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 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.
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Authors | 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 |
Journal | PloS one
(PLoS One)
Vol. 10
Issue 12
Pg. e0144811
( 2015)
ISSN: 1932-6203 [Electronic] United States |
PMID | 26669558
(Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
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Chemical References |
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Topics |
- Chromosomes, Human, Pair 21
(genetics)
- Computer Simulation
- Down Syndrome
(genetics)
- Female
- High-Throughput Nucleotide Sequencing
(methods)
- Humans
- Ions
- Pregnancy
- Prenatal Diagnosis
(methods)
- Reproducibility of Results
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