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
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