas by adding cell-free DNA (cfDNA) isolated from culture media of prenatal cells with chromosomal abnormalities to the plasmas from non-pregnant women. Thirty-eight positive plasmas with various chromosomal abnormalities, including autosomal and sex chromosomal aneuploidies, large deletions and duplications, were synthesized. The synthetic plasmas were characterized side-by-side with real positive plasmas from pregnant women and commercially available synthetic positive plasmas using the Illumina VeriSeq NIPT v2 system. All chromosomal abnormalities in the synthetic plasmas were correctly identified with the same testing sensitivity and specificity as in the real and commercial synthetic plasmas. The findings demonstrate that the synthetic positive plasmas are excellent alternatives of real positive plasmas for validation and QA of NIPS. The method described here is simple and straightforward, and can be readily used in clinical genetics laboratories with accessibility to prenatal cultures. Frontiers Media S.A. 2023-01-16 /pmc/articles/PMC9886268/ /pubmed/36726805 http://dx.doi.org/10.3389/fgene.2023.971087 Text en Copyright © 2023 Qi and Yu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Qi, Zhongxia
Yu, Jingwei
Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening
title Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening
title_full Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening
title_fullStr Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening
title_full_unstemmed Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening
title_short Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening
title_sort synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9886268/
https://www.ncbi.nlm.nih.gov/pubmed/36726805
http://dx.doi.org/10.3389/fgene.2023.971087
work_keys_str_mv AT qizhongxia synthesisofpositiveplasmaswithknownchromosomalabnormalitiesforvalidationofnoninvasiveprenatalscreening
AT yujingwei synthesisofpositiveplasmaswithknownchromosomalabnormalitiesforvalidationofnoninvasiveprenatalscreening