@article{MTMT:3092307,
	title = {Cell-Free DNA Analysis of Targeted Genomic Regions in Maternal Plasma for Non-Invasive Prenatal Testing of Trisomy 21, Trisomy 18, Trisomy 13, and Fetal Sex},
	url = {https://m2.mtmt.hu/api/publication/3092307},
	author = {Koumbaris, G and Kypri, E and Tsangaras, K and Achilleos, A and Mina, P and Neofytou, M and Velissariou, V and Christopoulou, G and Kallikas, I and Gonzalez-Linan, A and Benusiene, E and Latos-Bielenska, A and Marek, P and Santana, A and Nagy, Nikoletta and Széll, Márta and Laudanski, P and Papageorgiou, EA and Ioannides, M and Patsalis, PC},
	doi = {10.1373/clinchem.2015.252502},
	journal-iso = {CLIN CHEM},
	journal = {CLINICAL CHEMISTRY},
	volume = {62},
	unique-id = {3092307},
	issn = {0009-9147},
	abstract = {BACKGROUND: There is great need for the development of highly accurate cost effective technologies that could facilitate the widespread adoption of noninvasive prenatal testing (NIPT). METHODS: We developed an assay based on the targeted analysis of cell-free DNA for the detection of fetal aneuploidies of chromosomes 21, 18, and 13. This method enabled the capture and analysis of selected genomic regions of interest. An advanced fetal fraction estimation and aneuploidy determination algorithm was also developed. This assay allowed for accurate counting and assessment of chromosomal regions of interest. The analytical performance of the assay was evaluated in a blind study of 631 samples derived from pregnancies of at least 10 weeks of gestation that had also undergone invasive testing. RESULTS: Our blind study exhibited 100% diagnostic sensitivity and specificity and correctly classified 52/52 (95% CI, 93.2%-100%) cases of trisomy 21, 16/16 (95% CI, 79.4%-100%) cases of trisomy 18, 5/5 (95% CI, 47.8%-100%) cases of trisomy 13, and 538/538 (95% CI, 99.3%-100%) normal cases. The test also correctly identified fetal sex in all cases (95% CI, 99.4%-100%). One sample failed prespecified assay quality control criteria, and 19 samples were nonreportable because of low fetal fraction. CONCLUSIONS: The extent to which free fetal DNA testing can be applied as a universal screening tool for trisomy 21, 18, and 13 depends mainly on assay accuracy and cost. Cell-free DNA analysis of targeted genomic regions in maternal plasma enables accurate and cost-effective noninvasive fetal aneuploidy detection, which is critical for widespread adoption of NIPT.},
	year = {2016},
	eissn = {1530-8561},
	pages = {848-855},
	orcid-numbers = {Széll, Márta/0000-0002-0730-714X}
}

@article{MTMT:2992681,
	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},
	url = {https://m2.mtmt.hu/api/publication/2992681},
	author = {Minarik, G and Repiska, G and Hyblova, M and Nagyova, E and Soltys, K and Budis, J and Duris, F and Sysak, R and Gerykova, Bujalkova M and Vlkova-Izrael, B and Biró, Orsolya and Nagy, Bálint and Szemes, T},
	doi = {10.1371/journal.pone.0144811},
	journal-iso = {PLOS ONE},
	journal = {PLOS ONE},
	volume = {10},
	unique-id = {2992681},
	issn = {1932-6203},
	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.},
	year = {2015},
	eissn = {1932-6203},
	orcid-numbers = {Biró, Orsolya/0000-0002-4300-3602; Nagy, Bálint/0000-0002-0295-185X}
}