We have collaborated on the following publications
2020
6.
Hyblova, M; Harsanyova, M; Nikulenkov-Grochova, D; Kadlecova, J; Kucharik, M; Budis, J; Minarik, G
In: Diagnostics, 10 (8), 2020, ISSN: 20754418.
Abstract | Links | BibTeX | Tags: Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation
@article{Hyblova2020,
title = {Validation of copy number variants detection from pregnant plasma using low-pass whole-genome sequencing in noninvasive prenatal testing-like settings},
author = {M Hyblova and M Harsanyova and D Nikulenkov-Grochova and J Kadlecova and M Kucharik and J Budis and G Minarik},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090251668&doi=10.3390%2fdiagnostics10080569&partnerID=40&md5=b34f5ed83d4c332d97149be1644573c0},
doi = {10.3390/diagnostics10080569},
issn = {20754418},
year = {2020},
date = {2020-01-01},
journal = {Diagnostics},
volume = {10},
number = {8},
publisher = {MDPI AG},
abstract = {Detection of copy number variants as an integral part of noninvasive prenatal testing is increasingly used in clinical practice worldwide. We performed validation on plasma samples from 34 pregnant women with known aberrations using cell-free DNA sequencing to evaluate the sensitivity for copy number variants (CNV) detection using an in-house CNV fraction-based detection algorithm. The sensitivity for CNVs smaller than 3 megabases (Mb), larger than 3Mb, and overall was 78.57%, 100%, and 90.6%, respectively. Regarding the fetal fraction, detection sensitivity in the group with a fetal fraction of less than 10% was 57.14%, whereas there was 100% sensitivity in the group with fetal fraction exceeding 10%. The assay is also capable of indicating whether the origin of an aberration is exclusively fetal or fetomaternal/maternal. This validation demonstrated that a CNV fraction-based algorithm was applicable and feasible in clinical settings as a supplement to testing for common trisomies 21, 18, and 13. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).},
keywords = {Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation},
pubstate = {published},
tppubtype = {article}
}
Detection of copy number variants as an integral part of noninvasive prenatal testing is increasingly used in clinical practice worldwide. We performed validation on plasma samples from 34 pregnant women with known aberrations using cell-free DNA sequencing to evaluate the sensitivity for copy number variants (CNV) detection using an in-house CNV fraction-based detection algorithm. The sensitivity for CNVs smaller than 3 megabases (Mb), larger than 3Mb, and overall was 78.57%, 100%, and 90.6%, respectively. Regarding the fetal fraction, detection sensitivity in the group with a fetal fraction of less than 10% was 57.14%, whereas there was 100% sensitivity in the group with fetal fraction exceeding 10%. The assay is also capable of indicating whether the origin of an aberration is exclusively fetal or fetomaternal/maternal. This validation demonstrated that a CNV fraction-based algorithm was applicable and feasible in clinical settings as a supplement to testing for common trisomies 21, 18, and 13. © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
5.
Kucharik, M; Gnip, A; Hyblova, M; Budis, J; Strieskova, L; Harsanyova, M; Pös, O; Kubiritova, Z; Radvanszky, J; Minarik, G; Szemes, T
Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions Journal Article
In: PLoS ONE, 15 (8 August), 2020, ISSN: 19326203.
