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

Gabriel Minarik, Gabriela Repiska, Michaela Hyblova, Emilia Nagyova, Katarina Soltys, Jaroslav Budis, Frantisek Duris, Rastislav Sysak, Maria Gerykova Bujalkova, Barbora Vlkova-Izrael, Orsolya Biro, B. Nagy, Tomas Szemes

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Objectives 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. Methods 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. Results 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 significantlyâ€"p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively. Conclusions Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on highto- 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.

Original languageEnglish
Article numbere0144811
JournalPLoS One
Volume10
Issue number12
DOIs
Publication statusPublished - Dec 1 2015

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trisomics
Chromosomes, Human, Pair 21
Trisomy
Chromosomes
Computer Simulation
Ions
ions
chromosomes
Testing
testing
Cost effectiveness
Down Syndrome
Genes
Throughput
Cost-Benefit Analysis
Pregnant Women
cost effectiveness
pregnant women
selection methods
sampling

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

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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. / Minarik, Gabriel; Repiska, Gabriela; Hyblova, Michaela; Nagyova, Emilia; Soltys, Katarina; Budis, Jaroslav; Duris, Frantisek; Sysak, Rastislav; Bujalkova, Maria Gerykova; Vlkova-Izrael, Barbora; Biro, Orsolya; Nagy, B.; Szemes, Tomas.

In: PLoS One, Vol. 10, No. 12, e0144811, 01.12.2015.

Research output: Contribution to journalArticle

Minarik, Gabriel ; Repiska, Gabriela ; Hyblova, Michaela ; Nagyova, Emilia ; Soltys, Katarina ; Budis, Jaroslav ; Duris, Frantisek ; Sysak, Rastislav ; Bujalkova, Maria Gerykova ; Vlkova-Izrael, Barbora ; Biro, Orsolya ; Nagy, B. ; Szemes, Tomas. / 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. In: PLoS One. 2015 ; Vol. 10, No. 12.
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AU - Minarik, Gabriel

AU - Repiska, Gabriela

AU - Hyblova, Michaela

AU - Nagyova, Emilia

AU - Soltys, Katarina

AU - Budis, Jaroslav

AU - Duris, Frantisek

AU - Sysak, Rastislav

AU - Bujalkova, Maria Gerykova

AU - Vlkova-Izrael, Barbora

AU - Biro, Orsolya

AU - Nagy, B.

AU - Szemes, Tomas

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N2 - Objectives 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. Methods 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. Results 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 significantlyâ€"p = 0.0141 and p = 0.025 for Ion Torrent PGM and MiSeq, respectively. Conclusions Noninvasive prenatal testing for chromosome 21 trisomy with the utilization of benchtop NGS systems led to results equivalent to previously published studies performed on highto- 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.

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