Advertisement

Evaluation of 13 rapidly mutating Y-STRs in endogamous Punjabi and Sindhi ethnic groups from Pakistan

  • Atif Adnan
  • Allah Rakha
  • Shahid Nazir
  • Muhammad Farhan Khan
  • Sibte Hadi
  • Jinfeng Xuan
Population Data

Abstract

Y-chromosomal short tandem repeats (Y-STRs) are commonly used to study population histories, discover ancestral relationships, and identify males for criminal justice purposes. Y-STRs being largely in forensic use have low haplotype diversity in some populations and cannot discriminate between paternal male relatives. Rapidly mutating Y-STRs (RM Y-STRs) were breakthrough and have been paid much attention. A set of 13 rapidly mutating (RM) Y-STRs (DYF387S1, DYF399S1, DYF403S1a/b1/b2, DYF404S1, DYS449, DYS518, DYS526I/II, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) typically reveals higher haplotype diversities than the commercially available Y-STR sets and allows differentiating male relatives for which commercial Y-STR sets are usually not informative. Here, we amplified the 13 RM Y-STRs in 168 (37 Sindhi and 131 Punjabi) individuals from Pakistani population, which is characterized by high rates of endogamy. The haplotype diversity and discrimination capacity were 1. Allelic frequencies ranged from 0.0060 to 0.5060, while gene diversity ranged from 0.6759 (DYS526a) to 0.9937 (DYF399S1). A total 319 different alleles were observed. Results of our study showed that RM Y-STRs provided substantially stronger discriminatory power in Pakistani populations.

Keywords

RM Y-STRs Paternal lineage Endogamous Punjabi Sindhi Pakistan 

Notes

Funding information

This study was financially supported by the University Health Sciences Lahore Pakistan and China Medical University Shenyang China.

Compliance with ethical standards

All participants gave their informed consent in writing after the study aims and procedures were carefully explained to them in their own language. Collaborative study was approved by the ethical review boards of the University of Health Sciences Lahore Pakistan and China Medical University, Shenyang Liaoning Province, People’s Republic of China and in accordance with the standards of the Declaration of Helsinki.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

414_2018_1997_MOESM1_ESM.xlsx (28 kb)
Supplementary Table 1 The haplotype distributions and haplotype frequencies of Sindhi (Pak_S_1–37) and Punjabi (Pak_P_38–168) populations from Pakistan (n = 168). (XLSX 27 kb)
414_2018_1997_MOESM2_ESM.xlsx (17 kb)
Supplementary Table 2 Allelic frequencies and GD values of 13 RM Y STRs in Pakistani population together (XLSX 16 kb)

