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...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/6/590 |
| _version_ | 1797567051890425856 |
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| author | Vera Belova Daria Plakhina Sergey Evfratov Kirill Tsukanov Gennady Khvorykh Alexander Rakitko Alexander Konoplyannikov Valery Ilinsky Denis Rebrikov Dmitriy Korostin |
| author_facet | Vera Belova Daria Plakhina Sergey Evfratov Kirill Tsukanov Gennady Khvorykh Alexander Rakitko Alexander Konoplyannikov Valery Ilinsky Denis Rebrikov Dmitriy Korostin |
| author_sort | Vera Belova |
| collection | DOAJ |
| 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). |
| first_indexed | 2024-03-10T19:35:10Z |
| format | Article |
| id | doaj.art-e82c6570346f43029866299c4c8a9b9e |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T19:35:10Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-e82c6570346f43029866299c4c8a9b9e2023-11-20T01:46:34ZengMDPI AGGenes2073-44252020-05-0111659010.3390/genes11060590NIPT Technique Based on the Use of Long Chimeric DNA ReadsVera Belova0Daria Plakhina1Sergey Evfratov2Kirill Tsukanov3Gennady Khvorykh4Alexander Rakitko5Alexander Konoplyannikov6Valery Ilinsky7Denis Rebrikov8Dmitriy Korostin9Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, 1 Ostrovityanova Street, 117997 Moscow, RussiaGenotek Ltd., 17-1-14 Nastavnicheskiy Pereulok, 105120 Moscow, RussiaGenotek Ltd., 17-1-14 Nastavnicheskiy Pereulok, 105120 Moscow, RussiaGenotek Ltd., 17-1-14 Nastavnicheskiy Pereulok, 105120 Moscow, RussiaGenotek Ltd., 17-1-14 Nastavnicheskiy Pereulok, 105120 Moscow, RussiaGenotek Ltd., 17-1-14 Nastavnicheskiy Pereulok, 105120 Moscow, RussiaCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, 1 Ostrovityanova Street, 117997 Moscow, RussiaGenotek Ltd., 17-1-14 Nastavnicheskiy Pereulok, 105120 Moscow, RussiaCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, 1 Ostrovityanova Street, 117997 Moscow, RussiaCenter for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, 1 Ostrovityanova Street, 117997 Moscow, RussiaNon-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).https://www.mdpi.com/2073-4425/11/6/590NIPTchimeric DNAcfDNANGSshort DNA fragmentsfetal fraction |
| spellingShingle | Vera Belova Daria Plakhina Sergey Evfratov Kirill Tsukanov Gennady Khvorykh Alexander Rakitko Alexander Konoplyannikov Valery Ilinsky Denis Rebrikov Dmitriy Korostin NIPT Technique Based on the Use of Long Chimeric DNA Reads Genes NIPT chimeric DNA cfDNA NGS short DNA fragments fetal fraction |
| 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 | NIPT chimeric DNA cfDNA NGS short DNA fragments fetal fraction |
| url | https://www.mdpi.com/2073-4425/11/6/590 |
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