Skip to main content

Y-Chromosomal STR Typing and Case Studies

  • Chapter
  • First Online:
DNA Fingerprinting: Advancements and Future Endeavors

Abstract

The basis of Y-STR DNA profiling is derived from Y chromosome, which is passed down to all the male child from the father almost intact, from generation to generation without changing (except mutations in Y-chromosome STRs). The beautiful aspect of Y-STRs is its consistent and allele amplification among close paternal male relatives as well as dispersed male relatives. Y chromosome has lower mutability rate than the mtDNA which is always transferred to all the children from the mother, thus making it more stable generation after generation. This chapter elaborately discussed various Y-STR kits developed, its application, and accuracy. We have also highlighted the various reasons and conditions for mutations in Y chromosomes. In this chapter, we tried to establish the application of Y-STRs profiling in forensic science and criminal justice system and its implication. Y-STR-related case studies have also documented to show its use and applicability in forensic sciences.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Abu-Amero KK, Hellani A, Gonzalez AM, Larruga JM, Cabrera VM, Underhill PA (2009) Saudi Arabian Y-chromosome diversity and its relationship with nearby regions. BMC Genet 10:59

    Article  Google Scholar 

  2. Applied Biosystems (2011)Amp FℓSTR Yfiler PCR Amplification Kit Users Manual

    Google Scholar 

  3. Badro DA, Douaihy B, Haber M et al (2013) Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern middle eastern populations with European and African populations. PLoS One 8:e54616

    Article  CAS  Google Scholar 

  4. Ballantyne KN, Kayser M (2013) Additional Y-STRs in forensic: why, which and when. In: Jaiprakash S and Ray L (ed) Forensic DNA typing (current practices and emerging technologies). https://doi.org/10.12012F015361

  5. Ballantyne KN, Goedbloed M, Fang R et al (2010) Mutability of Y-chromosome microsatellites: rates, characteristics, molecular basis, and forensic application. Americ J Hum Genet 82:341–353

    Article  Google Scholar 

  6. Ballantyne KN, Keerl V, Wollstein A et al (2012) A new future of forensic Y-chromosome analysis: rapidly mutating Y-STRs for differentiating male relatives and paternal lineages. Forensic Sci Int Genet 6:208–218

    Article  CAS  Google Scholar 

  7. Ballantyne KN, Ralf A, Aboukhalid R et al (2014) Towards male individualization with rapidly mutating y-chromosomal short tandem repeats. Hum Mutat 35:1021–1032

    Article  CAS  Google Scholar 

  8. Brenner CH (2010) Fundamental problem of forensic mathematics-the evidential value of a rare haplotype. Forensic Sci Int Genet 4:281–291

    Article  Google Scholar 

  9. Burgarella C, Navascues M (2010) Mutation rate estimates for 110 Y-chromosome STRs combining population and father-son pair data. Eur J Hum Genet 19:70–75

    Article  Google Scholar 

  10. Calafell F, Larmuseau MHD (2016) The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 136:559. https://doi.org/10.1007/s00439-016-1740-0

    Article  PubMed  Google Scholar 

  11. Carvalho M, Brito P, Lopes V et al (2011) Analysis of paternal lineages in Brazilian and African populations. Genet Mol Biol 33:422–427

    Article  Google Scholar 

  12. Cho S, Seo HJ, Lee J, Yu HJ, Lee SD (2016) Kinship testing based on SNPs using microarray system. Transfus Med Hemother 43:429–432

    Article  Google Scholar 

  13. Coble MD, Loreille OM, Wadhams MJ et al (2009) Mystery solved: the identification of the two missing Romanov children using DNA analysis. PLoS One 4(3):e4838

    Article  Google Scholar 

  14. Davis C, Ge J, Sprecher C, Chidambaram A, Thompson JM et al (2013) Prototype PowerPlex1 Y23 system: a concordance study. Forensic Sci Int 7:204–208

