Skip to main content
SpringerLink
Log in

Development and characterization of a new 12-plex ChrX miniSTR system

  • Short Communication
  • Published:
International Journal of Legal Medicine Aims and scope Submit manuscript

Abstract

Short tandem repeat (STR) markers are extensively used for human identification as well as paternity and forensic casework. X-chromosome STR (X-STR) markers are a powerful complementary system especially in deficiency paternity testing. This study presents the development and characterization of a new X-chromosomal short tandem repeat (STR) multiplex using short amplicon (<200 bp). A total of 366 samples from Punjabi population and 346 samples from Sindhi population were typed for 11 X-chromosomal STR markers: DXS101, DXS6789, DXS6793, DXS7132, DXS7423, DXS7424, DXS8378, DXS9902, GATA31E08, GATA172D05, and HPRTB along with sex-typing locus, amelogenin. Each marker showed a high degree of polymorphism, and the multiplex was sensitive down to 250 pg of human DNA. A total of 78 alleles were found with 5–11 alleles for each marker. The population data can be used as reference database for Sindhi and Punjabi populations.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

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

    CAS  PubMed  Google Scholar 

  2. Coble MD, Butler JM (2005) Characterization of new miniSTR loci to aid analysis of degraded DNA. J Forensic Sci 50:43–53

    Article  CAS  PubMed  Google Scholar 

  3. Grubwieser P, Muhlmann R, Berger B, Niederstatter H, Pavlic M, Parson W (2006) A new “miniSTR-multiplex” displaying reduced amplicon lengths for the analysis of degraded DNA. Int J Legal Med 120:115–120

    Article  CAS  PubMed  Google Scholar 

  4. Holland MM, Cave CA, Holland CA, Bille TW (2003) Development of a quality, high throughput DNA analysis procedure for skeletal samples to assist with the identification of victims from the World Trade Center attacks. Croat Med J 44:264–272

    PubMed  Google Scholar 

  5. Parsons TJ, Huel R, Davoren J, Katzmarzyk C, Milos A, Selmanovic A, Smajlovic L, Coble MD, Rizvic A (2007) Application of novel “mini-amplicon” STR multiplexes to high volume casework on degraded skeletal remains. Forensic Sci Int Genet 1:175–179

    Article  PubMed  Google Scholar 

  6. Szibor R, Hering S, Kuhlisch E, Plate I, Demberger S, Krawczak M, Edelmann J (2005) Haplotyping of STR cluster DXS6801–DXS6809–DXS6789 on Xq21 provides a powerful tool for kinship testing. Int J Legal Med 119:363–369

    Article  PubMed  Google Scholar 

  7. Gomes C, Magalhaes M, Alves C, Amorim A, Pinto N, Gusmao L (2012) Comparative evaluation of alternative batteries of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs. Int J Legal Med 1–5

  8. Barbaro A, Cormaci P (2006) X-STR typing for an identification casework. Int Cong Ser 1288:513–515

    Article  CAS  Google Scholar 

  9. Toni C, Presciuttini S, Spinetti I, Domenici R (2003) Population data of four X-chromosome markers in Tuscany, and their use in a deficiency paternity case. Forensic Sci Int 137:215

    Article  CAS  PubMed  Google Scholar 

  10. Toni C, Presciuttini S, Spinetti I, Rocchi A, Domenici R (2006) Usefulness of X-chromosome markers in resolving relationships: report of a court case involving presumed half sisters. Int Cong Ser 1288:301–303

    Article  Google Scholar 

  11. Edelmann J, Lessig R, Klintschar M, Szibor R (2004) Advantages of X-chromosomal microsatellites in deficiency paternity testing: presentation of cases. Int Cong Ser 1261:257–259

    Article  CAS  Google Scholar 

  12. Haas-Rochholz H, Weiler G (1997) Additional primer sets for an amelogenin gene PCR-based DNA-sex test. Int J Legal Med 110:312–315

    Article  CAS  PubMed  Google Scholar 

  13. Asamura H, Sakai H, Kobayashi K, Ota M, Fukushima H (2006) MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis. Int J Legal Med 120:174–181

    Article  CAS  PubMed  Google Scholar 

  14. Israr M, Shahid AA, Rahman Z, Shahzad MS, Ullah O, Husnain T (2012) Punjabi population data for seven X-chromosome short tandem repeat (X-STR) loci using a new miniplex system. Afr J Biotechnol 11:10513–10516

