TY  - JOUR
AU  - Kloska, Anna
AU  - Giełczyk, Agata
AU  - Grzybowski, Tomasz
AU  - Płoski, Rafał
AU  - Kloska, Sylwester
AU  - Marciniak, Tomasz
AU  - Pałczynski, Krzysztof
AU  - Rogalla-Ładniak, Urszula
AU  - Malyarchuk, Boris
AU  - Derenko, Miroslava
AU  - Kovačević-Grujičić, Nataša
AU  - Stevanović, Milena
AU  - Drakulić, Danijela
AU  - Davidović, Slobodan
AU  - Spólnicka, Magdalena
AU  - Zubanska, Magdalena
AU  - Wozniak, Marcin
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6321
AB  - Abstract

Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used—Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846–1.000 for all classes.
PB  - Basel: MDPI
T2  - International Journal of Molecular Sciences
T1  - A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe
IS  - 20
VL  - 24
DO  - 10.3390/ijms242015095
SP  - 15095
ER  - 

@article{
author = "Kloska, Anna and Giełczyk, Agata and Grzybowski, Tomasz and Płoski, Rafał and Kloska, Sylwester and Marciniak, Tomasz and Pałczynski, Krzysztof and Rogalla-Ładniak, Urszula and Malyarchuk, Boris and Derenko, Miroslava and Kovačević-Grujičić, Nataša and Stevanović, Milena and Drakulić, Danijela and Davidović, Slobodan and Spólnicka, Magdalena and Zubanska, Magdalena and Wozniak, Marcin",
year = "2023",
abstract = "Abstract

Data obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used—Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846–1.000 for all classes.",
publisher = "Basel: MDPI",
journal = "International Journal of Molecular Sciences",
title = "A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe",
number = "20",
volume = "24",
doi = "10.3390/ijms242015095",
pages = "15095"
}

Kloska, A., Giełczyk, A., Grzybowski, T., Płoski, R., Kloska, S., Marciniak, T., Pałczynski, K., Rogalla-Ładniak, U., Malyarchuk, B., Derenko, M., Kovačević-Grujičić, N., Stevanović, M., Drakulić, D., Davidović, S., Spólnicka, M., Zubanska, M.,& Wozniak, M.. (2023). A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe. in International Journal of Molecular Sciences
Basel: MDPI., 24(20), 15095.
https://doi.org/10.3390/ijms242015095

Kloska A, Giełczyk A, Grzybowski T, Płoski R, Kloska S, Marciniak T, Pałczynski K, Rogalla-Ładniak U, Malyarchuk B, Derenko M, Kovačević-Grujičić N, Stevanović M, Drakulić D, Davidović S, Spólnicka M, Zubanska M, Wozniak M. A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe. in International Journal of Molecular Sciences. 2023;24(20):15095.
doi:10.3390/ijms242015095 .

Kloska, Anna, Giełczyk, Agata, Grzybowski, Tomasz, Płoski, Rafał, Kloska, Sylwester, Marciniak, Tomasz, Pałczynski, Krzysztof, Rogalla-Ładniak, Urszula, Malyarchuk, Boris, Derenko, Miroslava, Kovačević-Grujičić, Nataša, Stevanović, Milena, Drakulić, Danijela, Davidović, Slobodan, Spólnicka, Magdalena, Zubanska, Magdalena, Wozniak, Marcin, "A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe" in International Journal of Molecular Sciences, 24, no. 20 (2023):15095,
https://doi.org/10.3390/ijms242015095 . .