Abstract | Links | BibTeX | Tags: Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation
@article{Kucharik2020,
title = {Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions},
author = {M Kucharik and A Gnip and M Hyblova and J Budis and L Strieskova and M Harsanyova and O Pös and Z Kubiritova and J Radvanszky and G Minarik and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85089990305&doi=10.1371%2fjournal.pone.0238245&partnerID=40&md5=56850bc0c9e9e5e266a3538da3dd5bed},
doi = {10.1371/journal.pone.0238245},
issn = {19326203},
year = {2020},
date = {2020-01-01},
journal = {PLoS ONE},
volume = {15},
number = {8 August},
publisher = {Public Library of Science},
abstract = {To study the detection limits of chromosomal microaberrations in non-invasive prenatal testing with aim for five target microdeletion syndromes, including DiGeorge, Prader-Willi/Angelman, 1p36, Cri-Du-Chat, and Wolf-Hirschhorn syndromes. We used known cases of pathogenic deletions from ISCA database to specifically define regions critical for the target syndromes. Our approach to detect microdeletions, from whole genome sequencing data, is based on sample normalization and read counting for individual bins. We performed both an in-silico study using artificially created data sets and a laboratory test on mixed DNA samples, with known microdeletions, to assess the sensitivity of prediction for varying fetal fractions, deletion lengths, and sequencing read counts. The in-silico study showed sensitivity of 79.3% for 10% fetal fraction with 20M read count, which further increased to 98.4% if we searched only for deletions longer than 3Mb. The test on laboratory-prepared mixed samples was in agreement with in-silico results, while we were able to correctly detect 24 out of 29 control samples. Our results suggest that it is possible to incorporate microaberration detection into basic NIPT as part of the offered screening/diagnostics procedure, however, accuracy and reliability depends on several specific factors. Copyright: © 2020 Kucharik et al.},
keywords = {Copy number variation, Fetal fraction, Non-invasive prenatal testing, Validation},
pubstate = {published},
tppubtype = {article}
}
To study the detection limits of chromosomal microaberrations in non-invasive prenatal testing with aim for five target microdeletion syndromes, including DiGeorge, Prader-Willi/Angelman, 1p36, Cri-Du-Chat, and Wolf-Hirschhorn syndromes. We used known cases of pathogenic deletions from ISCA database to specifically define regions critical for the target syndromes. Our approach to detect microdeletions, from whole genome sequencing data, is based on sample normalization and read counting for individual bins. We performed both an in-silico study using artificially created data sets and a laboratory test on mixed DNA samples, with known microdeletions, to assess the sensitivity of prediction for varying fetal fractions, deletion lengths, and sequencing read counts. The in-silico study showed sensitivity of 79.3% for 10% fetal fraction with 20M read count, which further increased to 98.4% if we searched only for deletions longer than 3Mb. The test on laboratory-prepared mixed samples was in agreement with in-silico results, while we were able to correctly detect 24 out of 29 control samples. Our results suggest that it is possible to incorporate microaberration detection into basic NIPT as part of the offered screening/diagnostics procedure, however, accuracy and reliability depends on several specific factors. Copyright: © 2020 Kucharik et al.
2019
4.
Gazdarica, J; Hekel, R; Budis, J; Kucharik, M; Duris, F; Radvanszky, J; Turna, J; Szemes, T
Combination of fetal fraction estimators based on fragment lengths and fragment counts in non-invasive prenatal testing Journal Article
In: International Journal of Molecular Sciences, 20 (16), 2019, ISSN: 16616596.
Abstract | Links | BibTeX | Tags: Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing
@article{Gazdarica2019,
title = {Combination of fetal fraction estimators based on fragment lengths and fragment counts in non-invasive prenatal testing},
author = {J Gazdarica and R Hekel and J Budis and M Kucharik and F Duris and J Radvanszky and J Turna and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85071515046&doi=10.3390%2fijms20163959&partnerID=40&md5=13c0a797eeb085dba097cea3d39680a9},
doi = {10.3390/ijms20163959},
issn = {16616596},
year = {2019},
date = {2019-01-01},
journal = {International Journal of Molecular Sciences},
volume = {20},
number = {16},
publisher = {MDPI AG},
abstract = {The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.},
keywords = {Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing},
pubstate = {published},
tppubtype = {article}
}
The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion. © 2019 by the authors. Licensee MDPI, Basel, Switzerland.
3.
Budis, J; Gazdarica, J; Radvanszky, J; Szucs, G; Kucharik, M; Strieskova, L; Gazdaricova, I; Harsanyova, M; Duris, F; Minarik, G; Sekelska, M; Nagy, B; Turna, J; Szemes, T
Combining count- And length-based z-scores leads to improved predictions in non-invasive prenatal testing Journal Article
In: Bioinformatics, 35 (8), pp. 1284-1291, 2019, ISSN: 13674803.