    Article  CAS  Google Scholar 

  15. Dogan S, Primorac D, Marjanovic D (2014) Genetic analysis of haplotype data for 23 Y-chromosome short tandem repeat loci in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina. Croat Med J 55:530–536

    Article  Google Scholar 

  16. Feng L, Xu C, Zeng X et al (2014) Y-chromosomal haplotyping of single sperm cells isolated from semen mixtures – a successful identification of three perpetrators in a multi-suspect sexual assault case. Croat Med J 55:537–541

    Article  CAS  Google Scholar 

  17. Garvin AM, Fischer A, Schnee-Griese J et al (2012) Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach. Investig Genet 3:25

    Article  CAS  Google Scholar 

  18. Ge J, Budowle B, Aranda XG, Planz JV, Eisenberg AJ, Chakraborty R (2009) Mutation rates at Y chromosome short tandem repeats in Texas populations. Forensic Sci Int Genet 3:179–184

    Article  CAS  Google Scholar 

  19. Ge J, Eisenberg A, Budowle B (2012) Developing criteria and data to determine best options for expanding the core CODIS loci. Investig Genet 3(1):1

    Article  Google Scholar 

  20. Ge JY, Yan JW, Xie Q, Sun HY, Zhou HG, Li B (2013) Development of Chinese forensic Y-STR DNA database. Fa Yi XueZaZhi 29:212–221

    Google Scholar 

  21. Ge J, Sun H, Li H, Liu C, Yan J, Budowle B (2014) Future directions of forensic DNA databases. Croat Med J 55:163–166

    Article  CAS  Google Scholar 

  22. Gill P, Jeffreys AJ, Werrett DJ (1985) Forensic application of DNA ‘fingerprints’. Nature 318:577–579

    Article  CAS  Google Scholar 

  23. Goedbloed M, Vermeulen M, Fang RN, Lembring M, Wollstein A, Ballantyne K, Lao O, Brauer S, Kru¨ger C, Roewer L et al (2009) Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTRYfiler PCR amplification kit. Int J Legal Med 123:471–482

    Article  Google Scholar 

  24. Hammer MF, Zegurea SL (2002) The human Y chromosome haplogroup tree: nomenclature and phylogeography of its major divisions. Annu Rev Anthropol 31:303–321

    Article  Google Scholar 

  25. Hammer MF, Behar DM, Karafet TM et al (2009) Extended Y chromosome haplotypes resolve multiple and unique lineages of the Jewish priesthood. Hum Genet 126:707–717

    Article  CAS  Google Scholar 

  26. Hanson EK, Ballantyne J (2004) A highly discriminating 21 locus Y-STR “megaplex” system designed to augment the minimal haplotype loci for forensic casework. J Forensic Sci 49:40–51

    Article  CAS  Google Scholar 

  27. Hanson EK, Ballantyne J (2007) An ultra-high discrimination Y chromosome short tandem repeat multiplex DNA typing system. PLoS One 2:e688

    Article  Google Scholar 

  28. Henry J, Simon C, Linacre A (2015) The benefits and limitations of expanded Y-chromosome short tandem repeat (Y-STR) loci. Forensic Sci Int Genet 5:e28–e30

    Article  Google Scholar 

  29. Hu N, Cong B, Li S, Ma C, Fu L, Zhang X (2014) Current developments in forensic interpretation of mixed DNA samples (review). Biomed Rep 2:309–316

    Article  CAS  Google Scholar 

  30. Jain T, Shrivastava P, Bansal DD, Dash HR, Trivedi VB (2016) PowerPlex Y23 system: a fast, sensitive and reliable Y-STR multiplex system for forensic and population genetic purpose. J Mol Biomark Diagon 7:3

    Google Scholar 

  31. Jobling MA, Pandya A, Tyler-Smith C (1997) The Y chromosome in forensic analysis and paternity testing. Int J Legal Med 110:118–124

