Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance.
<h4>Objectives</h4>The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods.&...
Saved in:
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2015-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0144811&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849723503184445440 |
|---|---|
| author | Gabriel Minarik Gabriela Repiska Michaela Hyblova Emilia Nagyova Katarina Soltys Jaroslav Budis Frantisek Duris Rastislav Sysak Maria Gerykova Bujalkova Barbora Vlkova-Izrael Orsolya Biro Balint Nagy Tomas Szemes |
| author_facet | Gabriel Minarik Gabriela Repiska Michaela Hyblova Emilia Nagyova Katarina Soltys Jaroslav Budis Frantisek Duris Rastislav Sysak Maria Gerykova Bujalkova Barbora Vlkova-Izrael Orsolya Biro Balint Nagy Tomas Szemes |
| author_sort | Gabriel Minarik |
| collection | DOAJ |
| description | <h4>Objectives</h4>The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods.<h4>Methods</h4>Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied.<h4>Results</h4>Using a z score value of 3 as the cut-off, 98.11%-100% (104-106/106) specificity and 100% (24/24) sensitivity and 99.06%-100% (105-106/106) specificity and 100% (24/24) sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantly--p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively.<h4>Conclusions</h4>Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide. |
| format | Article |
| id | doaj-art-a67abece423847cebb702a881176d7fe |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-a67abece423847cebb702a881176d7fe2025-08-20T03:11:01ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-011012e014481110.1371/journal.pone.0144811Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance.Gabriel MinarikGabriela RepiskaMichaela HyblovaEmilia NagyovaKatarina SoltysJaroslav BudisFrantisek DurisRastislav SysakMaria Gerykova BujalkovaBarbora Vlkova-IzraelOrsolya BiroBalint NagyTomas Szemes<h4>Objectives</h4>The aims of this study were to test the utility of benchtop NGS platforms for NIPT for trisomy 21 using previously published z score calculation methods and to optimize the sample preparation and data analysis with use of in silico and physical size selection methods.<h4>Methods</h4>Samples from 130 pregnant women were analyzed by whole genome sequencing on benchtop NGS systems Ion Torrent PGM and MiSeq. The targeted yield of 3 million raw reads on each platform was used for z score calculation. The impact of in silico and physical size selection on analytical performance of the test was studied.<h4>Results</h4>Using a z score value of 3 as the cut-off, 98.11%-100% (104-106/106) specificity and 100% (24/24) sensitivity and 99.06%-100% (105-106/106) specificity and 100% (24/24) sensitivity were observed for Ion Torrent PGM and MiSeq, respectively. After in silico based size selection both platforms reached 100% specificity and sensitivity. Following the physical size selection z scores of tested trisomic samples increased significantly--p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively.<h4>Conclusions</h4>Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on high-to-ultrahigh throughput NGS systems. The in silico size selection led to higher specificity of the test. Physical size selection performed on isolated DNA led to significant increase in z scores. The observed results could represent a basis for increasing of cost effectiveness of the test and thus help with its penetration worldwide.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0144811&type=printable |
| spellingShingle | Gabriel Minarik Gabriela Repiska Michaela Hyblova Emilia Nagyova Katarina Soltys Jaroslav Budis Frantisek Duris Rastislav Sysak Maria Gerykova Bujalkova Barbora Vlkova-Izrael Orsolya Biro Balint Nagy Tomas Szemes Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance. PLoS ONE |
| title | Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance. |
| title_full | Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance. |
| title_fullStr | Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance. |
| title_full_unstemmed | Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance. |
| title_short | Utilization of Benchtop Next Generation Sequencing Platforms Ion Torrent PGM and MiSeq in Noninvasive Prenatal Testing for Chromosome 21 Trisomy and Testing of Impact of In Silico and Physical Size Selection on Its Analytical Performance. |
| title_sort | utilization of benchtop next generation sequencing platforms ion torrent pgm and miseq in noninvasive prenatal testing for chromosome 21 trisomy and testing of impact of in silico and physical size selection on its analytical performance |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0144811&type=printable |
| work_keys_str_mv | AT gabrielminarik utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT gabrielarepiska utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT michaelahyblova utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT emilianagyova utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT katarinasoltys utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT jaroslavbudis utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT frantisekduris utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT rastislavsysak utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT mariagerykovabujalkova utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT barboravlkovaizrael utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT orsolyabiro utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT balintnagy utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance AT tomasszemes utilizationofbenchtopnextgenerationsequencingplatformsiontorrentpgmandmiseqinnoninvasiveprenataltestingforchromosome21trisomyandtestingofimpactofinsilicoandphysicalsizeselectiononitsanalyticalperformance |