TY - JOUR AU - Budis, Jaroslav AU - Krampl, Werner AU - Kucharik, Marcel AU - Hekel, Rastislav AU - Goga, Adrian AU - Sitarcik, Jozef AU - Lichvar, Michal AU - Smol'ak, David AU - Boehmer, Miroslav AU - Balaz, Andrej AU - Duris, Frantisek AU - Gazdarica, Juraj AU - Soltys, Katarina AU - Turna, Jan AU - Radvanszky, Jan AU - Szemes, Tomas TI - SnakeLines: integrated set of computational pipelines for sequencing reads JF - Journal of Integrative Bioinformatics J2 - Journal of Integrative Bioinformatics PY - 2023 PG - 12 SN - 1613-4516 DO - 10.1515/jib-2022-0059 UR - https://m2.mtmt.hu/api/publication/34293998 ID - 34293998 AB - With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, which is often too demanding for clinicians and researchers without a computational background. Another problem represents the reproducibility of computational analyses across separated computational centres with inconsistent versions of installed libraries and bioinformatics tools. We propose an easily extensible set of computational pipelines, called SnakeLines, for processing sequencing reads; including mapping, assembly, variant calling, viral identification, transcriptomics, and metagenomics analysis. Individual steps of an analysis, along with methods and their parameters can be readily modified in a single configuration file. Provided pipelines are embedded in virtual environments that ensure isolation of required resources from the host operating system, rapid deployment, and reproducibility of analysis across different Unix-based platforms. SnakeLines is a powerful framework for the automation of bioinformatics analyses, with emphasis on a simple set-up, modifications, extensibility, and reproducibility. The framework is already routinely used in various research projects and their applications, especially in the Slovak national surveillance of SARS-CoV-2. LA - English DB - MTMT ER - TY - JOUR AU - Chang, Liang AU - Jiao, Haining AU - Chen, Jiucheng AU - Wu, Guanlin AU - Liu, Ping AU - Li, Rong AU - Guo, Jianying AU - Long, Wenqing AU - Tang, Xiaojian AU - Lu, Bingjie AU - Xu, Haibin AU - Wu, Han TI - Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases JF - LIFE SCIENCE ALLIANCE J2 - LIFE SCI ALLIANCE VL - 6 PY - 2023 IS - 5 PG - 11 SN - 2575-1077 DO - 10.26508/lsa.202201761 UR - https://m2.mtmt.hu/api/publication/33903397 ID - 33903397 AB - Monogenic inherited diseases are common causes of congenital disabilities, leading to severe economic and mental burdens on affected families. In our previous study, we demonstrated the validity of cell-based noninvasive prenatal testing (cbNIPT) in prenatal diagnosis by single-cell targeted sequencing. The present research further explored the feasibility of single-cell whole-genome sequencing (WGS) and haplotype analysis of various monogenic diseases with cbNIPT. Four families were recruited: one with inherited deafness, one with hemophilia, one with large vestibular aqueduct syndrome (LVAS), and one with no disease. Circulating trophoblast cells (cTBs) were obtained from maternal blood and analyzed by single-cell 15X WGS. Haplotype analysis showed that CFC178 (deafness family), CFC616 (hemo-philia family), and CFC111 (LVAS family) inherited haplotypes from paternal and/or maternal pathogenic loci. Amniotic fluid or fetal villi samples from the deafness and hemophilia families confirmed these results. WGS performed better than targeted sequencing in genome coverage, allele dropout (ADO), and false-positive (FP) ratios. Our findings suggest that cbNIPT by WGS and haplotype analysis have great potential for use in prenatally diagnosing various monogenic diseases. LA - English DB - MTMT ER - TY - JOUR AU - Jayashankar, Siva Shantini AU - Nasaruddin, Muhammad Luqman AU - Hassan, Muhammad Faiz AU - Dasrilsyah, Rima Anggrena AU - Shafiee, Mohamad Nasir AU - Ismail, Noor Akmal Shareela AU - Alias, Ekram TI - Non-Invasive Prenatal Testing (NIPT): Reliability, Challenges, and Future Directions JF - DIAGNOSTICS J2 - DIAGNOSTICS VL - 13 PY - 2023 IS - 15 PG - 21 SN - 2075-4418 DO - 10.3390/diagnostics13152570 UR - https://m2.mtmt.hu/api/publication/34293999 ID - 34293999 AB - Non-invasive prenatal testing was first discovered in 1988; it was primarily thought to be able to detect common aneuploidies, such as Patau syndrome (T13), Edward Syndrome (T18), and Down syndrome (T21). It comprises a simple technique involving the analysis of cell-free foetal DNA (cffDNA) obtained through maternal serum, using advances in next-generation sequencing. NIPT has shown promise as a simple and low-risk screening test, leading various governments and private organizations worldwide to dedicate significant resources towards its integration into national healthcare initiatives as well as the formation of consortia and research studies aimed at standardizing its implementation. This article aims to review the reliability of NIPT while discussing the current challenges prevalent among different communities worldwide. LA - English DB - MTMT ER - TY - JOUR AU - Dong, Zaizai AU - Wang, Yu AU - Yin, Dedong AU - Hang, Xinxin AU - Pu, Lei AU - Zhang, Jianfu AU - Geng, Jia AU - Chang, Lingqian TI - Advanced techniques for gene heterogeneity research: Single-cell sequencing and on-chip gene analysis systems JF - View J2 - View VL - 3 PY - 2022 IS - 1 PG - 21 SN - 2688-268X DO - 10.1002/VIW.20210011 UR - https://m2.mtmt.hu/api/publication/33305082 ID - 33305082 AB - Gene heterogeneity leads to the differences in cellular behaviors in a wide range, such as tumor drug-resistant mutation, epithelial-mesenchymal transition, and migration, posing significant challenges to the development of biomedicine. Traditional gene analysis methods, such as polymerase chain reaction, employ a mass of cells as the gene source, resulting in that the gene properties from a specific single cell are hidden in massive gene information. Recent decades have seen the emerging single-cell gene analysis techniques with their unprecedented opportunities to study gene heterogeneity with high precision and high throughput. In this review, we summarized the state-of-the-art techniques for single-cell sequencing and on-chip gene analysis systems. The principles of each technique are introduced in detail, with the focus on the application scenarios in gene heterogeneity research. Looking forward, we also introduced the challenges in current technologies and point out the future direction for facilitating the technical improvement and clinical applications of single-cell gene analysis techniques. LA - English DB - MTMT ER - TY - JOUR AU - Forgacova, Natalia AU - Gazdarica, Juraj AU - Budis, Jaroslav AU - Kucharik, Marcel AU - Sekelska, Martina AU - Szemes, Tomas TI - Non-intuitive trends of fetal fraction development related to gestational age and fetal gender, and their practical implications for non-invasive prenatal testing JF - MOLECULAR AND CELLULAR PROBES J2 - MOL CELL PROBE VL - 66 PY - 2022 PG - 7 SN - 0890-8508 DO - 10.1016/j.mcp.2022.101870 UR - https://m2.mtmt.hu/api/publication/33903398 ID - 33903398 AB - Discovery of fetal cell-free DNA fragments in maternal blood revolutionized prenatal diagnostics. Although noninvasive prenatal testing (NIPT) is already a matured screening test with high specificity and sensitivity, the accurate estimation of the proportion of fetal fragments, called fetal fraction, is crucial to avoid false-negative results. In this study, we collected 6999 samples from women undergoing NIPT testing with a single male fetus to demonstrate the influence of fetal fraction by the maternal and fetal characteristics. We show several fetal fraction discrepancies that contradict the generally presented conventional view. At first, the fetal fraction is not consistently rising with the maturity of the fetus due to a drop in 15 weeks of maturation. Secondly, the male samples have a lower fetal fraction than female fetuses, arguably due to the smaller gonosomal chromosomes. Finally, we discuss not only the possible reasons why this inconsistency exists but we also outline why these differences have not yet been identified and published. We demonstrate two non-intuitive trends to better comprehend the fetal fraction development and more precise selection of patients with sufficient fetal fraction for accurate testing. LA - English DB - MTMT ER - TY - JOUR AU - Forgacova, Natalia AU - Gazdarica, Juraj AU - Budis, Jaroslav AU - Radvanszky, Jan AU - Szemes, Tomas TI - Repurposing non-invasive prenatal testing data: Population study of single nucleotide variants associated with colorectal cancer and Lynch syndrome JF - ONCOLOGY LETTERS J2 - ONCOL LETT VL - 22 PY - 2021 IS - 5 PG - 14 SN - 1792-1074 DO - 10.3892/ol.2021.13040 UR - https://m2.mtmt.hu/api/publication/32295169 ID - 32295169 AB - In our previous work, genomic data generated through non-invasive prenatal testing (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA of pregnant women in Slovakia was described as a valuable source of population specific data. In the present study, these data were used to determine the population allele frequency of common risk variants located in genes associated with colorectal cancer (CRC) and Lynch syndrome (LS). Allele frequencies of identified variants were compared with six world populations to detect significant differences between populations. Finally, variants were interpreted, functional consequences were searched for and clinical significance of variants was investigated using publicly available databases. Although the present study did not identify any pathogenic variants associated with CRC or LS in the Slovak population using NIPT data, significant differences were observed in the allelic frequency of risk CRC variants previously reported in genome-wide association studies and common variants located in genes associated with LS. As Slovakia is one of the leading countries with the highest incidence of CRC among male patients in the world, there is a need for studies dedicated to investigating the cause of such a high incidence of CRC in Slovakia. The present study also assumed that extensive cross-country data aggregation of NIPT results would represent an unprecedented source of information