TY  - JOUR
AU  - Holub, Karolina
AU  - Malyarchuk, Boris
AU  - Derenko, Miroslava
AU  - Kovačević-Grujičić, Nataša
AU  - Stevanović, Milena
AU  - Drakulić, Danijela
AU  - Davidović, Slobodan
AU  - Grzybowski, Tomasz
PY  - 2022
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5555
AB  - Genetic markers for the prediction of biogeographical ancestry have proved to be effective tools for law enforcement agencies for many years now. In this study, we attempted to assess the potential of insertion-deletion markers (InDel) and microsatellites (STRs) as subsidiary polymorphisms for inference of Slavic population ancestry. For that purpose, we genotyped Slavic-speaking populations samples from Belarus, the Czech Republic, Poland, Serbia, Ukraine and Russia in 46 InDels and 15 STRs by PCR and capillary electrophoresis and analyzed for between-population differentiation with the use of distance-based methods (FST, principal component analysis and multidimensional scaling).
Additionally, we studied a sample from a Polish individual of well-documented genealogy whose biogeographic ancestry had previously been inferred by commercial genomic services using autosomal single nucleotide polymorphisms (SNPs), mitochondrial DNA and Y-SNP markers. For comparative purposes, we used genotype data collected in the “forInDel” browser and allele frequencies from previously published papers. The results obtained for InDels and STRs show that the Slavic populations constitute a genetically homogeneous group, with the exception of the Czechs differing clearly from the other tested populations. The analysis of the known Polish sample in the Snipper application proves the usefulness of the InDel markers on the continental level only. Conversely, microsatellites not only improve prediction, but are also informative if considered as an independent set of ancestry markers.
PB  - Polish Society of Forensic Medicine and Criminology
T2  - Archives of Forensic Medicine and Criminology
T1  - Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry
IS  - 3
VL  - 72
DO  - 10.4467/16891716AMSIK.22.015.17393
SP  - 120
EP  - 137
ER  - 

@article{
author = "Holub, Karolina and Malyarchuk, Boris and Derenko, Miroslava and Kovačević-Grujičić, Nataša and Stevanović, Milena and Drakulić, Danijela and Davidović, Slobodan and Grzybowski, Tomasz",
year = "2022",
abstract = "Genetic markers for the prediction of biogeographical ancestry have proved to be effective tools for law enforcement agencies for many years now. In this study, we attempted to assess the potential of insertion-deletion markers (InDel) and microsatellites (STRs) as subsidiary polymorphisms for inference of Slavic population ancestry. For that purpose, we genotyped Slavic-speaking populations samples from Belarus, the Czech Republic, Poland, Serbia, Ukraine and Russia in 46 InDels and 15 STRs by PCR and capillary electrophoresis and analyzed for between-population differentiation with the use of distance-based methods (FST, principal component analysis and multidimensional scaling).
Additionally, we studied a sample from a Polish individual of well-documented genealogy whose biogeographic ancestry had previously been inferred by commercial genomic services using autosomal single nucleotide polymorphisms (SNPs), mitochondrial DNA and Y-SNP markers. For comparative purposes, we used genotype data collected in the “forInDel” browser and allele frequencies from previously published papers. The results obtained for InDels and STRs show that the Slavic populations constitute a genetically homogeneous group, with the exception of the Czechs differing clearly from the other tested populations. The analysis of the known Polish sample in the Snipper application proves the usefulness of the InDel markers on the continental level only. Conversely, microsatellites not only improve prediction, but are also informative if considered as an independent set of ancestry markers.",
publisher = "Polish Society of Forensic Medicine and Criminology",
journal = "Archives of Forensic Medicine and Criminology",
title = "Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry",
number = "3",
volume = "72",
doi = "10.4467/16891716AMSIK.22.015.17393",
pages = "120-137"
}

Holub, K., Malyarchuk, B., Derenko, M., Kovačević-Grujičić, N., Stevanović, M., Drakulić, D., Davidović, S.,& Grzybowski, T.. (2022). Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry. in Archives of Forensic Medicine and Criminology
Polish Society of Forensic Medicine and Criminology., 72(3), 120-137.
https://doi.org/10.4467/16891716AMSIK.22.015.17393

Holub K, Malyarchuk B, Derenko M, Kovačević-Grujičić N, Stevanović M, Drakulić D, Davidović S, Grzybowski T. Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry. in Archives of Forensic Medicine and Criminology. 2022;72(3):120-137.
doi:10.4467/16891716AMSIK.22.015.17393 .

Holub, Karolina, Malyarchuk, Boris, Derenko, Miroslava, Kovačević-Grujičić, Nataša, Stevanović, Milena, Drakulić, Danijela, Davidović, Slobodan, Grzybowski, Tomasz, "Verification of insertion-deletion markers (InDels) and microsatellites (STRs) as subsidiary tools for inferring Slavic population ancestry" in Archives of Forensic Medicine and Criminology, 72, no. 3 (2022):120-137,
https://doi.org/10.4467/16891716AMSIK.22.015.17393 . .

