Null Allele in the D18S51 Locus Responsible for False Homozygosities and Discrepancies in Forensic STR Analysis

  • Eom, Yong-Bin (Department of Biomedical Laboratory Science, Korea Nazarene University)
  • Received : 2011.05.09
  • Accepted : 2011.06.21
  • Published : 2011.06.30

Abstract

Short tandem repeats (STRs) loci are the genetic markers used for forensic human identity test. With multiplex polymerase chain reaction (PCR) assays, STRs are examined and measured PCR product length relative to sequenced allelic ladders. In the repeat region and the flanking region of the commonly-used STR may have DNA sequence variation. A mismatch due to sequence variation in the DNA template may cause allele drop-out (i.e., a "null" or "silent" allele) when it falls within PCR primer binding sites. The STR markers were co-amplified in a single reaction by using commercial PowerPlex$^{(R)}$ 16 system and AmpFlSTR$^{(R)}$ Identifiler$^{(R)}$ PCR amplification kits. Separation of the PCR products and fluorescence detection were performed by ABI PRISM$^{(R)}$ 3100 Genetic Analyzer with capillary electrophoresis. The GeneMapper$^{TM}$ ID software were used for size calling and analysis of STR profiles. Here, this study described a forensic human identity test in which allelic drop-out occurred in the STR system D18S51. During the course of human identity test, two samples with a homozygous (16, 16 and 21, 21) genotype at D18S51 locus were discovered using the PowerPlex$^{(R)}$ 16 system. The loss of alleles was confirmed when the samples were amplified using AmpFlSTR$^{(R)}$ Identifiler$^{(R)}$ PCR amplification kit and resulted in a heterozygous (16, 20 and 20, 21) genotype at this locus each other. This discrepancy results suggest that appropriate measures should be taken for database comparisons and that allele should be further investigated by sequence analysis and be reported to the forensic community.

Keywords

References

  1. Amorin A, Alves C, Pereira L, Gusmao L. Progress in forensic genetics: Genotyping inconsistencies and null alleles using $AmpFlSTR^{\circledR}$ $Identifiler^{\circledR}$ and $PowerPlex^{\circledR}$ 16 kits (Doutremepuich C, Morling N, Eds). 2004. Vol 10, pp. 176-178. Experta Medica, Elsevier. Amsterdam, Nederland.
  2. Boutrand L, Egyed B, Furedi S, Mommers N, Mertens G, Vandenberghe A. Variations in primer sequences are the origin of allele drop-out at loci D13S317 and CD4. Int J Legal Med. 2001. 114: 295-297. https://doi.org/10.1007/s004140000183
  3. Budowle B, Moretti TR, Baumstark AL, Defenbaugh DA, Keys KM. Population data on the thirteen CODIS core short tandem repeat loci in African Americans, US Caucasians, Hispanics, Bahamians, Jamaicans and Trinidadians. J Forensic Sci. 1999. 44: 1277-1286.
  4. Budowle B, Masibay A, Anderson SJ, Barna C, Biega L, Brenneke S, Brown BL, Cramer J, DeGroot GA, Douglas D, Duceman B, Eastman A, Giles R, Hamill J, Haase DJ, Janssen DW, Kupferschmid TD, Lawton T, Lemire C, Llewellyn B, Moretti T, Neves J, Palaski C, Schueler S, Sgueglia J, Sprecher C, Tomsey C, Yet D. STR primer concordance study. Forensic Sci Int. 2001. 124: 47-54. https://doi.org/10.1016/S0379-0738(01)00563-1
  5. Clayton T, Hill S, Denton L, Watson S, Urquhart A. Primer binding site mutation affecting the typing of STR loci contained within the $AmpFlSTR^{\circledR}$ $SGM^{TM}$ Plus kit. Forensic Sci Int. 2004. 139: 255-259. https://doi.org/10.1016/j.forsciint.2003.10.004
  6. Delamoye M, Duverneuil C, Riva K, Leterreux M, Taieb S, De Mazancourt P. False homozygosities at various loci revealed by discrepancies between commercial kits: implications for genetic databases. Forensic Sci Int. 2004. 143: 47-52. https://doi.org/10.1016/j.forsciint.2004.02.001
  7. Eom YB. Evaluation of DNA Extraction Methods from Low Copy Number (LCN) DNA Samples for Forensic DNA Typing. J Exp Biomed Sci. 2009. 15: 229-232.
  8. Eom YB. Forensic STR analysis of mixed chimerism after allogeneic bone marrow transplantation. J Exp Biomed Sci. 2010. 16: 193-196.
  9. Han GR, Song ES, Hwang JJ. Non-amplification of an allele of the D8S1179 locus due to a point mutation. Int J Legal Med. 2001. 115: 45-47. https://doi.org/10.1007/s004140100213
  10. Heinrich M, Muller M, Rand S, Brinkmann B, Hohoff C. Allelic drop-out in the STR system ACTBP2 (SE33) as a result of mutations in the primer binding region. Int J Legal Med. 2004. 118: 361-363. https://doi.org/10.1007/s00414-004-0473-0
  11. Kline MC, Jenkins B, Rodgers S. Non-amplification of a vWA allele. J Forensic Sci. 1998. 43: 250.
  12. Kwok S, Kellogg D, McKinney N, Spasic D, Goda L, Levenson C, Sninsky J. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acid Res. 1990. 18: 999-1005. https://doi.org/10.1093/nar/18.4.999
  13. Leibelt C, Budowle B, Collins P, Daoudi Y, Moretti T, Nunn G, Reeder D, Roby R. Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles. Forensic Sci Int. 2003. 133: 220-227. https://doi.org/10.1016/S0379-0738(03)00035-5
  14. Masibay A, Mozer TJ, Sprecher C. Promega Corporation reveals primer sequences in its testing kits. J Forensic Sci. 2000. 45: 1360-1362.
  15. Nelson MS, Levedakou EN, Matthews JR, Early BE, Freeman DA, Kuhn CA, Sprecher CJ, Amin AS, McElfresh KC, Schumm JW. Detection of a primer-binding site polymorphism for the STR locus D16S539 using the Powerplex 1.1 system and validation of a degenerate primer to correct for the polymorphism. J Forensic Sci. 2002. 47: 345-349.
  16. Oberacher H, Pitterl F, Huber G, Niederstatter H, Steinlechner M, Parson W. Increased forensic efficiency of DNA fingerprints through simultaneous resolution of length and nucleotide variability by high-performance mass spectrometry. Hum Mutat. 2008. 29: 427-432. https://doi.org/10.1002/humu.20627
  17. Roberson JM, Walsh-Weller J. Forensic DNA Profiling Protocols: An introduction to PCR primer design and optimization of amplification reactions (Thomson J, Eds). 1998. pp. 121-154. Humana. Totowa, USA.
  18. Rubocki RJ, Duffy KJ, Shepard KL, McCue BJ, Shepherd SJ, Wisecarver JL. Loss of heterozygosity detected in a short tandem repeat (STR) locus commonly used for human DNA identification. J Forensic Sci. 2000. 45: 1087-1089.
  19. Schlenk J, Seidl S, Braunschweiger G, Betz P, Lederer T. Development of a 13-locus PCR multiplex system for paternity testing. Int J Legal Med. 2004. 118: 55-61. https://doi.org/10.1007/s00414-003-0420-5