Evaluation of InnoTyper® 21 in a sample of Rio de Janeiro population as an alternative forensic panel

  • R. S. Moura-Neto
  • I. C. T. Mello
  • R. Silva
  • A. P. C. Maette
  • C. G. Bottino
  • A. Woerner
  • J. King
  • F. Wendt
  • B. Budowle
Population Data

Abstract

The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls (for insertion/null) can overcome some limitations of short tandem repeat (STR) loci in typing forensic biological evidence. This study investigated the efficiency of the InnoTyper® 21 Innul markers in an urban admixed population sample in Rio de Janeiro (n = 40) and one highly compromised sample collected as evidence by the Rio de Janeiro police. No significant departures from Hardy-Weinberg equilibrium were detected after the Bonferroni correction (α′ ≈ 0.05/20, p < 0.0025), and no significant linkage disequilibrium was observed between markers. Assuming loci independence, the cumulative random match probability (RMP) was 2.3 × 10−8. A lower mean Fis value was obtained for this sample population compared with those of three North American populations (African-American, Southwest Hispanic, US Caucasian). Principal component analysis with the three North American populations and one from 21 East Asian population showed that African Americans segregated as an independent group while US Caucasian, Southwest Hispanic, East Asian, and Rio de Janeiro populations are in a single large heterogeneous group. Also, a full Innuls profile was produced from an evidence sample, despite the DNA being highly degraded. In conclusion, this system is a useful complement to standard STR kits.

Keywords

Forensic genetics Transposable element markers Innuls Rio de Janeiro Brazil 

Supplementary material

414_2017_1642_MOESM1_ESM.docx (85 kb)
ESM 1(DOCX 84 kb).
414_2017_1642_MOESM2_ESM.docx (28 kb)
Supplementary Table S1(DOCX 27 kb).
414_2017_1642_MOESM3_ESM.docx (39 kb)
Supplementary Table S2(DOCX 39 kb).
414_2017_1642_MOESM4_ESM.docx (17 kb)
Supplementary Table S3(DOCX 16 kb).
414_2017_1642_MOESM5_ESM.docx (70 kb)
Supplementary Figure S1(DOCX 70 kb).
414_2017_1642_MOESM6_ESM.docx (714 kb)
Supplementary Figure S2(DOCX 714 kb).
414_2017_1642_MOESM7_ESM.docx (1.1 mb)
Supplementary Figure S3(DOCX 1094 kb).
414_2017_1642_MOESM8_ESM.docx (1005 kb)
Supplementary Figure S4(DOCX 1005 kb).
414_2017_1642_MOESM9_ESM.docx (507 kb)
Supplementary Figure S5(DOCX 507 kb).
414_2017_1642_MOESM10_ESM.docx (47 kb)
Supplementary Figure S6(DOCX 47 kb).
414_2017_1642_MOESM11_ESM.docx (519 kb)
Supplementary Figure S7(DOCX 518 kb).

