Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Belova, Vera, Plakhina, Daria, Evfratov, Sergey, Tsukanov, Kirill, Khvorykh, Gennady, Rakitko, Alexander, Konoplyannikov, Alexander, Ilinsky, Valery, Rebrikov, Denis, Korostin, Dmitriy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
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
_version_ 1783557040757538816
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
work_keys_str_mv AT belovavera nipttechniquebasedontheuseoflongchimericdnareads
AT plakhinadaria nipttechniquebasedontheuseoflongchimericdnareads
AT evfratovsergey nipttechniquebasedontheuseoflongchimericdnareads
AT tsukanovkirill nipttechniquebasedontheuseoflongchimericdnareads
AT khvorykhgennady nipttechniquebasedontheuseoflongchimericdnareads
AT rakitkoalexander nipttechniquebasedontheuseoflongchimericdnareads
AT konoplyannikovalexander nipttechniquebasedontheuseoflongchimericdnareads
AT ilinskyvalery nipttechniquebasedontheuseoflongchimericdnareads
AT rebrikovdenis nipttechniquebasedontheuseoflongchimericdnareads
AT korostindmitriy nipttechniquebasedontheuseoflongchimericdnareads