International Journal of Bioinformatics and Biomedical Engineering
Articles Information
International Journal of Bioinformatics and Biomedical Engineering, Vol.4, No.1, Mar. 2018, Pub. Date: Aug. 20, 2018
Establishing Human Identification by Short Tandem Repeat (STR) and Mitochondrial DNA (mtDNA)
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[01] Yousef Alrajhi, Microbiology Department, College of Medicine, Howard University, Washington DC, USA.
The usage of DNA sequencing and fingerprinting has given rise to many powerful techniques that are extremely useful in the modern world, two particular areas where these have become vitally important is in the determination of paternity and in the investigation of ancestral roots. STR allele frequency and mtDNA HVR sequencing are both used for human identification purposes, they can also be applied to determine the area an individual most likely came from and the lineage they originated from tracking inheritance patterns over several generations. In this study we tested twenty related individuals of Arabic descent for both mtDNA and STR allele frequency to confirm their racial status, comparing and contrasting to existing data to verify the results and to localise their lineage. The data collected was also analysed for unusual results in both STR and mtDNA output. The results indicated that the individuals were in fact of Arabic descent, with very close matching to published Iraqi and Kuwaiti STR frequency population data. Furthermore, analysis of the mtDNA further confirmed likely Arabic status and location of origin in the Middle East. Analysis also determined that there was one unusual result for the D19S433 locus where a particularly lengthy allele was discovered in one allele. This allele had been previously reported and was not present in any other individuals in the sample group. Two of the single nucleotide mismatches in the mtDNA sequence appeared to be unique to the individual and were not definitive mutations for any known haplogroup; these may be truly unique or symptomatic of an undiscovered haplogroup or sub-clade. These results indicate that use of STR frequency is more accurate in determining lineage in small groups, whereas it is likely that in large groups mtDNA may be more useful due to its internal self-referencing in family groups, lower cost and timescale.
STR, mtDNA, HVR, Saudi Arabia
[01] Abdin, L., Dewab, K., Rand, S., Hohoff, C., Brinkmann, B., 2003. Analysis of 13 Y-chromosomal STRs in an Arab population sample from Syria. International Congress Series, 1239, pp. 319-321.
[02] Abu-Amero, K. K., González, A. M., Larruga, J. M., Bosley, T. M., Cabrera, V. M., 2007. Eurasian and African mitochondrial DNA influences in the Saudi Arabian population. BMC Evolutionary Biology, 7, pp. 32, doi: 10.1186/1471-2148-7-32.
[03] Achilli, A., Olivieri, A., Pala, M., Metspalu, E., Fornarino, S., Battaglia, V., Accetturo, M., Kutuev, I., Khusnutdinova, E., Pennarun, E., Cerutti, N., Di Gaetano, C., Crobu, F., Palli, D., Matullo, G., Santachiara-Benerecetti, A. S., Cavalli-Sforza, L. L., Semino, O., Villems, R., Bandelt, H. J., Piazza, A., Torroni. A., 2007. Mitochondrial DNA variation of modern Tuscans supports the near eastern origin of Etruscans. Am J Hum Genet., 80 (4), pp. 759-68.
[04] Alenizi, M., Goodwin, W., Ismael, S., Hadi, S., 2008. STR data for the AmpF‘STR® Identifiler loci in Kuwaiti population. Legal Medicine, 10, pp. 321–325.
[05] Alshamali, F., Pereira, L., Budowle, B., Poloni, E. S., Currat, M., 2009. Local Population Structure in Arabian Peninsula Revealed by Y-STR Diversity. Human Heredity, 68 (1), pp. 45-54.
[06] Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M., Howell, N., 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet., 23 (2), pp. 147.
[07] Anon, 2010. Restriction Fragment Length Polymorphism (RFLP). NCBI [Online] Available at: [Accessed 23rd June 2010].
[08] Barni, F., Berti, A., Pianese, A., Boccellino, A., Miller, M. P., Caperna, A., Lago, G., 2007. Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region. Forensic Science International, 167, pp. 87–92.
[09] Behar, D. M., Metspalu, E., Kivisild, T., Rosset, S., Tzur, S., Hadid, Y., Yudkovsky, G., Rosengarten, D., Pereira, L., Amorim, A., Kutuev, I., Gurwitz, D., Bonne-Tamir, B., Villems, R., Skorecki, K. (2008) Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. PLoS One., 3 (4), pp. e2062.
[10] Butler, J. M., Schoske, R., Vallone, P. M., Redman, J. W., Kline, M. C., 2003. Allele Frequencies for 15 Autosomal STR Loci on U.S. Caucasian, African American, and Hispanic Populations. Forensic Sci, 48 (4), pp. 1-4.
[11] Butler, J. M. 2007. Short tandem repeat typing technologies used in human identity testing. BioTechniques, 43 (4), pp. 1-5. Butler, J. M. 2010. Short Tandem Repeat DNA Internet DataBase. [Online] Available at: [Accessed 26th June 2010].
