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.
abstract: OBJECTIVE
  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 significantly--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 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.
authors.affiliation: Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia.|Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.|Geneton Ltd., Bratislava, Slovakia.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Minarik
authors.affiliation: Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Repiska
authors.affiliation: Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Michaela
authors.initials: M
authors.lastname: Hyblova
authors.affiliation: Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Emilia
authors.initials: E
authors.lastname: Nagyova
authors.affiliation: Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Katarina
authors.initials: K
authors.lastname: Soltys
authors.affiliation: Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Budis
authors.affiliation: Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.|Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Frantisek
authors.initials: F
authors.lastname: Duris
authors.affiliation: 1st Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia.
authors.forename: Rastislav
authors.initials: R
authors.lastname: Sysak
authors.affiliation: Department of Clinical Genetics, Medirex Inc., Bratislava, Slovakia.|Outpatient Clinic for Medical Genetics, Nemocnicna Inc., Malacky, Slovakia.
authors.forename: Maria
authors.initials: M
authors.lastname: Gerykova Bujalkova
authors.affiliation: Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia.|Geneton Ltd., Bratislava, Slovakia.
authors.forename: Barbora
authors.initials: B
authors.lastname: Vlkova-Izrael
authors.affiliation: 1st Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary.
authors.forename: Orsolya
authors.initials: O
authors.lastname: Biro
authors.affiliation: 1st Department of Obstetrics and Gynecology, Semmelweis University, Budapest, Hungary.
authors.forename: Balint
authors.initials: B
authors.lastname: Nagy
authors.affiliation: Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.|Geneton Ltd., Bratislava, Slovakia.
authors.forename: Tomas
authors.initials: T
authors.lastname: Szemes
mesh_terms: D002891:Chromosomes, Human, Pair 21 / Q000235:genetics*; D003198:Computer Simulation; D004314:Down Syndrome / Q000235:genetics*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007477:Ions; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D007477:Ions