concerning human genome variation in cancer research. LA - English DB - MTMT ER - TY - JOUR AU - Hekel, Rastislav AU - Budis, Jaroslav AU - Kucharik, Marcel AU - Radvanszky, Jan AU - Pos, Zuzana AU - Szemes, Tomas TI - Privacy-preserving storage of sequenced genomic data JF - BMC GENOMICS J2 - BMC GENOMICS VL - 22 PY - 2021 IS - 1 PG - 13 SN - 1471-2164 DO - 10.1186/s12864-021-07996-2 UR - https://m2.mtmt.hu/api/publication/32411369 ID - 32411369 AB - Background The current and future applications of genomic data may raise ethical and privacy concerns. Processing and storing of this data introduce a risk of abuse by potential offenders since the human genome contains sensitive personal information. For this reason, we have developed a privacy-preserving method, named Varlock providing secure storage of sequenced genomic data. We used a public set of population allele frequencies to mask the personal alleles detected in genomic reads. Each personal allele described by the public set is masked by a randomly selected population allele with respect to its frequency. Masked alleles are preserved in an encrypted confidential file that can be shared in whole or in part using public-key cryptography. Results Our method masked the personal variants and introduced new variants detected in a personal masked genome. Alternative alleles with lower population frequency were masked and introduced more often. We performed a joint PCA analysis of personal and masked VCFs, showing that the VCFs between the two groups cannot be trivially mapped. Moreover, the method is reversible and personal alleles in specific genomic regions can be unmasked on demand. Conclusion Our method masks personal alleles within genomic reads while preserving valuable non-sensitive properties of sequenced DNA fragments for further research. Personal alleles in the desired genomic regions may be restored and shared with patients, clinics, and researchers. We suggest that the method can provide an additional security layer for storing and sharing of the raw aligned reads. LA - English DB - MTMT ER - TY - JOUR AU - Kucharík, M. AU - Budiš, J. AU - Hýblová, M. AU - Minárik, G. AU - Szemes, T. TI - Copy number variant detection with low-coverage whole-genome sequencing represents a viable alternative to the conventional array-cgh JF - DIAGNOSTICS J2 - DIAGNOSTICS VL - 11 PY - 2021 IS - 4 SN - 2075-4418 DO - 10.3390/diagnostics11040708 UR - https://m2.mtmt.hu/api/publication/32159983 ID - 32159983 N1 - Export Date: 26 August 2021 Correspondence Address: Kucharík, M.; Geneton s.r.o.Slovakia; email: marcel.kucharik@geneton.sk Funding details: European Regional Development Fund, ERDF, 313011F988, NFP313010Q927 Funding text 1: This publication was supported by the project ?Long-term strategic research and development focused on the occurrence of Lynch syndrome in the Slovak population and possibilities of prevention of tumors associated with this syndrome? (ITMS 313011V578) co-financed by the European Regional Development Fund (ERDF). The article was also created with the support of the OP Integrated Infrastructure for the project: Introduction of an innovative test for screening and monitoring of cancer patients-GenoScan LBquant, ITMS: NFP313010Q927, co-financed by the ERDF. The data infrastructure was built with the support of the Operational Program Integrated Infrastructure within the following project: ?Horizontal ICT support and centralized infrastructure for research and development institutions?, ITMS code 313011F988, co-financed by the ERDF. Funding text 2: Funding: This publication was supported by the project “Long-term strategic research and development focused on the occurrence of Lynch syndrome in the Slovak population and possibilities of prevention of tumors associated with this syndrome” (ITMS 313011V578) co-financed by the European Regional Development Fund (ERDF). The article was also created with the support of the OP Integrated Infrastructure for the project: Introduction of an innovative test for screening and monitoring of cancer patients—GenoScan LBquant, ITMS: NFP313010Q927, co-financed by the ERDF. The data infrastructure was built with the support of the Operational Program Integrated Infrastructure within the following project: “Horizontal ICT support and centralized infrastructure for research and development institutions”, ITMS code 313011F988, co-financed by the ERDF. AB - Copy number variations (CNVs) represent a type of structural variant involving alterations in the number of copies of specific regions of DNA that can either be deleted or duplicated. CNVs contribute substantially to normal population variability, however, abnormal CNVs cause numerous genetic disorders. At present, several methods for CNV detection are applied, ranging from the conventional cytogenetic analysis, through microarray-based methods (aCGH), to next-generation sequencing (NGS). In this paper, we present GenomeScreen, an NGS-based CNV detection method for low-coverage, whole-genome sequencing. We determined the theoretical limits of its accuracy and obtained confirmation in an