    CAS  Google Scholar 

  15. Edelmann J, Hering S, Michael M, Lessig R, Deischel D, Meier-Sundhausen G, Roewer L, Plate I, Szibor R (2001) 16 X-chromosome STR loci frequency data from a German population. Forensic Sci Int 124:215–218

    Article  Google Scholar 

  16. Edelmann J, Deichsel D, Hering S, Plate I, Szibor R (2002) Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377. Forensic Sci Int 129:99–103

    Article  CAS  PubMed  Google Scholar 

  17. Tariq M, Ullah O, Riazuddin SA, Riazuddin S (2008) Allele frequency distribution of 13 X-chromosomal STR loci in Pakistani population. Int J Legal Med 122:525–528

    Article  PubMed  Google Scholar 

  18. Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12:656–664

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37:226–231

    CAS  PubMed  Google Scholar 

  20. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning : a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

    Google Scholar 

  21. Bender K, Farfán MJ, Schneider PM (2004) Preparation of degraded human DNA under controlled conditions. Forensic Sci Int 139:135–140

    Article  CAS  PubMed  Google Scholar 

  22. Poetsch M, Sabule A, Petersmann H, Volksone V, Lignitz E (2006) Population data of 10 X-chromosomal loci in Latvia. Forensic Sci Int 157:206–209

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  24. Szibor R, Hering S, Edelmann J (2006) A new Web site compiling forensic chromosome X research is now online. Int J Legal Med 120:252–254

    Article  PubMed  Google Scholar 

  25. 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

    Article  CAS  PubMed  Google Scholar 

  26. Kashyap V, Guha S, Sitalaximi T, Bindu GH, Hasnain S, Trivedi R (2006) Genetic structure of Indian populations based on fifteen autosomal microsatellite loci. BMC Genet 7:28

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Nadeem A, Babar ME, Hussain M, Tahir MA (2009) Development of pentaplex PCR and genetic analysis of X chromosomal STRs in Punjabi population of Pakistan. Mol Bio Rep 36:1671–1675

    Article  CAS  Google Scholar 

  28. Lee HY, Park MJ, Jeong CK, Lee SY, Yoo JE, Chung U, Choi JH, Kim CY, Shin KJ (2004) Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898. Int J Legal Med 118:355–360

    Article  PubMed  Google Scholar 

  29. Edelmann J, Hering S, Kuhlisch E, Szibor R (2002) Validation of the STR DXS7424 and the linkage situation on the X-chromosome. Forensic Sci Int 125:217–222

    Article  CAS  PubMed  Google Scholar 

  30. Tariq MA, Sabir MF, Riazuddin SA, Riazuddin S (2009) Haplotype analysis of two X-chromosome STR clusters in the Pakistani population. Int J Legal Med 123:85–87

    Article  PubMed  Google Scholar 

  31. Martins JA, Costa JC, Paneto GG, Gusmão L, Sánchez-Diz P, Carracedo A, Cicarelli RMB (2009) Genetic data of 10 X-chromosomal loci in Vitória population (Espírito Santo State, Brazil). Forensic Sci Int Genet Supp 2:394–395

    Article  Google Scholar 

Download references

Acknowledgments

The authors would like to acknowledge all individuals who participated in this study. The authors would like to thank Dr. Shaheen N. Khan, Obaid Ullah, and M. Akram Tariq for their support in this study. This work was partially supported by Higher Education Commission (HEC), Islamabad, Pakistan.

Author information

Authors and Affiliations

  1. National Centre of Excellence in Molecular Biology, University of the Punjab, 87-West Canal Bank Road, Lahore, -53700, Pakistan

    Muhammad Israr, Ahmad Ali Shahid, Ziaur Rahman, Mian Sahib Zar & Tayyab Husnain

  2. Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan

    Muhammad Israr

  3. cInstitute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan

    Muhammad Saqib Shahzad

  4. Abteilung für Rechtsmedizin, Universitätsklinikum Ulm, Prittwitzstraße 6, 9075, Ulm, Germany

    Celine Pfeifer & Peter Wiegand

Authors
  1. Muhammad Israr
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ahmad Ali Shahid
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ziaur Rahman
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mian Sahib Zar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Muhammad Saqib Shahzad
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Tayyab Husnain
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Celine Pfeifer
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Peter Wiegand
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Muhammad Israr or Ahmad Ali Shahid.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 1028 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Israr, M., Shahid, A.A., Rahman, Z. et al. Development and characterization of a new 12-plex ChrX miniSTR system. Int J Legal Med 128, 595–598 (2014). https://doi.org/10.1007/s00414-014-1009-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00414-014-1009-x

Keywords

Search

Navigation