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Bratislava Biocenter

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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 ofImpact of In Silico and Physical Size Selection on Its Analytical Performance. PLoS One, 10(12):e0144811. 2015.

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Download from publisher: https://doi.org/10.1371/journal.pone.0144811

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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.