TY  - JOUR
AU  - Davidović, Slobodan
AU  - Malyarchuk, Boris
AU  - Grzybowski, Tomasz
AU  - Aleksić, Jelena M.
AU  - Derenko, Miroslava
AU  - Litvinov, Andrey
AU  - Rogalla-Ładniak, Urszula
AU  - Stevanović, Milena
AU  - Kovačević-Grujičić, Nataša
PY  - 2020
UR  - http://link.springer.com/10.1007/s00414-020-02324-x
UR  - http://www.ncbi.nlm.nih.gov/pubmed/32504149
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3685
AB  - Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
PB  - Springer
T2  - International Journal of Legal Medicine
T1  - Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases.
VL  - 134
DO  - 10.1007/s00414-020-02324-x
SP  - 1581
EP  - 1590
ER  - 

@article{
author = "Davidović, Slobodan and Malyarchuk, Boris and Grzybowski, Tomasz and Aleksić, Jelena M. and Derenko, Miroslava and Litvinov, Andrey and Rogalla-Ładniak, Urszula and Stevanović, Milena and Kovačević-Grujičić, Nataša",
year = "2020",
abstract = "Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.",
publisher = "Springer",
journal = "International Journal of Legal Medicine",
title = "Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases.",
volume = "134",
doi = "10.1007/s00414-020-02324-x",
pages = "1581-1590"
}

Davidović, S., Malyarchuk, B., Grzybowski, T., Aleksić, J. M., Derenko, M., Litvinov, A., Rogalla-Ładniak, U., Stevanović, M.,& Kovačević-Grujičić, N.. (2020). Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases.. in International Journal of Legal Medicine
Springer., 134, 1581-1590.
https://doi.org/10.1007/s00414-020-02324-x

Davidović S, Malyarchuk B, Grzybowski T, Aleksić JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanović M, Kovačević-Grujičić N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases.. in International Journal of Legal Medicine. 2020;134:1581-1590.
doi:10.1007/s00414-020-02324-x .

Davidović, Slobodan, Malyarchuk, Boris, Grzybowski, Tomasz, Aleksić, Jelena M., Derenko, Miroslava, Litvinov, Andrey, Rogalla-Ładniak, Urszula, Stevanović, Milena, Kovačević-Grujičić, Nataša, "Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases." in International Journal of Legal Medicine, 134 (2020):1581-1590,
https://doi.org/10.1007/s00414-020-02324-x . .

TY  - CONF
AU  - Kovačević-Grujičić, Nataša
AU  - Davidović, Slobodan
AU  - Malyarchuk, Boris
AU  - Grzybowski, Tomasz
AU  - Aleksić, Jelena
AU  - Derenko, Miroslava
AU  - Litvinov, Andrey
AU  - Rogalla-Ladniak, Urszula
AU  - Stevanović, Milena
PY  - 2019
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5886
AB  - Mitochondrial DNA (mtDNA) is used in forensics for over three decades and is particularly
suitable when STR profiling cannot be performed due to the degraded and/or scarce nuclear
DNA. Traditionally, mtDNA typing is based on ~600 bp of the hypervariable segments I and
II (HVS-I and HVS-II) of the control region (CR, ~1100 bp). Nowadays, it is possible to use
variability of complete mtDNAs which enables maximum resolution of distinct maternal
lineages. However, the number of complete mitogenomes in reference databases such as
EMPOP is still insufficient, and that hampers their wider usage in forensic casework. In order
to fill in the gap in the reference database, which, considering Slavic-speaking populations,
currently comprises only mitogenomes of East and West Slavs, we present population data
for 226 Serbian mitogenomes, representatives of South Slavs from the Balkan Peninsula. We
support previous findings on both high levels of genetic diversity in the Serbian population
and patterns of genetic differentiation among Serbian and ten studied European populations.
However, increased genetic differentiation was observed among Serbian and two European
populations (Russians and Poles) with our high resolution data. We demonstrate that
the inclusion of indel polymorphisms into analysis contributed towards nearly complete
resolution of mtDNA haplotypes (97.1% vs. 86.3% without indels), and that the random
match probability was as low as 0.53%. Bayesian skyline analysis of Serbian mitogenomes
revealed population expansion after the Last Glacial Maximum and during the Migration
period (IV-IX century A.D.). Phylogenetic analysis of the Serbian and relevant West Eurasian
haplotypes contributed towards the improvement of the worldwide mtDNA phylogeny to
the certain extent, which is essential for the interpretation of the mtDNA casework. Lineages
of a putative Balkan origin as well as those shared among Serbian and other European
populations were observed.
PB  - Belgrade: Serbian Genetic Society
C3  - 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia
T1  - Whole mitochondrial genome diversity in serbian population: phylogenetic and forensic aspects
SP  - 157
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5886
ER  - 

