Journal Article

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

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

2015

Overview

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. 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. 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. 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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Bioinformatics / Chromosome 21 / Chromosomes / Chromosomes, Human, Pair 21 - genetics / Collaboration / Computer science / Computer Simulation / Cost effectiveness / Data analysis / Data processing / Deoxyribonucleic acid / DNA / DNA sequencing / Down Syndrome - genetics / Feasibility studies / Female / Gene sequencing / Genomes / Gynecology / Health aspects / High-Throughput Nucleotide Sequencing - methods / Human chromosome 21 / Humans / Informatics / Ions / Laboratories / Mathematical analysis / Medicine / Molecular biology / Obstetrics / Plasma / Pregnancy / Pregnant women / Prenatal diagnosis / Prenatal Diagnosis - methods / Reproducibility of Results / Sample preparation / Sampling methods / Sensitivity / Trisomy