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NIPT Technique Based on the Use of Long Chimeric DNA Reads
Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still r...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7349339/ https://www.ncbi.nlm.nih.gov/pubmed/32466452 http://dx.doi.org/10.3390/genes11060590 |
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author | Belova, Vera Plakhina, Daria Evfratov, Sergey Tsukanov, Kirill Khvorykh, Gennady Rakitko, Alexander Konoplyannikov, Alexander Ilinsky, Valery Rebrikov, Denis Korostin, Dmitriy |
author_facet | Belova, Vera Plakhina, Daria Evfratov, Sergey Tsukanov, Kirill Khvorykh, Gennady Rakitko, Alexander Konoplyannikov, Alexander Ilinsky, Valery Rebrikov, Denis Korostin, Dmitriy |
author_sort | Belova, Vera |
collection | PubMed |
description | Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an increasing trend in the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140–160 bp, it is not possible to effectively use long reads. The authors used high-performance sequencing of cell-free DNA (cfDNA) libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples from pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of the results. The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99.93% and 99.14% for T21; 100% and 98.34% for T18; 100% and 99.17% for T13, respectively). |
format | Online Article Text |
id | pubmed-7349339 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-73493392020-07-22 NIPT Technique Based on the Use of Long Chimeric DNA Reads Belova, Vera Plakhina, Daria Evfratov, Sergey Tsukanov, Kirill Khvorykh, Gennady Rakitko, Alexander Konoplyannikov, Alexander Ilinsky, Valery Rebrikov, Denis Korostin, Dmitriy Genes (Basel) Article Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an increasing trend in the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140–160 bp, it is not possible to effectively use long reads. The authors used high-performance sequencing of cell-free DNA (cfDNA) libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples from pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of the results. The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99.93% and 99.14% for T21; 100% and 98.34% for T18; 100% and 99.17% for T13, respectively). MDPI 2020-05-26 /pmc/articles/PMC7349339/ /pubmed/32466452 http://dx.doi.org/10.3390/genes11060590 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Belova, Vera Plakhina, Daria Evfratov, Sergey Tsukanov, Kirill Khvorykh, Gennady Rakitko, Alexander Konoplyannikov, Alexander Ilinsky, Valery Rebrikov, Denis Korostin, Dmitriy NIPT Technique Based on the Use of Long Chimeric DNA Reads |
title | NIPT Technique Based on the Use of Long Chimeric DNA Reads |
title_full | NIPT Technique Based on the Use of Long Chimeric DNA Reads |
title_fullStr | NIPT Technique Based on the Use of Long Chimeric DNA Reads |
title_full_unstemmed | NIPT Technique Based on the Use of Long Chimeric DNA Reads |
title_short | NIPT Technique Based on the Use of Long Chimeric DNA Reads |
title_sort | nipt technique based on the use of long chimeric dna reads |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7349339/ https://www.ncbi.nlm.nih.gov/pubmed/32466452 http://dx.doi.org/10.3390/genes11060590 |
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