[12] Brinkmann, C., Forster, P., Schürenkamp, M., Horst, J., Rolf, B., Brinkmann, B. 1999. Human Y-chromosomal STR haplotypes in a Kurdish population sample. Int J Legal Med., 112 (3), pp. 181-183.
[13] Coudray, C., Guitard, E., El-Chennawi, F., Larrouy, G., Dugoujon, J. M., 2007. Allele frequencies of 15 short tandem repeats (STRs) in three Egyptian populations of different ethnic groups. Forensic Science International, 169, pp. 260–265.
[14] Dauber, E. M., Bär, W., Klintschar, M., Neuhuber, F., Parson, W., Mueller-van der Spruit, E., Mayr, W. R., 2004. New sequence data of allelic variants at the STR loci ACTBP2 (SE33), D21S11, FGA, vWA, CSF1PO, D2S1338, D16S539, D18S51 and D19S433 in Caucasoids. Progress in Forensic Genetics 10, 1261, pp. 191-193.
[15] Dauber, E. M., Dorner, G., Wenda, S., Schwartz-Jungl, E. M., Glock, B., Bär, W., Mayr, W. R., 2008. Unusual FGA and D19S433 off-ladder alleles and other allelic variants at the STR loci D8S1132, vWA, D18S51 and ACTBP2 (SE33). Progress in Forensic Genetics 12 – Proceedings of the 22nd International ISFG Congress, 1 (1), pp. 109-111.
[16] Diez-Sanchez, C., Ruiz-Pesini, E., Lapena, A. C., Montoya, J., Perez-Martos, A., Enrıquez, J. A., Lopez-Perez, M. J. 2003. Mitochondrial DNA Content of Human Spermatozoa. Biology of Reproduction, 68, pp. 180–185.
[17] Edwards, A., Civitello, A., Hammond, H. A., Caskey, C. T., 1991. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet., 49 (4), pp. 746-756.
[18] Einum, D. D. and Scarpetta, M. A., 2004. Genetic analysis of large data sets of North American Black, Caucasian, and Hispanic populations at 13 CODIS STR loci. J Forensic Sci, 49 (6), pp. 1381-1385. Eupedia,
[19] Ferdous, A., Ali, M. E., Alam, S., Hasan, M., Hossain, T., Akhteruzzaman, S., 2010. Allele Frequencies of 10 Autosomal STR Loci from Chakma and Tripura Tribal Populations in Bangladesh. Molecular Biology International, 2010, Article ID 740152, doi: 10.4061/2010/740152.
[20] Giles, R. E., Blanc, H., Can, H. M., Wallace, D. C. 1980. Maternal inheritance of human mitochondrial DNA. Proc. Natl. Acad. Sci., 77 (11), pp. 6715-6719.
[21] Heinrich, M., Felske-Zech, H., Bernd Brinkmann, B., Hohoff, C., 2005. Characterisation of variant alleles in the STR systems D2S1338, D3S1358 and D19S433. Int Journal of Legal Medicine, 119 (5), pp. 310-313.
[22] Immel, U. D., Kleiber, M., Klintschar, M., 2003. Y-chromosomal STR haplotypes in an Arab population from Yemen. International Congress Series, 1261, pp. 340-343.
[23] Iudica, C., Maris, S., Jaureguiberry, M., Parolin, L., Sambuco, L., 2009. Forensic Science International: Genetics Supplement Series. Manuscript number FSIGSS-D-09-00005, ISSN: 18751768.
[24] Katsuyama, Y., Inoko, H., Imanishi, T., Mizuki, N., Gojoboric, T., Ota, M., 1998. Genetic Relationships among Japanese, Northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian, and Italian Populations Based on Allelic Frequencies at Four VNTR (D1S80, D4S43, COL2A1, D17S5) and One STR (ACTBP2) Loci. Human Heredity, 48, pp. 126–137.
[25] Klintschar, M., al-Hammadi, N., Reichenpfader, B. 2001. Significant differences between Yemenite and Egyptian STR profiles and the influence on frequency estimations in Arabs. Int J Legal Med., 114 (4-5), pp. 211-214.
[26] Kivisild, T., Reidla, M., Metspalu, E., Rosa, A., Brehm, A., Pennarun, E., Parik, J., Geberhiwot, T., Usanga, E., Villems, R., 2004. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet., 75 (5), pp. 752-70.
[27] Li, H., Schmidt, L., Wei, M. H., Hustad, T., Lerman, M. I., Zbar, B., Tory, K., 1993. Three tetranucleotide polymorphisms for loci: D3S1352; D3S1358; D3S1359. Hum Mol Genet., 2, pp. 1327.
[28] Leibelt, C., Budowle, B., Collins, P., Daoudi, Y., Moretti, T., Nunn, G., Reeder, D., Roby, R., 2003. Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles. Forensic Sci Int., 133 (3), pp. 220-227.