extensive in silico study and in real patient samples with known genotypes. In theory, at least 6 M uniquely mapped reads are required to detect a CNV with the length of 100 kilobases (kb) or more with high confidence (Z-score > 7). In practice, the in silico analysis required at least 8 M to obtain >99% accuracy (for 100 kb deviations). We compared GenomeScreen with one of the currently used aCGH methods in diagnostic laboratories, which has mean resolution of 200 kb. GenomeScreen and aCGH both detected 59 deviations, while GenomeScreen furthermore detected 134 other (usually) smaller variations. When compared to aCGH, overall performance of the proposed GenemoScreen tool is comparable or superior in terms of accuracy, turn-around time, and cost-effectiveness, thus providing reasonable benefits, particularly in a prenatal diagnosis setting. © 2021 by the authors. Licensee MDPI, Basel, Switzerland. LA - English DB - MTMT ER - TY - JOUR AU - Hyblova, Michaela AU - Harsanyova, Maria AU - Nikulenkov-Grochova, Diana AU - Kadlecova, Jitka AU - Kucharik, Marcel AU - Budis, Jaroslav AU - Minarik, Gabriel TI - Validation of Copy Number Variants Detection from Pregnant Plasma Using Low-Pass Whole-Genome Sequencing in Noninvasive Prenatal Testing-Like Settings JF - DIAGNOSTICS J2 - DIAGNOSTICS VL - 10 PY - 2020 IS - 8 PG - 8 SN - 2075-4418 DO - 10.3390/diagnostics10080569 UR - https://m2.mtmt.hu/api/publication/31710298 ID - 31710298 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Kucharik, Marcel AU - Gnip, Andrej AU - Hyblova, Michaela AU - Budis, Jaroslav AU - Strieskova, Lucia AU - Harsanyova, Maria AU - Pos, Ondrej AU - Kubiritova, Zuzana AU - Radvanszky, Jan AU - Minarik, Gabriel AU - Szemes, Tomas TI - Non-invasive prenatal testing (NIPT) by low coverage genomic sequencing: Detection limits of screened chromosomal microdeletions JF - PLOS ONE J2 - PLOS ONE VL - 15 PY - 2020 IS - 8 PG - 15 SN - 1932-6203 DO - 10.1371/journal.pone.0238245 UR - https://m2.mtmt.hu/api/publication/31710299 ID - 31710299 AB - 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 anin-silicostudy 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. Thein-silicostudy 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 within-silicoresults, 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. LA - English DB - MTMT ER - TY - JOUR AU - Xue, Ying AU - Zhao, Guodong AU - Qiao, Longwei AU - Lu, Jiafeng AU - Yu, Bin AU - Wang, Ting TI - Sequencing Shorter cfDNA Fragments Decreases the False Negative Rate of Non-invasive Prenatal Testing JF - FRONTIERS IN GENETICS J2 - FRONT GENET VL - 11 PY - 2020 PG - 7 SN - 1664-8021 DO - 10.3389/fgene.2020.00280 UR - https://m2.mtmt.hu/api/publication/31461958 ID - 31461958 AB - Circulating fetal cell-free DNA (cfDNA) is generally shorter than maternal cfDNA. Size selection of shorter cfDNA in total cfDNA could significantly increase the fetal fraction, but there are few reports of using this method to decrease the false negative rate for NIPT. In this study, nine false negative cases were retrospectively analyzed by NIPT retesting and E-gel based size-selection NIPT and the fetal cfDNA fraction in maternal total cfDNA was evaluated by calculating the proportion of reads from chromosome Y. Fetal placenta karyotypes were confirmed by CNVplex assays to analysis the reasons for false negative cases. Of the 81,601 pregnancies who underwent NIPT, nine false negative cases (0.01%) were found. Of eight retested cases, two (25%) had positive NIPT retest results, and five (62.5%) had positive size-selection NIPT results. For fetal cfDNA fraction, 100% cases had improvement after size-selection NIPT compared with the initial NIPT and retest results, and the fetal cfDNA fraction growth ratio ranged from 99 to 359%. For one twin pregnancy with one T18 fetus, size selection improved the fetal cfDNA fraction to 23.10%, and successfully detected the T18 fetus in NIPT. Placental tissue analysis results for two cases indicated both had confined placental mosaicism (CPM), which was confirmed with size-selection NIPT. In conclusion, size selection can significantly enrich the fetal cfDNA fraction and decrease the false negative rate of NIPT, especially for CPM and twin pregnancies. LA - English DB - MTMT ER - TY - JOUR AU - Budis, Jaroslav AU - Gazdarica, Juraj AU - Radvanszky, Jan AU - Harsanyova, Maria AU - Gazdaricova, Iveta AU - Strieskova, Lucia AU - Frno, Richard AU - Duris, Frantisek AU - Minarik, Gabriel AU - Sekelska, Martina AU - Nagy, Bálint AU - Szemes, Tomas TI - Non-invasive prenatal testing as a valuable source of population specific allelic frequencies JF - JOURNAL OF BIOTECHNOLOGY J2 - J BIOTECHNOL VL - 299 PY - 2019 SP - 72 EP - 78 PG - 7 SN - 0168-1656 DO - 10.1016/j.jbiotec.2019.04.026 UR - https://m2.mtmt.hu/api/publication/30728593 ID - 30728593 AB - Low-coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted and relatively low-cost DNA tests. Since aggregation of reads from a large number of samples allows overcoming the problems of extremely low coverage of individual samples, we describe the possible re-use of the data