Limit Detection of Short Tandem Repeats (STR) Analysis on Touch DNA Samples

Vira Saamia; Ahmad Yudianto; Muktiningsih Nurjayadi; Novitasari Novitasari; Abdul Hadi Furqoni

doi:10.22146/ijc.94081

Limit Detection of Short Tandem Repeats (STR) Analysis on Touch DNA Samples

https://doi.org/10.22146/ijc.94081

Vira Saamia⁽¹⁾, Ahmad Yudianto^(2*), Muktiningsih Nurjayadi⁽³⁾, Novitasari Novitasari⁽⁴⁾, Abdul Hadi Furqoni⁽⁵⁾

(1) Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen Prof. Dr. Moestopo 47, Surabaya 60131, Indonesia; Center Forensic Laboratory of Indonesia National Police, Jl. Raya Babakan Madang 67, Sentul, Bogor 16810, Indonesia
(2) Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen Prof. Dr. Moestopo 47, Surabaya 60131, Indonesia; Forensic Study Program, Magister Program of Postgraduate School of Forensics Study, Universitas Airlangga, Jl. Airlangga 4–6, Surabaya 60286, Indonesia
(3) Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta, Jl. Rawamangun Muka, Jakarta Timur 13220, Indonesia
(4) Research Center for Testing Technology and Standard, National Research and Innovation Agency (BRIN), Jl. Raya Puspitek Serpong, Tangerang Selatan 15314, Indonesia
(5) Center for Biomedical Research, Research Organization for Health, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta Bogor KM 46, Cibinong, Jawa Barat 16911, Indonesia
(*) Corresponding Author

Abstract

Forensic short tandem repeats (STR) profiling on touch DNA samples has emerged as a primary method for human identification. The stability and uniqueness of STR combination from the targeted locus in each individual make it a precision marker for human identification. Touch DNA samples can be found in traces of biological material shed from a person. This work aimed to identify the lowest concentration limit required for generating an interpretable DNA profile and the sensitivity of the STR loci applied. Touch DNA samples were collected from donors who were asked to hold a rope for 5 min. A double swab technique was used to lift the touch samples from the rope. These samples are subjected to DNA extraction and quantification. Two STR amplification cycles, 29 and 34 cycles, were used. DNA concentration greatly influences the success of amplifying the target allele at each STR locus to be interpreted into a complete DNA profile, shown by its allele peak. Touch DNA concentration >0.25 ng can produce a complete DNA profile. LCN method successfully amplified touch DNA with a concentration 0.0625–0.25 ng/µL. Limit detection of touch DNA analysis is 0.25 ng/µL. Low-copy DNA can still be analyzed within 0.0625–0.25 ng/µL.

Keywords

short tandem repeats; touch DNA; DNA concentration

Full Text:

Full Text PDF

References

[1] Putri, D.F.A., and Yudianto, A., 2019, The use of kinship analysis on paternity testing through CODIS STR loci ‘CSF1PO’ and ‘THO1’, BHSJ, 2 (2), 113–116.

[2] Butler, J.M., and Willis, S., 2020, Interpol review of forensic biology and forensic DNA typing 2016-2019, Forensic Sci. Int.: Synergy, 2, 352–367.

[3] Jordan, D., and Mills D., 2021, Past, present, and future of DNA typing for analyzing human and non-human forensic samples, Front. Ecol. Evol., 9, 646130.

[4] Yudianto, A., and Setiawan, F., 2020, The Effectiveness of mini primer STR CODIS in DNA Degradation as the Effect of High-Temperature Exposure, Anal. Cell. Pathol., 2020 (1), 2417693.

[5] Yudianto, A., Sispitasri, Y.E., and Margaret, N., 2016, Analysis of earphone swab mitochondrial DNA as an alternative material for identification examination, Folia Medica Indonesiana, 52 (3), 169–173.

[6] Yudianto, A., Nzilibili, S.M.M., Harjanto, P., and Setiawan, F., 2020, The use of touch DNA analysis in forensic identification focusing on STR CODIS loci THO1, CSF1PO and TPOX, Indian J. Forensic Med. Toxicol., 14 (3), 1740–1744.

[7] Furqoni, A.H., Megasari, N.L.A., Yudianto, A., Azizah, F., Maulidiyanti, E.T.S., Fahmi, N.F., Solihah, R., and Arimurti, A.R.R., 2023, Amplification of vWA, FGA, and TH01 loci of DNA samples isolated from ring stored at room temperature, Malays. J. Med. Health Sci., 19 (5), 97–101.

[8] Prasad, E., Atwood, L., van Oorschot, R.A.H., McNevin, D., Barash, M., and Raymond, J., 2023, Trace DNA recovery rates from firearms and ammunition as revealed by casework data, Aust. J. Forensic Sci., 55 (1), 73–88.

[9] van Oorschot, R.A.H., and Jones, M.K., 1997, DNA fingerprints from fingerprints, Nature, 387 (6635), 767.

