Skip to main content
SpringerLink
Log in

Characterization of human short tandem repeats (STRs) for individual identification using the Ion Torrent

  • Original Article
  • Published:
BioChip Journal Aims and scope Submit manuscript

Abstract

Human genomic short tandem repeats (STRs) are specific gene sequences containing base pairs that are repeatedly arranged. From the various methods available for identifying individuals, STR analysis is the method most widely used in forensic science. Conventional polymerase chain reaction (PCR) was used for STR typing, and the PCR products, consisting of amplified STR loci (amplicons) were electrophoresed with a DNA analysis device. About ten STR markers were used as standards for STR characterization and analysis of size. Extensive efforts are currently being made to explore the STR sequence diversity by analyzing multiple chromosomal loci using next generation sequencing (NGS). NGS greatly facilitates STR marker analysis for individual identification and the complete sequencing of any given sample through concurrent high-throughput sequencing of multiple loci. As a result, NGS data are more accurate and comprehensive compared to that in a conventional database. In order to overcome the limitations of the currently used size-based STR analysis method, we have typed the DNA of 13 combined DNA index system (CODIS) STR markers using Ion PGM. This kit, developed by Ion Torrent, enables the analysis of STR alleles and the sequencing of corresponding genes. We then analyzed the alleles using the HID_STR_Genotyper plugin. Through this, we determined the sequence of the allele type 15 at the D3S1358 locus in all NIST SRM 2391b samples. This allowed for the verification of the exact type of allele, which the conventional size-based STR typing methods could not resolve.

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

Similar content being viewed by others

References

  1. Lygo, J. et al. The validation of short tandem repeat (STR) loci for use in forensic casework. Int. J. Legal Med. 107, 77–89 (1994).

    Article  CAS  Google Scholar 

  2. Weber, J. L. Informativeness of human (dC-dA)n· (dG-dT)n polymorphisms. Genomics 7, 524–530 (1990).

    Article  CAS  Google Scholar 

  3. Weber, J.L. & Wong, C. Mutation of human short tandem repeats. Hum. Mol. Genet. 2, 1123–1128 (1993).

    Article  CAS  Google Scholar 

  4. Denis F., Alexander C., Sergey S., Tatyana, N. & Alexander, Z. Biochip for genotyping SNPs defining core Y-chromosome haplogroups in Russian population groups. BioChip J. 8, 171–178 (2014).

    Article  CAS  Google Scholar 

  5. Urquhart A., Kimpton C., Downes, T. & Gill, P. Variation in short tandem repeat sequences-a survey of twelve microsatellite loci for use as forensic identification markers. Int. J. Legal Med. 107, 13–20 (1994).

    Article  CAS  Google Scholar 

  6. Hammond, H.A., Jin L., Zhong Y., Caskey, C.T. & Chakraborty, R. Evaluation of 13 short tandem repeat loci for use in personal identification applications. Am. J. Hum. Genet. 55, 175 (1994).

    CAS  Google Scholar 

  7. Lazaruk, K. et al. Genotyping of forensic short tandem repeat (STR) systems based on sizing precision in a capillary electrophoresis instrument. Electrophoresis 19, 86–93 (1998).

    Article  CAS  Google Scholar 

  8. Kimpton, C.P. et al. Automated DNA profiling employing multiplex amplification of short tandem repeat loci. Genome Res. 3, 13–22 (1993).

    Article  CAS  Google Scholar 

  9. Schoske R., Vallone, P. M., Ruitberg, C.M. & Butler, J.M. Multiplex PCR design strategy used for the simultaneous amplification of 10 Y chromosome short tandem repeat (STR) loci. Anal. Bioanal. Chem. 375, 333–343 (2003).

    CAS  Google Scholar 

  10. Butler, J.M., Buel E., Crivellente, F. & McCord, B.R. Forensic DNA typing by capillary electrophoresis using the ABI Prism 310 and 3100 genetic analyzers for STR analysis. Electrophoresis 25, 1397–1412 (2004).