[29] Martín, P., García, O., Albarrán, C., García, P., Sancho, M., Alonso, A., 1999. Spanish population data on the four STR loci D8S1179, D16S539, D18S51 and D21S11. Int. Journal of Legal Medicine, 112 (5), pp. 340-341.
[30] Mills, K. A., Even, D., Murray, J. C., 1992. Tetranucleotide repeat polymorphism at the human alpha fibrinogen locus (FGA). Hum. Mol. Genet., 1 (9), pp. 779.
[31] MITOMAP. 2010. Report of the Committee on the Human Mitochondrial Genome. [Online] Available at: [Accessed 23rd June 2010].
[32] Moss, B. 2010. Nucleic Acid Structure and Function. [Online] Nature Education. Available at: [Accessed 23rd June 2010].
[33] Nasidze, I., Quinque, D., Ozturk, M., Bendukidze, N., Stoneking, Mark. 2005. MtDNA and Y-chromosome Variation in Kurdish Groups. Annals of Human Genetics, 69 (4), pp. 401-412.
[34] Norrgard, K. 2008. Forensics, DNA fingerprinting, and CODIS. Nature Education 1 (1) [Online] Available at: [Accessed 23rd June 2010].
[35] Omran, G. A., Rutty, G. N., Jobling, M. A., 2009. Genetic variation of 15 autosomal STR loci in Upper (Southern) Egyptians. FSI Genetics, 3 (2), pp. E39-e44. Paabo, S. 1995. The Y chromosome and the origin of all of us (men). Science, 268 (5214), pp. 1141-1142.
[36] Parsons, T. J. and Coble, M. D. 2001. Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croatian Medical Journal, 42 (3), pp. 304-309.
[37] Pereira, L., Richards, M., Goios, A., Alonso, A., Albarrán, C., Garcia, O., Behar, D. M., Gölge, M., Hatina, J., Al-Gazali, L., Bradley, D. G., Macaulay, V., Amorim, A., 2005. High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. Genome Res., 15 (1), pp. 19-24.
[38] Pray, L. J. 2008. Eukaryotic genome complexity. [Online] Nature Education 1 (1). Available at: [Accessed 23rd June 2010].
[39] Promega Technical Resources Promega IQ system [Online] Available at: [Accessed 28 July 2010].
[40] Sambrook, J. And Russel, D. W., 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, N. Y.: Cold Spring Harbor Laboratory Press. (3rd ed.). Chapter 8: In vitro Amplification of DNA by the Polymerase Chain Reaction. ISBN 0-87969-576-5.
[41] Schwartz, M., Vissing, J. 2002. Paternal inheritance of mitochondrial DNA. New England Journal of Medicine, 347 (8), pp. 576–580.
[42] Sharma, V., Guo, Z., Litt, M., 1992. Dinucleotide repeat polymorphism at the D18S37 locus. Hum. Mol. Genet., 1 (4), pp. 289.
[43] Shoubridge, E. A., Wai, T. 2007. Mitochondrial DNA and the mammalian oocyte. Current Topics in Developmental Biology, 77, pp. 87-111.
[44] Sinha, S., Amjad, M., Rogers, C., Hamby, J. E., Tahir, U. A., Balamurugan, K., Al-Kubaidan, N. A., Choudhry, A. R., Budowle B., Tahirb, M. A., 1999. Typing of eight short tandem repeat (STR) loci in a Saudi Arabian population. Forensic Science International, 104, pp. 143-146.
[45] Straub, R. E., Speer, M. C., Luo, Y., Rojas, K., Overhauser, J., Ott, J., Gilliam, T. C., 1993. A Microsatellite Genetic Linkage Map of Human Chromosome 18. Genomics, 15 (1), pp. 48-56.
[46] Sullivan, K. M., Mannucci, A., Kimpton, C. P., Gill, P., 1993. A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin. BioTechniques., 15 (4), pp. 637-641.
[47] Triki-Fendri, S., Alfadhli, S., Ayadi, I., Kharrat, N., Ayadi, H., Rebai, A. 2010. Genetic structure of Kuwaiti population revealed by Y-STR diversity. Annals of Human Biology, (doi: 10.3109/03014461003720296).
[48] Tsuji, A., Ishiko, A., Umehara, T., Usumoto, Y., Hikiji, W., Kudo, K., Ikeda, N., 2010. A silent allele in the locus D19S433 contained within the AmpFℓSTR® Identifiler™ PCR Amplification Kit. Legal Medicine, 12 (2), pp. 94-96.
[49] Yao, Y. G., Bravi, C. M., Bandelt, H. J. 2004. A call for mtDNA data quality control in forensic science. Forensic Science International, 141, pp. 1-6.
[50] Ambers, A., Wiley, R., Novroski, N., & Budowle, B. (2018). Direct PCR amplification of DNA from human bloodstains, saliva, and touch samples collected with microFLOQ ® swabs. Forensic Science International: Genetics, 32, 80-87. doi: 10.1016/j.fsigen.2017.10.010.
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