generated during NIPT testing for genome scale population specific frequency determination of small DNA variants, requiring no additional costs except of those for the NIPT test itself. We applied our method to a data set comprising of 1501 original NIPT test results and evaluated the findings on different levels, from in silico population frequency comparisons up to wet lab validation analyses using a gold-standard method based on Sanger sequencing. The revealed high reliability of variant calling and allelic frequency determinations suggest that these NIPT data could serve as valuable alternatives to large scale population studies even for smaller countries around the world. LA - English DB - MTMT ER - TY - JOUR AU - Chin, Re-I AU - Chen, Kevin AU - Usmani, Abul AU - Chua, Chanelle AU - Harris, Peter K. AU - Binkley, Michael S. AU - Azad, Tej D. AU - Dudley, Jonathan C. AU - Chaudhuri, Aadel A. TI - Detection of Solid Tumor Molecular Residual Disease(MRD) Using Circulating Tumor DNA (ctDNA) JF - MOLECULAR DIAGNOSIS & THERAPY J2 - MOL DIAGN THER VL - 23 PY - 2019 IS - 3 SP - 311 EP - 331 PG - 21 SN - 1177-1062 DO - 10.1007/s40291-019-00390-5 UR - https://m2.mtmt.hu/api/publication/31064987 ID - 31064987 N1 - Funding Agency and Grant Number: NCIUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [K08CA238711]; Cancer Research Foundation Young Investigator Award; Washington University SPORE in Pancreatic Cancer Career Enhancement Program; Conquer Cancer Foundation ASCO Young Investigator Award - Takeda Pharmaceuticals; NATIONAL CANCER INSTITUTEUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [K08CA238711, P50CA196510] Funding Source: NIH RePORTER Funding text: This work was funded by the NCI under award number K08CA238711 (A. A. Chaudhuri), a Cancer Research Foundation Young Investigator Award (A. A. Chaudhuri), the Washington University SPORE in Pancreatic Cancer Career Enhancement Program (A. A. Chaudhuri), and the Conquer Cancer Foundation ASCO Young Investigator Award (A. A. Chaudhuri), supported by Takeda Pharmaceuticals. Any opinions, findings and conclusions expressed in this material are those of the authors and do not necessarily reflect those of the American Society of Clinical - Oncology (R), Conquer - Cancer (R), or - Takeda (R). AB - Circulating tumor DNA (ctDNA) is a component of cell-free DNA that is shed by malignant tumors into the bloodstream and other bodily fluids. Levels of ctDNA are typically low, particularly in patients with localized disease, requiring highly sophisticated methods for detection and quantification. Multiple liquid biopsy methods have been developed for ctDNA analysis in solid tumor malignancies and are now enabling detection and assessment of earlier stages of disease, post-treatment molecular residual disease (MRD), resistance to targeted systemic therapy, and tumor mutational burden. Understanding ctDNA biology, mechanisms of release, and clearance and size characteristics, in conjunction with the application of molecular barcoding and targeted error correction, have increased the sensitivity and specificity of ctDNA detection techniques. Combinatorial approaches including integration of ctDNA data withcirculating protein biomarkers may further improve assay sensitivity and broaden the scope of ctDNA applications. Circulating viral DNA may be utilized to monitor disease in some virally induced malignancies. In spite of increasingly accurate methods of ctDNA detection, results need to be interpreted with caution given that somatic mosaicisms such as clonal hematopoiesis of indeterminate potential (CHIP) may give rise to genetic variants in the bloodstream unrelated to solid tumors, and the limited concordance observed between different commercial platforms. Overall, highly precise ctDNA detection and quantification methods have the potential to transform clinical practice via non-invasive monitoring of solid tumor malignancies, residual disease detection at earlier timepoints than standard clinical and/or imaging surveillance, and treatment personalization based on real-time assessment of the tumor genomic landscape. LA - English DB - MTMT ER - TY - JOUR AU - Gazdarica, Juraj AU - Budis, Jaroslav AU - Duris, Frantisek AU - Turna, Jan AU - Szemes, Tomas TI - Adaptable Model Parameters in Non-Invasive Prenatal Testing Lead to More Stable Predictions JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 20 PY - 2019 IS - 14 PG - 11 SN - 1661-6596 DO - 10.3390/ijms20143414 UR - https://m2.mtmt.hu/api/publication/31064983 ID - 31064983 AB - Recent advances in massively parallel shotgun sequencing opened up new options for affordable non-invasive prenatal testing (NIPT) for fetus aneuploidy from DNA material extracted from maternal plasma. Tests typically compare chromosomal distributions of a tested sample with a control set of healthy samples with unaffected fetuses. Deviations above certain threshold levels are concluded as positive findings. The main problem with this approach is that the variance of the control set is dependent on the number of sequenced fragments. The higher the amount, the more