Display options
Cite
Bornman DM, Hester ME, Schuetter JM, et al. Short-read, high-throughput sequencing technology for STR genotyping. Biotech Rapid Dispatches. 2012;2012:1-6
Bornman, D. M., Hester, M. E., Schuetter, J. M., Kasoji, M. D., Minard-Smith, A., Barden, C. A., Nelson, S. C., Godbold, G. D., Baker, C. H., Yang, B., Walther, J. E., Tornes, I. E., Yan, P. S., Rodriguez, B., Bundschuh, R., Dickens, M. L., Young, B. A., & Faith, S. A. (2012). Short-read, high-throughput sequencing technology for STR genotyping. BioTechniques. Rapid dispatches, 20121-6.
Bornman, Daniel M, et al. "Short-read, high-throughput sequencing technology for STR genotyping." BioTechniques. Rapid dispatches vol. 2012 (2012): 1-6.
Bornman DM, Hester ME, Schuetter JM, Kasoji MD, Minard-Smith A, Barden CA, Nelson SC, Godbold GD, Baker CH, Yang B, Walther JE, Tornes IE, Yan PS, Rodriguez B, Bundschuh R, Dickens ML, Young BA, Faith SA. Short-read, high-throughput sequencing technology for STR genotyping. Biotech Rapid Dispatches. 2012 Apr;2012:1-6. PMID: 25621315; PMCID: PMC4301848.
Copy Download .nbib Format: NLM
Share it on

Biotech Rapid Dispatches. 2012 Apr;2012:1-6.

Short-read, high-throughput sequencing technology for STR genotyping.

BioTechniques. Rapid dispatches

Daniel M Bornman, Mark E Hester, Jared M Schuetter, Manjula D Kasoji, Angela Minard-Smith, Curt A Barden, Scott C Nelson, Gene D Godbold, Christine H Baker, Boyu Yang, Jacquelyn E Walther, Ivan E Tornes, Pearlly S Yan, Benjamin Rodriguez, Ralf Bundschuh, Michael L Dickens, Brian A Young, Seth A Faith

Affiliations

  1. Battelle Memorial Institute, Columbus, OH, USA.
  2. Battelle Memorial Institute, Charlottesville, VA, USA.
  3. Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
  4. Department of Physics and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, USA.

PMID: 25621315 PMCID: PMC4301848

Abstract

DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples.

Keywords: Bridge PCR; Illumina; SNP; STR; forensic; genotyping; high-throughput sequencing; next-generation sequencing

References

  1. Biotechniques. 2007 Oct;43(4):ii-v - PubMed
  2. Forensic Sci Int Genet. 2010 Feb;4(2):122-9 - PubMed
  3. Leg Med (Tokyo). 2010 May;12(3):137-43 - PubMed
  4. J Forensic Sci. 2001 May;46(3):453-89 - PubMed
  5. PCR Methods Appl. 1993 Aug;3(1):13-22 - PubMed
  6. Int J Legal Med. 1998;111(5):267-72 - PubMed
  7. Bioinformatics. 2009 Aug 15;25(16):2078-9 - PubMed
  8. Biotechniques. 2011 Aug;51(2):127-33 - PubMed
  9. Electrophoresis. 2004 Jun;25(10-11):1397-412 - PubMed
  10. Bioinformatics. 2010 Mar 15;26(6):841-2 - PubMed
  11. J Forensic Sci. 2004 Jan;49(1):71-80 - PubMed
  12. J Forensic Sci. 1997 Mar;42(2):213-22 - PubMed
  13. J Forensic Sci. 2009 Jul;54(4):810-21 - PubMed
  14. J Forensic Sci Soc. 1991 Jan-Mar;31(1):41-7 - PubMed
  15. Am J Hum Genet. 1991 Oct;49(4):746-56 - PubMed
  16. Genome Biol. 2009;10(3):R25 - PubMed
  17. Forensic Sci Int. 2001 Dec 15;124(1):47-54 - PubMed
  18. Electrophoresis. 2008 Dec;29(23):4618-26 - PubMed
  19. Nat Rev Genet. 2004 Oct;5(10):739-51 - PubMed
  20. J Appl Genet. 2012 Feb;53(1):41-60 - PubMed
  21. Biotechniques. 1993 Jul;15(1):100-19 - PubMed
  22. Nat Rev Genet. 2004 Jun;5(6):435-45 - PubMed
  23. Int J Legal Med. 2010 Nov;124(6):551-8 - PubMed

Publication Types

Grant support