Full Text (PDF)
Review Article

Y-Chromosome Short Tandem Repeats: A Review

Kajol Bhati, Christo S. Cherian, Mansi Mishra

Author Information

Licence:

Attribution-Non-commercial 4.0 International (CC BY-NC 4.0)

This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.


Indian Journal of Forensic Medicine and Pathology 18((2 Suppl)):p 251-259, April-June 2025. | DOI: https://doi.org/10.21088/ijfmp.0974.3383.18225.26

How Cite This Article:

Cherian CS, Mishra M, Bhati K. Y-Chromosome Short Tandem Repeats: A Review. Indian J Forensic Med Pathol. 2025;18(2 Suppl):251-259.

Timeline

Received : June 28, 2024         Accepted : June 28, 2025          Published : June 30, 2025

Abstract

Since the early 1990s, the effective development of forensic Y-chromosome examination has led to its widespread use as a standard procedure in labs handling cases involving crime worldwide. The Y-chromosome is a powerful tool in forensic genetics since it can spot the masculine DNA through the most likely to vary genomic sequence the so called STRs. These sequences could be considered to be an irreplaceable asset to the generally worldwide used array of non-sex chromosomal loci used in the study of genetics with respect to forensics. The focus on the masculine part of the chromosome makes it specifically of huge regard in cases of the lumping up of feminine and masculine cell, such as in scenarios of defilement in sexual aspect. However, single set stature of chromosome and the father to son passover of the masculine genetic material can make the detection and study of the short tandem repeats spotted on the male chromosomal gene difficult when males have the exact same Y-chromosomal make up for n number of generations. This may complicate the very understanding of the fact that whether a DNA profile belongs to a suspect or a paternal relative. On the other hand, Y-chromosome research can be used to study the very formation of a DNA profile in a given population which further enables us to study population genetics. As it is also evident that the people falling in the same patrilineal line generally do stay in the same place they were born indicating that there could not be much of a change in their culture and habitat, study of the masculine genetic material thus could be of great significance in understanding the habitat and culture of an entire population. The study of forensic Y-chromosome analysis includes the disciplines of application of Y-genome haplotyping, the evaluation of outcomes, making a track of data of new projects and efforts. This field has played a critical role in criminal investigations, and its continued development promises to bring even greater benefits to forensic genetics.