precise the estimation of actual chromosomal proportions is. Testing a sample with a highly different number of sequenced reads as used in training may thus lead to over- or under-estimation of their variance, and so lead to false predictions. We propose the calculation of a variance for each tested sample adaptively, based on the actual number of its sequenced fragments. We demonstrate how it leads to more stable predictions, mainly in real-world diagnostics with the highly divergent inter-sample coverage. LA - English DB - MTMT ER - TY - JOUR AU - Gazdarica, Juraj AU - Hekel, Rastislav AU - Budis, Jaroslav AU - Kucharik, Marcel AU - Duris, Frantisek AU - Radvanszky, Jan AU - Turna, Jan AU - Szemes, Tomas TI - Combination of Fetal Fraction Estimators Based on Fragment Lengths and Fragment Counts in Non-Invasive Prenatal Testing JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 20 PY - 2019 IS - 16 PG - 13 SN - 1661-6596 DO - 10.3390/ijms20163959 UR - https://m2.mtmt.hu/api/publication/31064982 ID - 31064982 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Jaroslav, Budis AU - Juraj, Gazdarica AU - Jan, Radvanszky AU - Gabor, Szucs AU - Marcel, Kucharik AU - Lucia, Strieskova Iveta AU - Gazdaricova, Iveta AU - Maria, Harsanyova AU - Frantisek, Duris AU - Gabriel, Minarik AU - Martina, Sekelska AU - Nagy, Bálint AU - Jan, Turna AU - Tomas, Szemes TI - Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing JF - BIOINFORMATICS J2 - BIOINFORMATICS VL - 35 PY - 2019 IS - 8 SP - 1284 EP - 1291 PG - 10 SN - 1367-4803 DO - 10.1093/bioinformatics/bty806 UR - https://m2.mtmt.hu/api/publication/3420877 ID - 3420877 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Pos, Ondrej AU - Budis, Jaroslav AU - Kubiritova, Zuzana AU - Kucharik, Marcel AU - Duris, Frantisek AU - Radvanszky, Jan AU - Szemes, Tomas TI - Identification of Structural Variation from NGS-Based Non-Invasive Prenatal Testing JF - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES J2 - INT J MOL SCI VL - 20 PY - 2019 IS - 18 PG - 9 SN - 1661-6596 DO - 10.3390/ijms20184403 UR - https://m2.mtmt.hu/api/publication/31064980 ID - 31064980 AB - Copy number variants (CNVs) are an important type of human genome variation, which play a significant role in evolution contribute to population diversity and human genetic diseases. In recent years, next generation sequencing has become a valuable tool for clinical diagnostics and to provide sensitive and accurate approaches for detecting CNVs. In our previous work, we described a non-invasive prenatal test (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA for detection of CNV aberrations >= 600 kbp. We reanalyzed NIPT genomic data from 5018 patients to evaluate CNV aberrations in the Slovak population. Our analysis of autosomal chromosomes identified 225 maternal CNVs (47 deletions; 178 duplications) ranging from 600 to 7820 kbp. According to the ClinVar database, 137 CNVs (60.89%) were fully overlapping with previously annotated variants, 66 CNVs (29.33%) were in partial overlap, and 22 CNVs (9.78%) did not overlap with any previously described variant. Identified variants were further classified with the AnnotSV method. In summary, we identified 129 likely benign variants, 13 variants of uncertain significance, and 83 likely pathogenic variants. In this study, we use NIPT as a valuable source of population specific data. Our results suggest the utility of genomic data from commercial CNV analysis test as background for a population study. LA - English DB - MTMT ER - TY - JOUR AU - Qiao, Longwei AU - Mao, Jun AU - Liu, Minjuan AU - Liu, Yinghua AU - Song, Xiaoyan AU - Tang, Hui AU - Zhang, Qing AU - Li, Hong AU - Lu, Yaojuan AU - Liang, Yuting AU - Wang, Ting TI - Experimental factors are associated with fetal fraction in size selection noninvasive prenatal testing JF - AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH J2 - AM J TRANSL RES VL - 11 PY - 2019 IS - 10 SP - 6370 EP - 6381 PG - 12 SN - 1943-8141 UR - https://m2.mtmt.hu/api/publication/31064979 ID - 31064979 AB - Every year, 4-6 million pregnant women undergo noninvasive prenatal testing (NIPT), which is used world-wide for fetal aneuploidy screening. Adequate fetal cell-free DNA (cfDNA) is the critically important factor to ensure high sensitivity and specificity. In this study, we sought to increase the fetal fraction by adjusting experimental factors in the size selection for NIPT. CfDNA was extracted from 1495 pregnant women at 12-26 weeks of gestation for sequencing of shorter cfDNA NIPT (< 140 bp). Multivariable linear regression models were used to evaluate the association between experimental factors and fetal fraction. Nomograms for the likelihood of high fetal fraction (> 20%) were constructed according to significant factors in multivariable regression models. Our results suggested that cfDNA and library concentrations were negatively correlated with fetal fraction, and uniquely mapped reads were positively correlated with fetal fraction. Lower cfDNA and library concentrations, shorter cfDNA fragments, and higher uniquely mapped reads may be more