    Article  CAS  Google Scholar 

  32. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830–838

    Article  CAS  Google Scholar 

  33. Kayser M (2003) The human Y-chromosome-introduction into genetics and applications. Forensic Sci Rev 15:78–90

    Google Scholar 

  34. Kayser M (2017) Forensic use of Y-chromosome DNA: a general overview. Hum Genet 136:621–635

    Article  CAS  Google Scholar 

  35. Kayser M, Ballantyne KN (2014) Y chromosome in forensic science. In: Primorac D, Shanfield M (eds) Forensic DNA applications: an interdisciplinary perspective. CRC Press Taylor & Francis Group, New York

    Google Scholar 

  36. Kayser M, Brauer S, Weiss G, Underhill PA, Roewer L, Schiefenhovel W, Stoneking M (2000) Melanesian origin of Polynesian Y chromosomes. Curr Biol 10:1237–1246

    Article  CAS  Google Scholar 

  37. Kayser M, Roewer L, Hedman M et al (2000b) Characteristics and frequency of germline mutations at microsatellite loci from the human Y chromosome, as revealed by direct observation in father/son pairs. Am J Hum Genet 66:1580–1588

    Article  CAS  Google Scholar 

  38. Kayser M, Krawczak M, Excoffier L et al (2001) An extensive analysis of Y-chromosomal microsatellite haplotypes in globally dispersed human populations. Am J Hum Genet 68:990–1018

    Article  CAS  Google Scholar 

  39. Kayser M, Lao O, Anslinger K et al (2005) Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis. Hum Genet 117:428–443

    Article  Google Scholar 

  40. Kayser M, Vermeulen M, Knoblauch H, Schuster H, Krawczak M, Roewer L (2007) Relating two deep-rooted pedigrees from Central Germany by high-resolution Y-STR haplotyping. Forensic Sci Int Genet 1:125–128

    Article  Google Scholar 

  41. King TE, Jobling MA (2009) What’s in a name? Y chromosomes, surnames and the genetic genealogy revolution. Trends Genet 25:351–360

    Article  CAS  Google Scholar 

  42. Lao O, Vallone PM, Coble MD et al (2010) Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA. Hum Mutat 31:E1875–E1893

    Article  Google Scholar 

  43. Magalhaes T, Dinis-Oliveira RJ, Silva B, Corte-Real F, Nuno Vieira D (2015) Biological evidence management for DNA analysis in cases of sexual assault. Sci World J 365674

    Google Scholar 

  44. Martinez-Gonzalez LJ, Martinez-Espin E, Alvarez JC et al (2011) Surname and Y chromosome in southern Europe: a case study with Colom/Colombo. Eur J Hum Genet 20:211–216

    Article  Google Scholar 

  45. Mrsic G, Grskovic B, Vrdoljak A et al (2012) Croatian national reference Y-STR haplotype database. Mol Biol Rep 39:7727–7741

    Article  CAS  Google Scholar 

  46. Prinz M, Boll K, Baum HJ, Shaler B (1997) Multiplexing of Y chromosome specific STRs and performance for mixed samples. Forensic Sci Int 85:209–218

    Article  CAS  Google Scholar 

  47. Purps J, Siegert S, Willuweit S et al (2014) A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet 12:12–23

    Article  CAS  Google Scholar 

  48. Rapone C, D’Atanasio E, Agostino A, Mariano M, Papaluca MT, Cruciani F, Berti A (2016) Forensic genetic value of a 27 Y-STR loci multiplex (Yfiler® plus kit) in an Italian population sample. Forensic Sci Int Genet 21:e1. https://doi.org/10.1016/j.fsigen.2015.11

    Article  CAS  PubMed  Google Scholar 

  49. Roewer L (2003) The use of the Y chromosome in forensic genetics-current practices and future perspectives. Int Congr Ser 1239:279–280

    Article  Google Scholar 

  50. Roewer L (2009) Y chromosome STR typing in crime casework. Forensic Sci Med Pathol 5:77–84

    Article  CAS  Google Scholar 

  51. Roewer L, Epplen JT (1992) Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts. Hum Genet 89:389–394

    Article  CAS  Google Scholar 

  52. Rong Y, Gao J, Jiang X, Zheng F (2012) Multiplex PCR for 17 Y-chromosome specific short tandem repeats (STR) to enhance the reliability of fetal sex determination in maternal plasma. Int J Mol Sci 13:5972–5981