References

  • 1.   Roewer, L. (2019). Y-chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA. Wiley Interdisciplinary Reviews: Forensic Science, 1(4), e1336. https:// doi.org/10.1002/wfs2.1336
  • 2.   Budowle, B., Sinha, S.K., Lee, H.S. and Chakraborty, R., 2003. Utility of Y-chromosome short tandemrepeat haplotypes in forensic applications. Forensic science review, 15(2), pp. 153-164.
  • 3.   Schlecht, J., Kaplan, M.E., Barnard, K., Karafet, T., Hammer, M.F. and Merchant, N.C., 2008. Machine learning approaches for classifying haplogroup from Y chromosome STR data. PLoSComputBiol, 4(6), p.e1000093.
  • 4.   Kareem, M.A., Hussein, A.O., & Hameed, I.H. (2015). Y-chromosome short tandem repeat, typing technology, locus information and allele frequency in different population: A review. African Journal of Biotechnology, 14(27), 2175- 2178
  • 5.   Butler, J.M. (2011). Advanced topics in forensic DNA typing: methodology. Academic press.
  • 6.   Butler J.M. (2012). Advanced Topics in Forensic DNA Typing: Methodology. Academic Press.,
  • 7.   Rai, N., Chaubey, G., Tamang, R., Pathak, A.K., Singh, V.K., Karmin, M., Singh, M., Rani, D.S., Anugula, S., Yadav, B.K. and Singh, A., 2012. The phylogeography of Y-chromosome haplogroup h1a1a-m82reveals the likely Indian origin of the European Romani populations. PloS one, 7(11), p.e48477.
  • 8.   de Knijff, P., 2000. Messages through bottlenecks: on the combined use of slow and fast evolvingpolymorphic markers on the human Y chromosome. The American Journal of Human Genetics, 67(5), pp. 1055-1061.
  • 9.   Sims, L.M., Garvey, D. and Ballantyne, J., 2009. Improved resolution haplogroup G phylogeny in the Ychromosome, revealed by a set of newly characterized SNPs. PLoS One, 4(6), p. e5792.
  • 10.   Järve, M., Zhivotovsky, L.A., Rootsi, S., Rogaev, E.I., Khusnutdinova, E.K., Kivisild, T. and Sanchez, J.J., 2009. Decreased rate of evolution in Y chromosome STR loci of increased size of the repeat unit. PLoSOne, 4(9), p. e7276.
  • 11.   Battaglia, V., Grugni, V., Perego, U.A., Angerhofer, N., Gomez-Palmieri, J.E., Woodward, S.R., Achilli,A., Myres, N., Torroni, A. and Semino, O., 2013. The first peopling of South America: new evidence fromYchromosome haplogroup Q. PLoS One, 8(8), p. e71390.
  • 12.   Calafell, F. and Larmuseau, M.H., 2017. The Y chromosome as the most popular marker in geneticgenealogy benefits interdisciplinary research. Human genetics, 136(5), pp. 559-573.
  • 13.   Kumar, V., Langstieh, B.T., Madhavi, K.V., Naidu, V.M., Singh, H.P., Biswas, S., Thangaraj, K., Singh, L.and Reddy, B.M., 2006. Global patterns in human mitochondrial DNA and Y-chromosome variationcaused by spatial instability of the local cultural processes. PLoS Genet, 2(4), p. e53
  • 14.   Dulik, M.C., Osipova, L.P. and Schurr, T.G., 2011. Y-chromosome variation in Altaian Kazakhs reveals acommon paternal gene pool for Kazakhs and the influence of Mongolian expansions. PLoS One, 6(3), p. e17548.
  • 15.   Hanson, E.K. and Ballantyne, J., 2007. An ultra-high discrimination Y chromosome short tandem repeatmultiplex DNA typing system. PloS one, 2(8), p. e688.
  • 16.   Olofsson, J.K., Pereira, V., Børsting, C. and Morling, N., 2015. Peopling of the North CircumpolarRegion–insights from Y chromosome STR and SNP typing of Greenlanders. PLoS One, 10(1), p. e0116573.
  • 17.   Badro, D.A., Douaihy, B., Haber, M., Youhanna, S.C., Salloum, A., Ghassibe-Sabbagh, M., Johnsrud, B.,Khazen, G., Matisoo-Smith, E.,Soria-Hernanz, D.F. and Wells, R.S., 2013. Y-chromosome and mtDNAgenetics reveal significant contrasts in affinities of modern Middle Eastern populations with European andAfrican populations. PloS one, 8(1), p. e54616.
  • 18.   Willuweit, S. and Roewer, L., 2015. The new Y chromosome haplotype reference database. Forensic Science International: Genetics, 15, pp. 43-48.
  • 19.   Varzari, A., Kharkov, V., Nikitin, A.G., Raicu, F., Simonova, K., Stephan, W., Weiss, E.H. and Stepanov, V., 2013. Paleo-Balkan and Slavic contributions to the genetic pool of Moldavians: insights from the Ychromosome PLoS One, 8(1), p. e53731.
  • 20.   Morelli, L., Contu, D., Santoni, F., Whalen, M.B., Francalacci, P. and Cucca, F., 2010. A comparison of Y-chromosome variation in Sardinia and Anatolia is more consistent with cultural rather than demic diffusionof agriculture. PLoS One, 5(4), p. e10419
  • 21.   Lacerenza, D., Aneli, S., Di Gaetano, C., Critelli, R., Piazza, A., Matullo, G., Culigioni, C., Robledo, R.,Robino, C. and Calo, C., 2017. Investigation of extended Y chromosome STR haplotypes in Sardinia. Forensic Science International: Genetics, 27, pp. 172-174.
  • 22.   Jin, H.J., Tyler-Smith, C. and Kim, W., 2009. The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers. PloS one, 4(1), p. e4210
  • 23.   Niederstatter, H., Rampl, G., Erhart, D., Pitterl, F., Oberacher, H., Neuhuber, F., Hausner, I., Gassner, C., Schennach, H., Berger, B. and Parson, W., 2012. Pasture names with Romance and Slavic roots facilitated is section of Y chromosome variation in an exclusively German-speaking alpine region. PLoS One, 7(7), p. e41885.
  • 24.   Kareem, M.A., Hussein, A.O. and Hameed, I.H., 2015. Y-chromosome short tandem repeat, typingtechnology, locus information, and allele frequency in different population: A review. African Journal of Biotechnology, 14(27), pp. 2175-2178
  • 25.   Palha, T., Gusmão, L., Ribeiro-Rodrigues, E., Guerreiro, J.F., Ribeiro-dos-Santos, A. and Santos, S., 2012. Disclosing the genetic structure of Brazil through analysis of male lineages with highly discriminatinghaplotypes. PLoS One, 7(7), p. e40007
  • 26.   Gusmão, L., Brion, M., González-Neira, A., Lareu, M. and Carracedo, A., 1999. Y chromosome specific polymorphisms in forensic analysis. Legal Medicine, 1(2), pp. 55-60.
  • 27.   Grugni, V., Battaglia, V., Kashani, B.H., Parolo, S., Al-Zahery, N., Achilli, A., Olivieri, A., Gandini, F.,Houshmand, M., Sanati, M.H. and Torroni, A., 2012. Ancient migratory events in the Middle East: newclues from the Y-chromosome variation of modern Iranians. PloS one, 7(7), p. e41252.
  • 28.   Brown, S.K., Pedersen, N.C., Jafarishorijeh, S., Bannasch, D.L., Ahrens, K.D., Wu, J.T., Okon, M. and Sacks, B.N., 2011. Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Ychromosomes illuminates dog origins. PloS one, 6(12), p.e28496.
  • 29.   Yang, Y., Wang, W., Cheng, F., Chen, M., Chen, T., Zhao, J., Chen, C., Shi, Y., Li, C., Chen, C. and Liu,Y., 2018. Haplotypic polymorphisms and mutation rate estimates of 22 Y-chromosome STRs in the Northern Chinese Han father–son pairs. Scientific reports, 8(1), pp. 1-6.
  • 30.   Ge, J., Budowle, B. and Chakraborty, R., 2010. Interpreting Y chromosome STR haplotype mixture. Legal Medicine, 12(3), pp. 137-143.
  • 31.   Just, R.S., Moreno, L.I., Smerick, J.B. and Irwin,J.A., 2017. Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-typespecimens. Forensic Science International: Genetics, 28, pp.1-9
  • 32.   Zhabagin, M., Sarkytbayeva, A., Tazhigulova, I., Yerezhepov, D., Li, S., Akilzhanov, R., Yeralinov, A., Sabitov, Z. and Akilzhanova, A., 2019. Development of the Kazakhstan Y-chromosome haplotypereference database: analysis of 27 Y-STR in Kazakh population. International journal of legal medicine,133(4), pp. 1029-1032.
  • 33.   Scozzari, R., Massaia, A., D’Atanasio, E., Myres, N.M., Perego, U.A., Trombetta, B. and Cruciani, F.,2012. Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree. PLoS One,7(11), p. e49170.
  • 34.   Henke, J., Henke, L., Chatthopadhyay, P., Kayser, M., Dulmer, M., Cleef, S., ... & FelskeZech, H. (2001). Application of Y-chromosomal STR haplotypes to forensic genetics. Croatian Medical Journal, 42(3), 292-297.
  • 35.   Xue, Y. and Tyler-Smith, C., 2017. Past successes and future opportunities for the genetics of the human Ychromosome.
  • 36.   Frank, K., Bana, N.Á., Bleier, N., Sugár, L., Nagy, J., Wilhelm, J., Kálmán, Z., Barta, E., Orosz, L., Horn,P. and Stéger, V., 2020. Mining the red deer genome (CerEla1. 0) to develop X-and Y-chromosome-linked STR markers. PLoS One, 15(11), p. e0242506
  • 37.   Roewer, L., 2019. Y-chromosome short tandem repeats in forensics—Sexing, profiling, and matching maleDNA. Wiley Interdisciplinary Reviews: Forensic Science, 1(4), p. e1336.
  • 38.   Tofanelli, S., Taglioli, L., Bertoncini, S., Francalacci, P., Klyosov, A. and Pagani, L., 2014. Mitochondrialand Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration. Frontiersin genetics, 5, p. 384.
  • 39.   Cai, X., Qin, Z., Wen, B., Xu, S., Wang, Y., Lu, Y., Wei, L., Wang, C., Li, S., Huang, X. and Jin, L., 2011. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximumrevealed by Y chromosomes. PloS one, 6(8), p. e24282
  • 40.   Kovatsi, L., Saunier, J.L. and Irwin, J.A., 2009. Population genetics of Y-chromosome STRs in apopulation of Northern Greeks. Forensic Science International: Genetics, 4(1), pp. e21-e22.
  • 41.   Butler, J.M., 2003. Recent developments in Y-short tandem repeat and Y-single nucleotide polymorphismanalysis. Forensic Science Review, 15(2), pp. 91-114.
  • 42.   Henry, J., Simon, C., & Linacre, A. (2015). The benefits and limitations of expanded Y-chromosome short tandem repeat (Y-STR) loci. Forensic Science International: Genetics Supplement Series, 5, e28-e30.
  • 43.   Xue, Y., Zerjal, T., Bao, W., Zhu, S., Lim, S. K., Shu, Q., ... & Tyler-Smith, C. (2005). Recent spread of a Y-chromosomal lineage in northern China and Mongolia. The American Journal of Human Genetics, 77(6), 1112-1116.