conducive to obtaining higher fetal fractions. Furthermore, we constructed easy-to-use nomograms incorporating the maternal, fetal characteristics and experimental factors to precisely predict the probability of high fetal fraction with an area under the curve (AUC) of 0.773 (95% confidence interval: 0.749-0.797). Collectively, our maternal plasma cfDNA-based nomograms consider experimental factors that can be adjusted and may improve a laboratory's ability to obtain higher fetal cfDNA concentrations. LA - English DB - MTMT ER - TY - JOUR AU - Sekelska, Martina AU - Izsakova, Anita AU - Kubosova, Katarina AU - Tilandyova, Petra AU - Csekes, Erika AU - Kuchova, Zaneta AU - Hyblova, Michaela AU - Harsanyova, Maria AU - Kucharik, Marcel AU - Budis, Jaroslav AU - Szemes, Tomas AU - Minarik, Gabriel TI - Result of Prospective Validation of the Trisomy Test((R)) for the Detection of Chromosomal Trisomies JF - DIAGNOSTICS J2 - DIAGNOSTICS VL - 9 PY - 2019 IS - 4 PG - 5 SN - 2075-4418 DO - 10.3390/diagnostics9040138 UR - https://m2.mtmt.hu/api/publication/31579246 ID - 31579246 AB - Noninvasive prenatal testing (NIPT) is one of the most common prenatal screening tests used worldwide. Trisomy Test (R) 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 (R) is fully comparable with other commercial NIPT tests available worldwide. LA - English DB - MTMT ER - TY - JOUR AU - Strieskova, Lucia AU - Gazdaricova, Iveta AU - Kajsik, Michal AU - Soltys, Katarina AU - Budis, Jaroslav AU - Pos, Ondrej AU - Lickova, Martina AU - Klempa, Boris AU - Szemes, Tomas TI - Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome JF - JOURNAL OF BIOTECHNOLOGY J2 - J BIOTECHNOL VL - 299 PY - 2019 SP - 8 EP - 12 PG - 5 SN - 0168-1656 DO - 10.1016/j.jbiotec.2019.04.019 UR - https://m2.mtmt.hu/api/publication/31064985 ID - 31064985 AB - The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA ( mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases. LA - English DB - MTMT ER - TY - JOUR AU - Xue, Ying AU - Zhao, Guodong AU - Li, Hong AU - Zhang, Qin AU - Lu, Jiafeng AU - Yu, Bin AU - Wang, Ting TI - Non-invasive prenatal testing to detect chromosome aneuploidies in 57,204 pregnancies JF - MOLECULAR CYTOGENETICS J2 - MOL CYTOGENET VL - 12 PY - 2019 PG - 7 SN - 1755-8166 DO - 10.1186/s13039-019-0441-5 UR - https://m2.mtmt.hu/api/publication/31064984 ID - 31064984 AB - BackgroundNon-invasive prenatal testing (NIPT) has been widely used to detect common fetal chromosome aneuploidies, such as trisomy 13, 18, and 21 (T13, T18, and T21), and has expanded to sex chromosome aneuploidies (SCAs) during recent years, but few studies have reported NIPT detection of rare fetal chromosome aneuploidies (RCAs). In this study, we evaluated the clinical practical performance of NIPT to analyze all 24 chromosome aneuploidies among 57,204 pregnancies in the Suzhou area of China.MethodsThis was a retrospective analysis of prospectively collected NIPT data from two next-generation sequencing (NGS) platforms (Illumina and Proton) obtained from The Affiliated Suzhou Hospital of Nanjing Medical University. NIPT results were validated by karyotyping or clinical follow-up.ResultsNIPT using the Illumina platform identified 586 positive cases; fetal karyotyping and follow-up results validated 178T21 cases, 49T18 cases, 4T13 cases, and 52 SCAs. On the Proton platform, 270 cases were positive during NIPT. Follow-up confirmed 85T21 cases, 17T18 cases, 4T13 cases, 28 SCAs, and 1 fetal chromosome 22 aneuploidy case as true positives. There were 5 false-negative results, including 4T21 and 1T18 cases. The NGS platforms showed similar sensitivities and positive predictive values (PPVs) in detecting T21, T18, T13 and SCAs (p>0.01). However, the Proton platform showed better specificity in detecting 45, X and the Illumina platform had better specificity in detecting T13 (p<0.01). The major factor contributing to NIPT false-positives on the Illumina platform was false SCAs cases (65.11%). Maternal chromosome aneuploidies, maternal cancers, and confined placental mosaicism caused discordant results between fetal karyotyping and NIPT.ConclusionNIPT with NGS showed good performance for detecting T13, T18, and T21. The Proton platform had better performance for detecting SCAs, but the NIPT accuracy rate for detecting RCAs was insufficient. LA - English DB - MTMT ER - TY - JOUR AU - Gaksch, Lukas AU - Kashofer, Karl AU - Heitzer, Ellen AU - Quehenberger, Franz AU - Daga, Shruti AU - Hofer, Sybille AU - Halbwedl, Iris AU - Graf, Ricarda AU - Krisper, Nina AU - Hoefler, Gerald AU - Zebisch, Armin AU - Sill, Heinz AU - Woelfler, Albert TI - Residual disease detection using targeted parallel sequencing predicts relapse in cytogenetically normal acute myeloid leukemia JF - AMERICAN JOURNAL OF HEMATOLOGY J2 - AM J HEMATOL VL - 93 PY - 2018 IS - 1 SP - 23 EP - 30 PG - 8 SN - 0361-8609 DO - 10.1002/ajh.24922 UR - https://m2.mtmt.hu/api/publication/27053562 ID - 27053562 LA - English DB - MTMT ER - TY - JOUR AU - He, Q Z AU - Wu, X J AU - He, Q Y AU - Xiang, J J AU - Zhang, C H AU - Lu, L AU - Wang, T AU - Li, H TI - A