    Article  CAS  Google Scholar 

  53. Ruitberg CM, Reeder DJ, Butler JM (2001) STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res 29:320–322

    Article  CAS  Google Scholar 

  54. Semino O, Magri C, Benuzzi G et al (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023–1034

    Article  CAS  Google Scholar 

  55. Serin A, Canan H, Alper B, Sertdemir Y (2011) Haplotype frequencies of 17 Y-chromosomal short tandem repeat loci from the Cukurova region of Turkey. Croat Med J 52:703–708

    Article  Google Scholar 

  56. Shewale JG, Sikka SC, Schneida E, Sinha SK (2003) DNA profiling of azoospermic semen samples from vasectomized males by using Y-PLEX 6 amplification kit. J Forensic Sci 48:127–129

    Article  CAS  Google Scholar 

  57. Shi W, Ayub Q, Vermeulen M et al (2010) A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations. Mol Biol Evol 27:385–393

    Article  CAS  Google Scholar 

  58. Shrivastava P, Trivedi VB, Jain T, Ali M (2015) An unusual occurrence of repeated single allele variation on Y-STR locus DYS458. Egypt J Forensic Sci 6:289. https://doi.org/10.1016/j.ejfs.2015.05.003

    Article  Google Scholar 

  59. Soares-Vieira JA, Billerbeck AE, Iwamura ES et al (2007) Y-STRs in forensic medicine: DNA analysis in semen samples of azoospermic individuals. J Forensic Sci 52:664–670

    Article  CAS  Google Scholar 

  60. Thompson JM, Ewing M, Frank W, Pogemiller J, Nolde C et al (2013) Developmental validation of the PowerPlex Y23 system: a single multiplex YSTR analysis system for casework and database samples. Forensic Sci Int Genet 7(2):240–250

    Article  CAS  Google Scholar 

  61. Thomson R, Pritchard JK, Shen P, Oefner PJ, Feldman MW (2000) Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc Natl Acad Sci USA 97:7360–7365

    Article  CAS  Google Scholar 

  62. Underhill PA, Kivisild T (2007) Use of Y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 41:539–564

    Article  CAS  Google Scholar 

  63. Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonne-Tamir B, Bertranpetit J, Francalacci P et al (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26:358–361

    Article  CAS  Google Scholar 

  64. Vanek D, Saskova L, Koch H (2009) Kinship and Y-chromosome analysis of 7th century human remains: novel DNA extraction and typing procedure for ancient material. Croat Med J 50:286–295

    Article  CAS  Google Scholar 

  65. Wang CC, Li H (2013) Inferring human history in East Asia from Y chromosome. Investig Genet 4:11

    Article  Google Scholar 

  66. Willuweit S, Caliebe A, Andersen MM, Roewer L (2011) Y-STR frequency surveying method: a critical reappraisal. Forensic Sci Int Genet 5:84–90

    Article  CAS  Google Scholar 

  67. Zastera J, Roewer L, Willuweit S, Sekerka P, Benesova L, Minarik M (2010) Assembly of a large Y-STR haplotype database for the Czech population and investigation of its substructure. Forensic Sci Int Genet 4:e75–e78

    Article  CAS  Google Scholar 

Download references

Acknowledgment

The authors are thankful to the director, State Forensic Science Laboratory, Ranchi, Jharkhand, for support.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Imam, J., Rana, A.K., Reyaz, R. (2018). Y-Chromosomal STR Typing and Case Studies. In: Dash, H., Shrivastava, P., Mohapatra, B., Das, S. (eds) DNA Fingerprinting: Advancements and Future Endeavors. Springer, Singapore. https://doi.org/10.1007/978-981-13-1583-1_13

Download citation

Publish with us

Policies and ethics