@conference{
author = "Kovačević-Grujičić, Nataša and Davidović, Slobodan and Malyarchuk, Boris and Grzybowski, Tomasz and Aleksić, Jelena and Derenko, Miroslava and Litvinov, Andrey and Rogalla-Ladniak, Urszula and Stevanović, Milena",
year = "2019",
abstract = "Mitochondrial DNA (mtDNA) is used in forensics for over three decades and is particularly
suitable when STR profiling cannot be performed due to the degraded and/or scarce nuclear
DNA. Traditionally, mtDNA typing is based on ~600 bp of the hypervariable segments I and
II (HVS-I and HVS-II) of the control region (CR, ~1100 bp). Nowadays, it is possible to use
variability of complete mtDNAs which enables maximum resolution of distinct maternal
lineages. However, the number of complete mitogenomes in reference databases such as
EMPOP is still insufficient, and that hampers their wider usage in forensic casework. In order
to fill in the gap in the reference database, which, considering Slavic-speaking populations,
currently comprises only mitogenomes of East and West Slavs, we present population data
for 226 Serbian mitogenomes, representatives of South Slavs from the Balkan Peninsula. We
support previous findings on both high levels of genetic diversity in the Serbian population
and patterns of genetic differentiation among Serbian and ten studied European populations.
However, increased genetic differentiation was observed among Serbian and two European
populations (Russians and Poles) with our high resolution data. We demonstrate that
the inclusion of indel polymorphisms into analysis contributed towards nearly complete
resolution of mtDNA haplotypes (97.1% vs. 86.3% without indels), and that the random
match probability was as low as 0.53%. Bayesian skyline analysis of Serbian mitogenomes
revealed population expansion after the Last Glacial Maximum and during the Migration
period (IV-IX century A.D.). Phylogenetic analysis of the Serbian and relevant West Eurasian
haplotypes contributed towards the improvement of the worldwide mtDNA phylogeny to
the certain extent, which is essential for the interpretation of the mtDNA casework. Lineages
of a putative Balkan origin as well as those shared among Serbian and other European
populations were observed.",
publisher = "Belgrade: Serbian Genetic Society",
journal = "6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia",
title = "Whole mitochondrial genome diversity in serbian population: phylogenetic and forensic aspects",
pages = "157",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5886"
}

Kovačević-Grujičić, N., Davidović, S., Malyarchuk, B., Grzybowski, T., Aleksić, J., Derenko, M., Litvinov, A., Rogalla-Ladniak, U.,& Stevanović, M.. (2019). Whole mitochondrial genome diversity in serbian population: phylogenetic and forensic aspects. in 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia
Belgrade: Serbian Genetic Society., 157.
https://hdl.handle.net/21.15107/rcub_ibiss_5886

Kovačević-Grujičić N, Davidović S, Malyarchuk B, Grzybowski T, Aleksić J, Derenko M, Litvinov A, Rogalla-Ladniak U, Stevanović M. Whole mitochondrial genome diversity in serbian population: phylogenetic and forensic aspects. in 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia. 2019;:157.
https://hdl.handle.net/21.15107/rcub_ibiss_5886 .

Kovačević-Grujičić, Nataša, Davidović, Slobodan, Malyarchuk, Boris, Grzybowski, Tomasz, Aleksić, Jelena, Derenko, Miroslava, Litvinov, Andrey, Rogalla-Ladniak, Urszula, Stevanović, Milena, "Whole mitochondrial genome diversity in serbian population: phylogenetic and forensic aspects" in 6th Congress of the Serbian genetic society: Book of abstracts; 2019 Oct 13-17; Vrnjačka Banja, Serbia (2019):157,
https://hdl.handle.net/21.15107/rcub_ibiss_5886 .