Publications

@article{Budiš20191310,

title = {Dante: Genotyping of known complex and expanded short tandem repeats},

author = {J Budiš and M Kucharík and F Duriš and J Gazdarica and M Zrubcová and A Ficek and T Szemes and B Brejová and J Radvanszky},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064435619&doi=10.1093%2fbioinformatics%2fbty791&partnerID=40&md5=7e873f64aff7726aeb724a3a0c37237f},

doi = {10.1093/bioinformatics/bty791},

issn = {13674803},

year  = {2019},

date = {2019-01-01},

journal = {Bioinformatics},

volume = {35},

number = {8},

pages = {1310-1317},

publisher = {Oxford University Press},

abstract = {Motivation: Short tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2-6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays. Results: We propose an alignment-free algorithm, called Dante, for genotyping and characterization of STR alleles at user-specified known loci based on sequence reads originating from STR loci of interest. The method accounts for natural deviations from the expected sequence, such as variation in the repeat count, sequencing errors, ambiguous bases and complex loci containing several different motifs. In addition, we implemented a correction for copy number defects caused by the polymerase induced stutter effect as well as a prediction of STR expansions that, according to the conventional view, cannot be fully captured by inherently short MPS reads. We tested Dante on simulated datasets and on datasets obtained by targeted sequencing of protein coding parts of thousands of selected clinically relevant genes. In both these datasets, Dante outperformed HipSTR and GATK genotyping tools. Furthermore, Dante was able to predict allele expansions in all tested clinical cases. Availability and implementation: Dante is open source software, freely available for download at https://github.com/jbudis/dante. © The Author(s) 2018. Published by Oxford University Press. All rights reserved.},

keywords = {Computational method, Genetic testing, Short tandem repeats, Variant calling},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{Kamodyová2013124,

title = {Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing},

author = {N Kamodyová and J Durdiaková and P Celec and T Sedláčková and G Repiská and B Sviežená and G Minárik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84869494452&doi=10.1016%2fj.fsigen.2012.07.007&partnerID=40&md5=f8e720ec77c4cb403c6ae43168224959},

doi = {10.1016/j.fsigen.2012.07.007},

issn = {18724973},

year  = {2013},

date = {2013-01-01},

journal = {Forensic Science International: Genetics},

volume = {7},

number = {1},

pages = {124-128},

abstract = {Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60 min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30 min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence. © 2012 Elsevier Ireland Ltd.},

keywords = {Body fluids, Short tandem repeats},

pubstate = {published},

tppubtype = {article}

}