[10] Lowe, A., Murray, C., Whitaker, J., Tully, G., and Gill, P., 2002, The propensity of individuals to deposit DNA and secondary transfer of low level DNA from individuals to inert surfaces, Forensic Sci. Int., 129 (1), 25–34.

[11] Dziak, R., Peneder, A., Buetter, A., and Hageman, C., 2018, Trace DNA sampling success from evidence items commonly encountered in forensic casework, J. Forensic Sci., 63 (3), 835–841.

[12] Budowle, B., Eisenberg, A.J., and van Daal, A., 2009, Validity of low copy number typing and applications to forensic science, Croat. Med. J., 50 (3), 207–217.

[13] Mateen, R.M., Tariq, A., and Hussain, M., 2020, Generating DNA profile from low copy number DNA: Strategies and associated risks, Acta Sci., Biol. Sci., 42, 1–7.

[14] Hedell, R., Dufva, C., Ansell, R., Mostad, P., and Hedman, J., 2015, Enhanced low-template DNA analysis conditions and investigation of allele dropout patterns, Forensic Sci. Int.: Genet., 14, 61–75.

[15] Kloosterman, A.D., and Kersbergen, P., 2003, Efficacy and limits of genotyping low copy number (LCN) DNA samples by multiplex PCR of STR loci, J. Soc. Biol., 197 (4), 351–359.

[16] Lee, L.Y.C., Tan, J., Lee, Y.S., and Syn, C.K.C., 2023, Shedder status—An analysis over time and assessment of various contributing factors, J. Forensic Sci., 68 (4), 1292–1301.

[17] Flores, S., Sun, J., King, J., and Budowle, B., 2014, Internal validation of the GlobalFiler™ Express PCR Amplification Kit for the direct amplification of reference DNA samples on a high-throughput automated workflow, Forensic Sci. Int.: Genet., 10, 33–39.

[18] Ziubrii, O., 2019, Comparative characteristic of effectiveness of some decontamination facilities used for carrying out of forensic molecular genetic examination, Theor. Pract. Forensic Sci. Crim., 19 (1), 489–502.

[19] Kallupurackal, V., Kummer, S., Voegeli, P., Kratzer, A., Dørum, G., Haas, C., and Hess, S., 2021, Sampling touch DNA from human skin following skin-to-skin contact in mock assault scenarios—A comparison of nine collection methods, J. Forensic Sci., 66 (5), 1889–1900.

[20] Hedman, J., Akel, Y., Jansson, L., Hedell, R., Wallmark, N., Forsberg, C., and Ansell, R., 2021, Enhanced forensic DNA recovery with appropriate swabs and optimized swabbing technique, Forensic Sci. Int.: Genet., 53, 102491.

[21] Cameron, C.J., Hymus, C.M., Quach, K., Blackwell, S.J., and Tay, J.W., 2022, Enhanced efficiency of PrepFiler™ BTA DNA extraction kit with PrepFiler™ lysis buffer top-up over sample remnants, Forensic Sci., 2 (4), 672–681.

[22] Puliatti, L., Handt, O., and Taylor, D., 2021, The level of DNA an individual transfers to untouched items in their immediate surroundings, Forensic Sci. Int.: Genet., 54, 102561.

[23] Cisana, S., Cerri, N., Bosetti, A., Verzeletti, A., and Cortellini, V., 2017, PowerPlex® Fusion 6C System: Evaluation study for analysis of casework and database samples, Croat. Med. J., 58 (1), 26–33.

[24] Gettings, K.B., Bodner, M., Borsuk, L.A., King, J.L., Ballard, D., Parson, W., Benschop, C.C.G., Børsting, C., Budowle, B., Butler, J.M., van der Gaag, K.J., Gill, P., Gusmão, L., Hares, D.R., Hoogenboom, J., Irwin, J., Prieto, L., Schneider, P.M., Vennemann, M., and Phillips, C., 2024, Recommendations of the DNA commission of the international society for forensic genetics (ISFG) on short tandem repeat sequence nomenclature, Forensic Sci. Int.: Genet., 68, 102946.

[25] Udogadi, N.S., Abdullahi, M.K., Bukola, A.T., Imose, O.P., and Esewi, A.D., 2020, Forensic DNA profiling: Autosomal short tandem repeat as a prominent marker in crime investigation, Malays. J. Med. Health Sci., 27 (4), 22–35.

[26] Gill, P., Haned, H., Bleka, O., Hansson, O., Dørum, G., and Egeland, T., 2015, Genotyping and interpretation of STR-DNA: Low-template, mixtures and database matches—Twenty years of research and development, Forensic Sci. Int.: Genet., 18, 100–117.

[27] Burrill, J., Daniel, B., and Frascione, N., 2019, A review of trace “Touch DNA” deposits: Variability factors and an exploration of cellular composition, Forensic Sci. Int.: Genet., 39, 8–18.

[28] Kim, J., Kim, H., Nam, Y.H., Lee, J.H., Kim, H.S., and Kim, E., 2021, Efficacy of reduced-size short tandem repeat PCR analysis for degraded DNA samples, Genes Genomics, 43 (7), 749–758.

DOI: https://doi.org/10.22146/ijc.94081