Abstract | Links | BibTeX | Tags: Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis
@article{Budis20191284,
title = {Combining count- And length-based z-scores leads to improved predictions in non-invasive prenatal testing},
author = {J Budis and J Gazdarica and J Radvanszky and G Szucs and M Kucharik and L Strieskova and I Gazdaricova and M Harsanyova and F Duris and G Minarik and M Sekelska and B Nagy and J Turna and T Szemes},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85067353429&doi=10.1093%2fbioinformatics%2fbty806&partnerID=40&md5=c63c304db3eb59cb922d0ca8e3a9e76a},
doi = {10.1093/bioinformatics/bty806},
issn = {13674803},
year = {2019},
date = {2019-01-01},
journal = {Bioinformatics},
volume = {35},
number = {8},
pages = {1284-1291},
publisher = {Oxford University Press},
abstract = {Motivation: Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. Results: We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. Availability and implementation: The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda. © The Author(s) 2018. Published by Oxford University Press. All rights reserved.},
keywords = {Aneuploidy, Computational method, Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis},
pubstate = {published},
tppubtype = {article}
}
Motivation: Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. Results: We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. Availability and implementation: The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda. © The Author(s) 2018. Published by Oxford University Press. All rights reserved.
2.
Sekelska, M; Izsakova, A; Kubosova, K; Tilandyova, P; Csekes, E; Kuchova, Z; Hyblova, M; Harsanyova, M; Kucharik, M; Budis, J; Szemes, T; Minarik, G
Result of prospective validation of the trisomy Test® for the detection of chromosomal trisomies Journal Article
In: Diagnostics, 9 (4), 2019, ISSN: 20754418.
Abstract | Links | BibTeX | Tags: Aneuploidy, Fetal fraction, Non-invasive prenatal testing, Validation
@article{Sekelska2019,
title = {Result of prospective validation of the trisomy Test® for the detection of chromosomal trisomies},
author = {M Sekelska and A Izsakova and K Kubosova and P Tilandyova and E Csekes and Z Kuchova and M Hyblova and M Harsanyova and M Kucharik and J Budis and T Szemes and G Minarik},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85076805864&doi=10.3390%2fdiagnostics9040138&partnerID=40&md5=ffdda3394730383358ea467fee4a90f8},
doi = {10.3390/diagnostics9040138},
issn = {20754418},
year = {2019},
date = {2019-01-01},
journal = {Diagnostics},
volume = {9},
number = {4},
publisher = {MDPI AG},
abstract = {Noninvasive prenatal testing (NIPT) is one of the most common prenatal screening tests used worldwide. Trisomy Test® belongs to NIPT tests based on low-coverage whole-genome sequencing. In our prospective study, 7279 samples of pregnant women collected during approximately two years were analyzed. In this cohort, 117 positive cases for trisomies 21, 18, and 13 were reported. An in-house designed bioinformatic pipeline and proprietary biostatistical approach was used for the detection of trisomies. The pooled sensitivity and specificity of our test reached 99.12% and 99.94%, respectively. The proportion of repeatedly uninformative results after repeated blood draws was 1.11%. Based on the presented results, we can confirm that the Trisomy Test® is fully comparable with other commercial NIPT tests available worldwide. © 2019 by the authors.},
keywords = {Aneuploidy, Fetal fraction, Non-invasive prenatal testing, Validation},
pubstate = {published},
tppubtype = {article}
}
Noninvasive prenatal testing (NIPT) is one of the most common prenatal screening tests used worldwide. Trisomy Test® belongs to NIPT tests based on low-coverage whole-genome sequencing. In our prospective study, 7279 samples of pregnant women collected during approximately two years were analyzed. In this cohort, 117 positive cases for trisomies 21, 18, and 13 were reported. An in-house designed bioinformatic pipeline and proprietary biostatistical approach was used for the detection of trisomies. The pooled sensitivity and specificity of our test reached 99.12% and 99.94%, respectively. The proportion of repeatedly uninformative results after repeated blood draws was 1.11%. Based on the presented results, we can confirm that the Trisomy Test® is fully comparable with other commercial NIPT tests available worldwide. © 2019 by the authors.