method for improving the accuracy of non-invasive prenatal screening by cell-free foetal DNA size selection JF - BRITISH JOURNAL OF BIOMEDICAL SCIENCE J2 - BRIT J BIOMED SCI VL - 75 PY - 2018 IS - 3 SP - 133 EP - 138 PG - 6 SN - 0967-4845 DO - 10.1080/09674845.2018.1468152 UR - https://m2.mtmt.hu/api/publication/27529099 ID - 27529099 LA - English DB - MTMT ER - TY - JOUR AU - Mouliere, Florent AU - Chandrananda, Dineika AU - Piskorz, Anna M. AU - Moore, Elizabeth K. AU - Morris, James AU - Ahlborn, Lise Barlebo AU - Mair, Richard AU - Goranova, Teodora AU - Marass, Francesco AU - Heider, Katrin AU - Wan, Jonathan C. M. AU - Supernat, Anna AU - Hudecova, Irena AU - Gounaris, Ioannis AU - Ros, Susana AU - Jimenez-Linan, Mercedes AU - Garcia-Corbacho, Javier AU - Patel, Keval AU - Ostrup, Olga AU - Murphy, Suzanne AU - Eldridge, Matthew D. AU - Gale, Davina AU - Stewart, Grant D. AU - Burge, Johanna AU - Cooper, Wendy N. AU - van der Heijden, Michiel S. AU - Massie, Charles E. AU - Watts, Colin AU - Corrie, Pippa AU - Pacey, Simon AU - Brindle, Kevin M. AU - Baird, Richard D. AU - Mau-Sorensen, Morten AU - Parkinson, Christine A. AU - Smith, Christopher G. AU - Brenton, James D. AU - Rosenfeld, Nitzan TI - Enhanced detection of circulating tumor DNA by fragment size analysis JF - SCIENCE TRANSLATIONAL MEDICINE J2 - SCI TRANSL MED VL - 10 PY - 2018 IS - 466 PG - 13 SN - 1946-6234 DO - 10.1126/scitranslmed.aat4921 UR - https://m2.mtmt.hu/api/publication/30559117 ID - 30559117 N1 - Funding Agency and Grant Number: University of CambridgeUniversity of Cambridge; Cancer Research UKCancer Research UK; EPSRC [CRUK]UK Research & Innovation (UKRI)Engineering & Physical Sciences Research Council (EPSRC) [A11906, A20240, A22905, A15601, A25177, A17242, A16465]; European Research Council under the European UnionEuropean Research Council (ERC) [337905]; National Institute for Health Research Cambridge; Hutchison Whampoa Limited; Target Ovarian Cancer; Medical Research CouncilUK Research & Innovation (UKRI)Medical Research Council UK (MRC)European Commission; AstraZenecaAstraZeneca; National Cancer Research Network; Cambridge Experimental Cancer Medicine Centre; MRCUK Research & Innovation (UKRI)Medical Research Council UK (MRC) [MR/L017415/1] Funding Source: UKRI Funding text: We would like to acknowledge the support of the University of Cambridge, Cancer Research UK, and the EPSRC [CRUK grant numbers A11906 (to N.R.), A20240 (to N.R.), A22905 (to J.D.B.), A15601 (to J.D.B.), A25177 (CRUK Cancer Centre Cambridge), A17242 (to K.M.B.), and A16465 (CRUK-EPSRC Imaging Centre in Cambridge and Manchester)]. The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP/2007-2013)/ERC grant agreement no. 337905. The research was supported by the National Institute for Health Research Cambridge, National Cancer Research Network, Cambridge Experimental Cancer Medicine Centre, and Hutchison Whampoa Limited. This research is also supported by Target Ovarian Cancer and the Medical Research Council through their Joint Clinical Research Training Fellowship for E.K.M. The CALIBRATE study was supported by funding from AstraZeneca. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. AB - Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4x). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC <0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA. LA - English DB - MTMT ER - TY - JOUR AU - Badeau, Mylene AU - Lindsay, Carmen AU - Blais, Jonatan AU - Nshimyumukiza, Leon AU - Takwoingi, Yemisi AU - Langlois, Sylvie AU - Legare, France AU - Giguere, Yves AU - Turgeon, Alexis F AU - Witteman, William AU - Rousseau, Francois TI - Genomics-based non-invasive prenatal testing for detection of fetal chromosomal aneuploidy in pregnant women JF - COCHRANE DATABASE OF SYSTEMATIC REVIEWS J2 - COCHRANE DATABASE SYST REV PY - 2017 IS - 11 PG - 345 SN - 1361-6137 DO - 10.1002/14651858.CD011767.pub2 UR - https://m2.mtmt.hu/api/publication/27055633 ID - 27055633 LA - English DB - MTMT ER - TY - JOUR AU - Lahens, Nicholas F AU - Ricciotti, Emanuela AU - Smirnova, Olga AU - Toorens, Erik AU - Kim, Eun Ji AU - Baruzzo, Giacomo AU - Hayer, Katharina E AU - Ganguly, Tapan AU - Schug, Jonathan AU - Grant, Gregory R TI - A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression JF - BMC GENOMICS J2 - BMC GENOMICS VL - 18 PY - 2017 PG - 13 SN - 1471-2164 DO - 10.1186/s12864-017-4011-0 UR - https://m2.mtmt.hu/api/publication/26929154 ID - 26929154 LA - English DB - MTMT ER - TY - JOUR AU - Shubina, J AU - Trofimov, DY AU - Barkov, IY AU - Stupko, OK AU - Goltsov, AY AU - Mukosey, IS AU - Tetruashvili, NK AU - Kim, LV AU - Bakharev, VA AU - Karetnikova, NA AU - Kochetkova, TO AU - Krasheninnikova, RV AU - Bystritskiy, AA AU - Sukhikh, GT TI - In silico size selection is effective in reducing false positive NIPS cases of monosomy X that are due to maternal mosaic monosomy X JF - PRENATAL DIAGNOSIS J2 - PRENATAL DIAG VL - 37 PY - 2017 IS - 13 SP - 1305 EP - 1310 PG - 6 SN - 0197-3851 DO - 10.1002/pd.5178 UR - https://m2.mtmt.hu/api/publication/27231043 ID - 27231043 LA - English DB - MTMT ER -