Male individualization using 12 rapidly mutating Y-STRs in Araein ethnic group and shared paternal lineage of Pakistani population


A multiplex assay has been developed with newly designed primer sets comprising high mutation rate 12 RM Y-STR markers (DYS570, DYF399S1, DYS547, DYS612, DYF387S1, DYS449, DYS576, DYS5626, DYF403S1 (a + b), DYS627, DYS526, and DYF404S1). Rapidly mutating Y-STRs were evaluated in 167 male individuals among 97 were unrelated from Araein ethnic group and 70 belonged to shared paternal lineage including 20 pairs of father-son and 15 pairs of brother-brother relationship collected from Punjabi population of Pakistan. Forensic competency parameters were implemented for each marker and exceptionally significant results found wherein polymorphism information content (PIC) was in range of 0.7494 (DYS576) to 0.8994 (DYS627). Samples were also analyzed with Y-filer kit for comparison and marked differentiations observed. Haplotype discrimination capacity was 100% as no haplotype shared among all the unrelated individuals of same ethnic group as compared to 17 Y-filer loci (78%). While in closely related males, discrimination capacity was 96.4% with haplotype diversity value of 0.98. Resulted high mutation rate 1 × 10−2 to 7.14 × 10−2 as compared to Y-filer (1 × 10−4 to 1 × 10−3) manifested the power of RM Y-STRs for considering absolute individualization of interrelated and unrelated male individuals. However, multiplex assay would be useful for male discrimination in mixed DNA specimen, azoospermic males, and multiple male DNA contributors in sexual assault cases and mass disasters victim’s identification as well as anthropological studies.

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


  1. 1.

    Underhill PA, Shen P, Lin AA, Li J, Passarino G, Yang WH, Kauffman E, Bonné-Tamir B, Bertranpetit J, Francalacci P (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26(3):358–361

    Article  CAS  Google Scholar 

  2. 2.

    Butler JM (2005) Forensic DNA typing: biology, technology, and genetics of STR markers. Academic Press

  3. 3.

    Liu P, Seo TS, Beyor N, Shin K-J, Scherer JR, Mathies RA (2007) Integrated portable polymerase chain reaction-capillary electrophoresis microsystem for rapid forensic short tandem repeat typing. Anal Chem 79(5):1881–1889

    Article  CAS  Google Scholar 

  4. 4.

    Ozbaran B, Erermis S, Bukusoglu N, Bildik T, Tamar M, Ercan ES, Aydin C, Cetin SK (2009) Social and emotional outcomes of child sexual abuse: a clinical sample in Turkey. J Interpers Violence 24(9):1478–1493

    Article  Google Scholar 

  5. 5.

    Coble MD, Loreille OM, Wadhams MJ, Edson SM, Maynard K, Meyer CE, Niederstätter H, Berger C, Berger B, Falsetti AB (2009) Mystery solved: the identification of the two missing Romanov children using DNA analysis. PLoS One 4(3):e4838

    Article  CAS  Google Scholar 

  6. 6.

    Gusmão L, Butler JM, Carracedo A, Gill P, Kayser M, Mayr W, Morling N, Prinz M, Roewer L, Tyler-Smith C (2006) DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Int J Legal Med 120(4):191–200

    Article  Google Scholar 

  7. 7.

    Roewer L (2009) Y chromosome STR typing in crime casework. Forensic Sci Med Pathol 5(2):77–84

    Article  CAS  Google Scholar 

  8. 8.

    Boattini A, Sarno S, Bini C, Pesci V, Barbieri C, De Fanti S, Quagliariello A, Pagani L, Ayub Q, Ferri G (2016) Mutation rates and discriminating power for 13 rapidly-mutating Y-STRs between related and unrelated individuals. PLoS One 11(11):e0165678

    Article  CAS  Google Scholar 

  9. 9.

    Ballantyne KN, Keerl V, Wollstein A, Choi Y, Zuniga SB, Ralf A, Vermeulen M, de Knijff P, Kayser M (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(2):208–218

    Article  CAS  Google Scholar 

  10. 10.

    Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B (2014) Toward male individualization with rapidly mutating Y-chromosomal short tandem repeats. Hum Mutat 35(8):1021–1032

    Article  CAS  Google Scholar 

  11. 11.

    Alghafri R, Pajnič IZ, Zupanc T, Balažic J, Shrivastava P (2018) Rapidly mutating Y-STR analyses of compromised forensic samples. Int J Legal Med 132(2):397–403

    Article  Google Scholar 

  12. 12.

    Signer E, Kuenzle CC, Thomann PE, Hübscher U (1988) DNA fingerprinting: improved DNA extraction from small blood samples. Nucleic Acids Res 16(15):7738

    Article  CAS  Google Scholar 

  13. 13.

    Alghafri R, Goodwin W, Ralf A, Kayser M, Hadi S (2015) A novel multiplex assay for simultaneously analysing 13 rapidly mutating Y-STRs. Forensic Sci Int Genet 17:91–98

    Article  CAS  Google Scholar 

  14. 14.

    Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21(9):2128–2129

    Article  CAS  Google Scholar 

  15. 15.

    Guo F, Shen H, Tian H, Jin P, Jiang X (2014) Development of a 24-locus multiplex system to incorporate the core loci in the CombinedDNA Index System (CODIS) and the European Standard Set (ESS). Forensic Sci Int Genet 8(1):44–54

    Article  CAS  Google Scholar 

  16. 16.

    Butler JM, Shen Y, McCord BR (2003) The development of reduced size STR amplicons as tools for analysis of degraded DNA. J Forensic Sci 48(5):1054–1064

    Article  CAS  Google Scholar 

  17. 17.

    Shafique M, Shahzad MS, Rahman Z, Shan MA, Perveen R, Shahzad M, Hussain M, Shahid AA, Husnain T (2016) Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs. Int J Legal Med 130(6):1409–1419

    Article  Google Scholar 

  18. 18.

    Alghafri R, Goodwin W, Hadi S (2013) Rapidly mutating Y-STRs multiplex genotyping panel to investigate UAE population. Forensic Sci Int Genet Suppl Ser 4(1):e200–e201

    Article  Google Scholar 

  19. 19.

    Brito P, Carvalho M, Bogas V, Bento A, Serra A, Andrade L, Balsa F, São-Bento M, Souto L, Corte-Real F (2013) Study of rapidly mutating Y-STRs in a Portuguese population. Forensic Sci Int Genet Suppl Ser 4(1):e83–e84

    Article  Google Scholar 

  20. 20.

    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(1):40–51

    Article  CAS  Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Muhammad Shafique.

Electronic supplementary material


(DOCX 25 kb)


(DOCX 47 kb)

Supplementary Figure 1

(DOCX 41 kb)

Supplementary Figure 2

(DOCX 258 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Javed, F., Sumbal, S., Shafique, M. et al. Male individualization using 12 rapidly mutating Y-STRs in Araein ethnic group and shared paternal lineage of Pakistani population. Int J Legal Med 132, 1621–1624 (2018).

Download citation


  • Rapidly mutating Y-STRs
  • Male individualization
  • Araein ethnic group
  • Paternal lineage
  • Haplotype diversity
  • Mutation rate