2015
1.
Repiská, G; Sedláčková, T; Szemes, T; Minárik, G
In: Fetal Diagnosis and Therapy, 37 (1), pp. 58-64, 2015, ISSN: 10153837.
Abstract | Links | BibTeX | Tags: Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis, Short tandem repeats
@article{Repiská201558,
title = {Effect of different DNA concentration methods on performance of non-invasive fetal y-chromosomal short tandem repeat profiling from maternal plasma},
author = {G Repiská and T Sedláčková and T Szemes and G Minárik},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922410960&doi=10.1159%2f000362664&partnerID=40&md5=7c7661ed02547b6c348c02c18d1f0b51},
doi = {10.1159/000362664},
issn = {10153837},
year = {2015},
date = {2015-01-01},
journal = {Fetal Diagnosis and Therapy},
volume = {37},
number = {1},
pages = {58-64},
publisher = {S. Karger AG},
abstract = {Background: The accuracy and reliability of detection of free fetal DNA in plasma of pregnant women can be significantly improved by increasing the overall DNA concentration following the isolation from maternal plasma. The aim of our study was to compare DNA concentration methods on samples with free fetal DNA. Materials and Methods: DNA isolated from plasma samples of pregnant women carrying a male fetus were concentrated by 3 different methods: vacuum concentration, centrifugal filters and spin columns. Their performance was evaluated using PCR-based Y-chromosomal short tandem repeat (Y-STR) genotyping of the fetus. Results: A statistically significant difference was found between the 3 tested methods (F = 15.57, p < 0.0001). Using vacuum concentration 85.3% of paternally inherited Y-STR alleles were correctly identified. A significantly smaller proportion of alleles was correctly identified in samples concentrated by centrifugal filters and spin columns - 75.9 and 66.5%, respectively. Discussion: The highest proportion of paternally inherited Y-STR alleles was found in samples concentrated with the use of vacuum concentration. This concentration procedure does not require further handling of the sample either, which is an advantage because it avoids potential sample contamination. On the other hand, when automation is considered, vacuum concentration is less suitable because of an uneven and unpredictable sample evaporation rate. © 2014 S. Karger AG, Basel.},
keywords = {Fetal fraction, Non-invasive prenatal testing, Prenatal diagnosis, Short tandem repeats},
pubstate = {published},
tppubtype = {article}
}
Background: The accuracy and reliability of detection of free fetal DNA in plasma of pregnant women can be significantly improved by increasing the overall DNA concentration following the isolation from maternal plasma. The aim of our study was to compare DNA concentration methods on samples with free fetal DNA. Materials and Methods: DNA isolated from plasma samples of pregnant women carrying a male fetus were concentrated by 3 different methods: vacuum concentration, centrifugal filters and spin columns. Their performance was evaluated using PCR-based Y-chromosomal short tandem repeat (Y-STR) genotyping of the fetus. Results: A statistically significant difference was found between the 3 tested methods (F = 15.57, p < 0.0001). Using vacuum concentration 85.3% of paternally inherited Y-STR alleles were correctly identified. A significantly smaller proportion of alleles was correctly identified in samples concentrated by centrifugal filters and spin columns - 75.9 and 66.5%, respectively. Discussion: The highest proportion of paternally inherited Y-STR alleles was found in samples concentrated with the use of vacuum concentration. This concentration procedure does not require further handling of the sample either, which is an advantage because it avoids potential sample contamination. On the other hand, when automation is considered, vacuum concentration is less suitable because of an uneven and unpredictable sample evaporation rate. © 2014 S. Karger AG, Basel.