    Article  CAS  Google Scholar 

  11. Sanger F., Nicklen, S. & Coulson, A.R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. 74, 5463–5467 (1977).

    Article  CAS  Google Scholar 

  12. Metzker, M.L. Sequencing technologies-the next generation. Nat. Rev. Genet. 11, 31–46 (2009).

    Article  Google Scholar 

  13. Park, J.Y. et al. Comparative study between Next Generation Sequencing Technique and identification of microarray for Species Identification within blended food products. Biochip J. 6, 354–361 (2012).

    Article  CAS  Google Scholar 

  14. Rothberg, J.M. et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348–352 (2011).

    Article  CAS  Google Scholar 

  15. Loman, N.J. et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30, 434–439 (2012).

    Article  CAS  Google Scholar 

  16. Shokralla S., Spall, J.L., Gibson, J.F. & Hajibabaei, M. Next-generation sequencing technologies for environmental DNA research. Mol. Ecol. 21, 1794–1805 (2012).

    Article  CAS  Google Scholar 

  17. Parson, W. et al. Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM). Forensic Sci. Int. Genet. 7, 543–549 (2013).

    Article  CAS  Google Scholar 

  18. Connors III, M. A. DNA Databases: The Case for the Combined DNA Index System. Wake Forest L. Rev. 29, 889 (1994).

    Google Scholar 

  19. Edwards A.,ia Hammond, H.A., Jin L., Caskey, C.T. & Chakraborty, R. Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12, 241–253 (1992).

    Article  CAS  Google Scholar 

  20. Sprecher, C.J., Puers C., Lins, A.M. & Schumm, J.W. General approach to analysis of polymorphic short tandem repeat loci. BioTechniques 20, 266–277 (1996).

    CAS  Google Scholar 

  21. Butler, J. & Hill, C. Biology and genetics of new autosomal STR loci useful for forensic DNA analysis. Analysis 24 (2012).

  22. Rockenbauer E., Hansen S., Mikkelsen M., Børsting, C. & Morling, N. Characterization of mutations and sequence variants in the D21S11 locus by next generation sequencing. Forensic Sci. Int. Genet. 8, 68–72(2014).

    CAS  Google Scholar 

  23. Ruitberg, C.M., Reeder, D.J. & Butler, J.M. STRBase: a short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res. 29, 320–322 (2001).

    Article  CAS  Google Scholar 

  24. http://www.cstl.nist.gov/strbase/str_D3S1358.htm.

  25. Sharma, V. & Litt, M. Tetranucleotide repeat polymorphism at the D21S11 locus. Hum. Mol. Genet. 1, 67–67 (1992).

    Article  CAS  Google Scholar 

  26. Farrer, M.J. et al. Allelic variability in D21S11, but not in APP or APOE, is associated with cognitive decline in Down syndrome. Neuroreport 8, 1645–1649(1997).

    Article  CAS  Google Scholar 

  27. Faas, B.H. et al. Non-invasive prenatal diagnosis of fetal aneuploidies using massively parallel sequencing- by-ligation and evidence that cell-free fetal DNA in the maternal plasma originates from cytotrophoblastic cells. Expert Opin. Biol. Ther. 12, S19-S26 (2012).

  28. http://ioncommunity.lifetechnologies.com/docs/DOC- 7671.

Download references

Author information

Authors and Affiliations

  1. Biocore Co. Ltd., Guro-gu, Seoul, Korea

    Seri Lim, Jong Pil Youn & Seung Yong Hwang

  2. Forensic DNA Division, National Forensic Service, Seoul, Korea

    Sang Ok Moon, Youn Hyung Nam, Seung Bum Hong, Dongho Choi & Myunsoo Han

  3. Department of Molecular and Life Science, Hanyang University, Hanyang, Korea

    Seri Lim & Seung Yong Hwang

Authors
  1. Seri Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jong Pil Youn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sang Ok Moon
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Youn Hyung Nam
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Seung Bum Hong
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Dongho Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Myunsoo Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Seung Yong Hwang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Myunsoo Han or Seung Yong Hwang.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lim, S., Youn, J.P., Moon, S.O. et al. Characterization of human short tandem repeats (STRs) for individual identification using the Ion Torrent. BioChip J 9, 164–172 (2015). https://doi.org/10.1007/s13206-015-9210-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13206-015-9210-7

Keywords

Search

Navigation