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001-es BibID:	BIBFORM078546
035-os BibID:	(WoS)000468162100005 (Scopus)85064934684
Első szerző:	Grendar, Marian
Cím:	Uncertainty of fetal fraction determination in Non-Invasive Prenatal Screening by highly polymorphic SNPs / Marian Grendár, Dušan Loderer, Zuzana Laučeková, Iveta Švecová, Michaela Hrtánková, Andrea Hornáková, Bálint Nagy, Pavol Žúbor, Zora Lasabová, Ján Danko
Dátum:	2019
ISSN:	0168-1656
Megjegyzések:	Fetal fraction and the chromosome representation are the two key quantities used in Non-Invasive Prenatal Screening (NIPS) to determine the aneuploidy status of a fetus. Several methods for fetal fraction determination have been proposed in the literature, including a class of the methods, denoted snpFF, based on high-coverage targeted sequencing of highly polymorphic Single Nucleotide Polymorphisms (SNPs). The variant of snpFF, investigated here, has similar properties as the other variants of snpFF. We point out that the variability of the individual informative SNPs-based estimates of fetal fraction increases with the increase of fetal fraction. At 4% fetal fraction the Inter-Quartile Range (IQR) of the individual estimates of fetal fraction is around 3% and it increases to 6% at 15% fetal fraction. snpFF cannot detect fetal fraction below 2.5% because the number of informative SNPs becomes too small, even zero.
Tárgyszavak:	Orvostudományok Klinikai orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk prenatal screening non-invasive SNP
Megjelenés:	Journal Of Biotechnology. - 299 (2019), p. 32-36. -
További szerzők:	Loderer, Dusan Laucekova, Zuzana Svecova, Iveta Hrtankova, Michaela Hornakova, Andrea Nagy Bálint (1956-) (molekuláris genetikus) Zubor, Pavol Lasabova, Zora Danko, Jan
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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001-es BibID:	BIBFORM078545
Első szerző:	Grendar, Marian
Cím:	Non-invasive prenatal screening : from counting chromosomes to estimation of the degree of mosaicism / Marian Grendar, Dusan Loderer, Iveta Svecova, Zuzana Laucekova, Michaela Hrtankova, Balint Nagy, Pavol Zubor, Zora Lasabova, Jan Danko
Dátum:	2019
Megjegyzések:	The read-counting approach to Non-Invasive Prenatal Screening(NIPS) for the common aneuploidies in the placenta rests on a corre-spondence between the number of copies of a chromosome (one, two,or three) and the number of sequencing reads aligned to the chromosome.The discreet, trichotomous NIPS implicitly assumes that a placenta is ei-ther monosomic, euploid or trisomic. If the placenta is affected by somedegree of mosaicism then the discreet NIPS forces it into one of the threecategories, and, in this sense, the placenta is misdiagnosed.The degree of mosaicism can be any number between 0 and 1 (or 0and 100 percent). Thus, a trisomy can be seen as the 100% mosaicism,euploidy as the 0% mosaicism, and the -100% mosaicism corresponds tomonosomy. This way, NIPS turns from counting the copies of a chromo-some (discrete NIPS) to estimation of the degree of mosaicism (continu-ous NIPS). The objective of the continuous NIPS is to measure the degreeof the placental mosaicism as accurately and as precisely as possible.In this work, quantitative foundations of the continuous NIPS are laiddown and explored. The mosaicism interval and the interval-based esti-mate of the degree of mosaicism are introduced. The uncertainty of theestimation of the degree of mosaicism can be quantified by the width ofthe mosaicism interval. Quality control criterion for the continuous NIPSis specified. Importance of using the well-calibrated NIPS is stressed.A small-scale study of a well-calibrated continuous NIPS pipeline im-plies that at the 5% fetal fraction a sample with the 70% trisomic mo-saicism on chromosome 21 can be indistinguishablefrom an euploid sam-ple. In order to attain an acceptable precision of the continuous NIPS,sequencing depth higher than that of the current use in the discreet NIPSwould be needed.
ISBN:	978-1-53615-335-4
Tárgyszavak:	Orvostudományok Klinikai orvostudományok könyvfejezet non-invasive prenatal mosaicism chromosomes
Megjelenés:	Advances in Medicine and Biology / Ed. Leon V. Berhardt. - p. 85-126. -
További szerzők:	Loderer, Dusan Svecova, Iveta Laucekova, Zuzana Hrtankova, Michaela Nagy Bálint (1956-) (molekuláris genetikus) Zubor, Pavol Lasabova, Zora Danko, Jan
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat
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001-es BibID:	BIBFORM074281
Első szerző:	Grendar, Marian
Cím:	Decreasing the no call rate of Non-Invasive Prenatal Testing / Marian Grendar, Dusan Loderer, Iveta Svecova, Zuzana Laucekova, Michaela Hrtankova, Andrea Hornakova, Balint Nagy, Zora Lasabova, Jan Danko
Dátum:	2018
Megjegyzések:	The no call (or failure) rate is an important characteristics of any diagnostic, testing, or screening method. Failures of the read counting approach to Non-Invasive Prenatal Testing (NIPT) are primarily caused by the low fetal fraction. If fetal fraction is below a value, known as the Limit of Detection (LoD), then NIPT cannot determine the aneuploidy status of a fetus. The LoD can be estimated experimentally or by the coverage method. The coverage method implies that the LoD, and hence also the no call rate due to the low fetal fraction, can be made arbitrarily small by increasing the sequencing depth. The no call rate can be made arbitrarily small also by excluding from NIPT the pregnancies suspect of having fetal fraction below the LoD (e.g., due to the low gestational age, high maternal BMI, etc.). These methods of decreasing the no call rate have obvious drawbacks.Explorations of the quantitative foundations of NIPT lead a variant of NIPT that for a fixed sequencing depth attains the no call rate lower than the conventional NIPT and is particularly useful for the subpopulation of pregnancies with the high maternal BMI, and/or low gestational week.
Tárgyszavak:	Orvostudományok Klinikai orvostudományok idézhető absztrakt Non-Invasive Prenatal Testing quantitative foundations
Megjelenés:	Biomedical Papers. - 162 : Suppl. 1 (2018), p. S3. -
További szerzők:	Loderer, Dusan Svecova, Iveta Laucekova, Zuzana Hrtankova, Michaela Hornakova, Andrea Nagy Bálint (1956-) (molekuláris genetikus) Lasabova, Zora Danko, Jan
Internet cím:	Intézményi repozitóriumban (DEA) tárolt változat
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