References

  1. 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 Paper ID JFS2003043_485PubMedGoogle Scholar
  2. 2.
    Kayser M, de Knijff P (2011) Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet 12:179–192. doi:10.1038/nrg2952 CrossRefPubMedGoogle Scholar
  3. 3.
    Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nat Rev Genet 3:370–379. doi:10.1038/nrg798 CrossRefPubMedGoogle Scholar
  4. 4.
    Gill P, Werrett DJ, Budowle B, Guerrieri R (2004) An assessment of whether SNPs will replace STRs in national DNA databases—joint considerations of the DNA working group of the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM). Sci Justice 44:51–53. doi:10.1016/S1355-0306(04)71685-8 CrossRefPubMedGoogle Scholar
  5. 5.
    LaRue BL, Sinha SK, Montgomery AH, Thompson R, Klaskala L, Ge J, King J, Turnbough M, Budowle B (2012) INNULs: a novel design amplification strategy for retrotransposable elements for studying population variation. Hum Hered 74:27–35. doi:10.1159/000343050 CrossRefPubMedGoogle Scholar
  6. 6.
    Sudhir K, Carter A (2010) Method for genetic detection using interspersed genetic elements. US patent # 7,794,983Google Scholar
  7. 7.
    Feng Q, Moran JV, Kazazian HH Jr, Boeke JD (1996) Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87:905–916CrossRefPubMedGoogle Scholar
  8. 8.
    Houck CM, Rinehart FP, Schmid CW (1979) A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol 132:289–306CrossRefPubMedGoogle Scholar
  9. 9.
    Kazazian HH, Moran JV (1998) The impact of L1 retrotransposons on the human genome. Nat Genet 19:19–24. doi:10.1038/ng0598-19 CrossRefPubMedGoogle Scholar
  10. 10.
    Mamedov IZ, Shagina IA, Kurnikova MA, Novozhilov SN, Shagin DA, Lebedev YB (2010) A new set of markers for human identification based on 32 polymorphic Alu insertions. Eur J Hun Genet 18:808–814. doi:10.1038/ejhg.2010.22 CrossRefGoogle Scholar
  11. 11.
    Hughes-Stamm R, Ashton KJ, van Daal A (2011) Assessment of DNA degradation and the genotyping success of highly degraded samples. Int J Legal Med 125:341–348. doi:10.1007/s00414-010-0455-3 CrossRefPubMedGoogle Scholar
  12. 12.
    Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, Shaikh TH, Novick GE, Ioannou PA, Scheer WD, Herrera RJ (1994) African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci U S A 91:12288–12292CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Brown H, Thompson R, Murphy G, Peters D, LaRue B, Kiing J, Montgomery AH, Carroll M, Baus J, Sinha S, Wendt FR, Song B, Chakraborty R, Budowle B, Sinha SK (2017) Development and validation of a novel multiplexed DNA analysis system, InnoTyper®21. Forens Sci Int Genet 29:80–99. doi:10.1016/j.fsigen.2017.03.017 CrossRefGoogle Scholar
  14. 14.
    Budowle B, Monson KL, Chakrabort R (1996) Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci. Int J Legal Med 108:173–176CrossRefPubMedGoogle Scholar
  15. 15.
    Chakraborty R (1992) Sample size requirements for addressing the population genetic issues of forensic use of DNA typing. Hum Biol 64:141–159PubMedGoogle Scholar
  16. 16.
    Oostdik K, Lenz K, Nye J, Schelling K, Yet D, Bruski S, Strong J, Buchanan C, Sutton J, Linner J, Frazier N, Young H, Matthies L, Sage A, Hahn J, Wells R, Williams N, Price M, Koehler J, Staples M, Swango KL, Hill C, Oyerly K, Duke W, Katzilierakis L, Ensenberger MG, Bourdeau JM, Sprecher CJ, Krenke B, Storts DR (2014) Developmental validation of the PowerPlex® fusion system for analysis of casework and reference samples: a 24-locus multiplex for new database standards. Forensic Sci Int Genet 12:69–76. doi:10.1016/j.fsigen.2014.04.013 CrossRefPubMedGoogle Scholar
  17. 17.
    Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370. doi:10.1086/667904 PubMedGoogle Scholar
  18. 18.
    Campbell CD, Eichler EE (2013) Properties and rates of germline mutations in humans. Trends Genet 29:575–584. doi:10.1016/j.tig.2013.04.005 CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    van den Berge M, Wiskerke D, Gerretsen RRR, Tabak J, Sijen T (2016) DNA and RNA profiling of excavated human remains with varying postmortem intervals. Int J Legal Med 130:1471–1480. doi:10.1007/s00414-016-1438-9 CrossRefPubMedGoogle Scholar
  20. 20.
    Sinha S, Murphy G, Brown H, Montgomery A, Carrol M, Tabak J (2015) Retrotransposable elements: novel and sensitive DNA markers and their application in human identity. Forensic Sci Int Genet Supp Ser 5:e627–e629. doi:10.1016/j.fsigss.2015.10.005 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • R. S. Moura-Neto
    • 1
  • I. C. T. Mello
    • 2
  • R. Silva
    • 2
  • A. P. C. Maette
    • 2
  • C. G. Bottino
    • 3
  • A. Woerner
    • 4
  • J. King
    • 4
  • F. Wendt
    • 4
  • B. Budowle
    • 4
    • 5
  1. 1.Laboratório de Biologia Molecular Forense, Instituto de BiologiaUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
  2. 2.Instituto de Biofisica Carlos Chagas FilhoUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
  3. 3.Policia Civil do Estado do Rio de JaneiroInstituto de Pesquisas e Perícias em Genética ForenseRio de JaneiroBrazil
  4. 4.Center for Human IdentificationUniversity of North Texas Health Science CenterFort WorthUSA
  5. 5.Center of Excellence in Genomic Medicine Research (CEGMR)King Abdulaziz UniversityJeddahSaudi Arabia

Personalised recommendations