Data Sharing Statement

There are no additional data available. All raw data and code are available upon request.

Funding

This research received no funding.

Author Contributions

All authors contributed significantly to the work and approve its publication.

Ethics Declaration

This article does not involve any human or animal subjects, and therefore does not require ethics approval.

Acknowledgements

We would like to express our gratitude to the patients, their families, and all those who have contributed to this study.

Conflicts of Interest

No conflicts of interest.


About this article


Cite this article

Cherian CS, Mishra M, Bhati K. Y-Chromosome Short Tandem Repeats: A Review. Indian J Forensic Med Pathol. 2025;18(2 Suppl):251-259.


Licence:

Attribution-Non-commercial 4.0 International (CC BY-NC 4.0)

This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.


Received Accepted Published
June 28, 2024 June 28, 2025 June 30, 2025

DOI: https://doi.org/10.21088/ijfmp.0974.3383.18225.26

Keywords

STRDNADNA profilehaplotypingY-chromosome haplotyping

Article Level Metrics

Last Updated

Saturday 30 May 2026, 13:15:09 (IST)


6268

Accesses

52
1637
00

Citations


NA
NA
NA

Download citation


Article Keywords


Keyword Highlighting

Highlight selected keywords in the article text.


Timeline


Received June 28, 2024
Accepted June 28, 2025
Published June 30, 2025

licence


Attribution-Non-commercial 4.0 International (CC BY-NC 4.0)

This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.


Access this article



Share