References

  1. 1.
    Underhill PA, Kivisild T (2007) Use of y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 41:539–564.  https://doi.org/10.1146/annurev.genet.41.110306.130407 CrossRefGoogle Scholar
  2. 2.
    Kayser M (2007) Uni-parental markers in human identity testing including forensic DNA analysis. BioTechniques Supplement to Vol. 43, No. 6, December 2007:Sxv-SxxiGoogle Scholar
  3. 3.
    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.  https://doi.org/10.1101/gr.7172008 CrossRefGoogle Scholar
  4. 4.
    Adnan A, Rakha A, Noor A, van Oven M, Ralf A, Kayser M (2017) Population data of 17 Y-STRs (Yfiler) from Punjabis and Kashmiris of Pakistan. Int J Legal Med 132:137–138.  https://doi.org/10.1007/s00414-017-1611-9 CrossRefGoogle Scholar
  5. 5.
    Adnan A, Rakha A, Kasim K, Noor A, Nazir S, Hadi S, Pang H (2018) Genetic characterization of Y-chromosomal STRs in Hazara ethnic group of Pakistan and confirmation of DYS448 null allele. Int J Legal Med.  https://doi.org/10.1007/s00414-018-1962-x
  6. 6.
    Atif Adnan KK, Rakha A et al (2018) Population data of 23 Y STRs from Manchu population of Liaoning Province, Northeast China. Int J Legal Med.  https://doi.org/10.1007/s00414-018-1957-7
  7. 7.
    Ye Y, Gao J, Fan G, Liao L, Hou Y (2015) Population genetics for 23 Y-STR loci in Tibetan in China and confirmation of DYS448 null allele. Forensic Sci Int Genet 16:e7–e10.  https://doi.org/10.1016/j.fsigen.2014.11.018 CrossRefGoogle Scholar
  8. 8.
    Gibson-Daw G, Albani P, Gassmann M, McCord B (2017) Rapid microfluidic analysis of a Y-STR multiplex for screening of forensic samples. Anal Bioanal Chem 409:939–947.  https://doi.org/10.1007/s00216-016-9950-9 CrossRefGoogle Scholar
  9. 9.
    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–e5.  https://doi.org/10.1016/j.fsigen.2015.11.006 CrossRefGoogle Scholar
  10. 10.
    Redd AJ, Agellon AB, Kearney VA, Contreras VA, Karafet T, Park H, de Knijff P, Butler JM, Hammer MF (2002) Forensic value of 14 novel STRs on the human Y chromosome. Forensic Sci Int 130:97–111CrossRefGoogle Scholar
  11. 11.
    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 49:40–51CrossRefGoogle Scholar
  12. 12.
    Hanson EK, Ballantyne J (2007) An ultra-high discrimination Y chromosome short tandem repeat multiplex DNA typing system. PLoS One 2:e688.  https://doi.org/10.1371/journal.pone.0000688 CrossRefGoogle Scholar
  13. 13.
    Vermeulen M, Wollstein A, van der Gaag K, Lao O, Xue Y, Wang Q, Roewer L, Knoblauch H, Tyler-Smith C, de Knijff P, Kayser M (2009) Improving global and regional resolution of male lineage differentiation by simple single-copy Y-chromosomal short tandem repeat polymorphisms. Forensic Sci Int Genet 3:205–213.  https://doi.org/10.1016/j.fsigen.2009.01.009 CrossRefGoogle Scholar
  14. 14.
    Lee EY, Lee HY, Kwon SY, Oh YN, Yang WI, Shin KJ (2016) A multiplex PCR system for 13 RM Y-STRs with separate amplification of two different repeat motif structures in DYF403S1a. Forensic Sci Int Genet 26:85–90.  https://doi.org/10.1016/j.fsigen.2016.10.019 CrossRefGoogle Scholar
  15. 15.
    Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567.  https://doi.org/10.1111/j.1755-0998.2010.02847.x CrossRefGoogle Scholar
  16. 16.
    Adnan A, Ralf A, Rakha A, Kousouri N, Kayser M (2016) Improving empirical evidence on differentiating closely related men with RM Y-STRs: a comprehensive pedigree study from Pakistan. Forensic Sci Int Genet 25:45–51.  https://doi.org/10.1016/j.fsigen.2016.07.005 CrossRefGoogle Scholar
  17. 17.
    Rakha A, Oh YN, Lee HY, Hussain S, Waryah AM, Adnan A, Shin KJ (2018) Discriminating power of rapidly mutating Y-STRs in deep rooted endogamous pedigrees from Sindhi population of Pakistan. Legal Med 34:17–20.  https://doi.org/10.1016/j.legalmed.2018.08.001 CrossRefGoogle Scholar
  18. 18.
    Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, de Ungria MCA, Decorte R, Dobosz T, Dupuy BM, Elmrghni S, Gliwiński M, Gomes SC, Grol L, Haas C, Hanson E, Henke J, Henke L, Herrera-Rodríguez F, Hill CR, Holmlund G, Honda K, Immel UD, Inokuchi S, Jobling MA, Kaddura M, Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovačević L, Kovatsi L, Krajewski P, Kravchenko S, Larmuseau MHD, Lee EY, Lessig R, Livshits LA, Marjanović D, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Munier P, Nagaraju J, Neuhuber F, Nie S, Nilasitsataporn P, Nishi T, Oh HH, Olofsson J, Onofri V, Palo JU, Pamjav H, Parson W, Petlach M, Phillips C, Ploski R, Prasad SPR, Primorac D, Purnomo GA, Purps J, Rangel-Villalobos H, Rębała K, Rerkamnuaychoke B, Gonzalez DR, Robino C, Roewer L, Rosa A, Sajantila A, Sala A, Salvador JM, Sanz P, Schmitt C, Sharma AK, Silva DA, Shin KJ, Sijen T, Sirker M, Siváková D, Škaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EPH, Yong RYY, Pajnič IZ, Kayser M (2014) Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Hum Mutat 35:1021–1032.  https://doi.org/10.1002/humu.22599 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Forensic Genetics and Biology, School of Forensic MedicineChina Medical UniversityShenyangPeople’s Republic of China
  2. 2.Department of Forensic SciencesUniversity of Health Sciences LahoreLahorePakistan
  3. 3.School of Forensic and Investigative SciencesUniversity of Central LancashirePrestonUK

Personalised recommendations