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1 Kor. J. Legal Med. Vol. 27, No. 1 = Abstract = A Korean population study for the COfiler STR loci (D3S1358, D16S539, TH01, TPOX, CSF1PO, D7S820) Jeong-Seung Kwon, Kyoung-Jin Shin 2, 4, 5, Yun-Seok Yang 2, Gil-Ro Han 3, 4, 5, Chong-Youl Kim 1, 2, 5 1, 2, 5, Jong-Hoon Choi Department of Oral Diagnosis and Oral Medicine, College of Dentistry, Yonsei University 2 Department of Forensic Medicine, College of Medicine, Yonsei University 3 Department of Forensic Medicine, National Institute of Scientific Investigation 4 Biometrics Engineering Research Center, Yonsei University 5 Human Identification Research Institute, Yonsei University In the United States, the Federal Bureau of Investigation (FBI) officially launched its national DNA database. This database, named the combined DNA Index System (CODIS), included one genderdetermining amelogenin and 13 polymorphic short tandem repeats (STR) loci. To introduce a new STR system, a population database for the relevant population must be established for the statistical analysis of forensic cases. AmpFlSTR Profiler Plus PCR Amplification Kit (Profiler Plus Kit) and AmpFlSTR COfiler PCR Amplification Kit (COfiler Kit) are required to obtain information from all the 13 CODIS core STR loci. Study on 9 STR loci using Profiler Plus kit was already performed in a Korean population, but not yet on 6 STR loci using COfiler Kit. This study intends to evaluate usefulness of 6 COfiler STR loci (D3S1358, D16S539, TH01, TPOX, CSF1PO, D7S820) in forensic identification. Buccal swab samples obtained from 300 randomly selected unrelated Koreans. DNA was extracted from the buccal swab samples and multiplex polymerase chain reaction (PCR) was performed using the COfiler Kit to amplify it. And using automated DNA sequencer and computer program, the allele and genotype frequency distribution is investigated and statistical analysis was performed for the PCR products. The following results were obtained: 65

2 1. The observed heterozygosity at each STR locus ranged from to and the expected heterozygosity at each STR locus ranged from to The polymorphism information content (PIC) at each STR locus ranged from to and is higher than 0.5 for all loci to have relatively high information content. 3. The power of discrimination (PD) at each STR locus ranged from to and the combined power of discrimination is calculated to be The mean exclusion chance (MEC) at each STR locus ranged from to and the combined mean exclusion chance is calculated to be Based on the results of this study, 6 COfiler STR loci may be useful in forensic identification including finding an individual in relation to criminal case and paternity testing. Key Words : COfiler, STR loci, CODIS, individual identification, D3S1358, D16S539, TH01, TPOX, CSF1PO, D7S820 66

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6 Table 1. Allele frequency distribution of the D3S1358 locus in a Korean population Allele Observed No Frequency Fig. 1. AmpFlSTR COfiler multiplex STR data for D3S1358 and D16S539 loci. 70

7 Table 2. Allele frequency distribution of the D16S539 locus in a Korean population Allele Observed No Frequency Fig. 2. AmpFlSTR COfiler multiplex STR data for TH01, TPOX and CSF1PO loci. 71

8 Table 3. Allele frequency distribution of the TH01 locus in a Korean population Allele Observed No Frequency Table 4. Allele frequency distribution of the TPOX locus in a Korean population Allele Observed No Frequency Table 5. Allele frequency distribution of the CSF1PO locus in a Korean population Allele Observed No Frequency

9 Fig. 3. AmpFlSTR COfiler multiplex STR data for D7S820 locus. Table 6. Allele frequency distribution of the D7S820 locus in a Korean population Allele Observed No Frequency Table 7. Statistical parameters for the COfiler STR loci Locus D3S1358 D16S539 TH01 TPOX CSF1PO D7S820 obs-h a exp-h b PIC c PD d MEC e a obs-h: Observed heterozygosity, b exp-h: Expected heterozygosity c PIC: Polymorphic information contents, d PD: Power of discrimination, e MEC: Mean exclusion chance 73

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16 1. Smith HO, Wilcox KW. A restriction enzyme from haemophilus influenza,. Purification and general properties. J Mol Biol 1970;51: Jeffreys AJ, Wilson V, Thein SL. Hypervariable minisatellite regions in human DNA. Nature 1985;314: Jeffreys AJ, Wilson V, Thein SL. Individual-specific fingerprints of human DNA. Nature 1985;316: Jeffreys AJ, Brookfield JFY, Semeonoff R. Positive identification of an immigration test-case using human DNA fingerprints. Nature 1985;317: Gill P, Jeffreys AJ, Werrett DJ. Forensic application of D- NA fingerprints. Nature 1985;318: Miesfield R, Krystal M, Arnheim N. A member of a new repeated sequence family which is conserved throughout eucaryote evolution is found between the human delta and beta globin genes. Nucleic Acids Res 1981;9: Nakamura Y, Leppert M, O Connell P et al. Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 1987;235: Tautz D. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 1989;17: Mullis KB, Faloona FA. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 1987;155: Craig J, Fowler S, Burgoyne LA, Scott AC, Hardig HWJ. 80

17 Repetitive deoxyribonucleic acid (DNA) and human genome variation. A concise review relevant to forensic biology. J Forensic Sci 1988;33: Litt M, Luty JA. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotied repeat within the cardiac muscle actin gene. Am J Hum Genet 1989; 44: Urquhart A, Kimpton CP, Downes TJ, Gill P. Variation in short tandem repeat sequences - a survey of twelve microsatellite loci for use as forensic identification markers. Int J Legal Med 1994;107: Smith LM, Sanders JZ, Kaiser RJ et al. Fluorescence detection in automated DNA sequence analysis. Nature 1986;321: Carrano AV, Lamerdin J, Ashworth LK et al. A high-resolution, fluorescence-based, semiautomated method for DNA fingerprinting. Genomics 1989;4: Sullivan KM, Pope S, Gill P, Robertson JM. Automated DNA profiling by fluorescent labeling of PCR products. PCR Methods and Applications 1992;2: Ziegle JS, Ying S, Corcoran KP et al. Application of automated DNA sizing technology for genotyping microsatellite loci. Genomics 1992;14: ,,. 9 STR (FGA, vwa, D3S1358, D18S51, D21S11, D8S1179, D7S820, 27. Jones DA. Blood samples: probability of discrimination. J Forens Sci Soc 1972;12: Ronald A, Garber, Jeffrey, Morris W. General equations for the average power of exclusion for genetic systems of n codominant alleles in one-parent and no-parent cases of disputed parentage. Inclusion probabilities in Parentage Testing 1983; Lewis PO, Zaykin S. Genetic data analysis, Computer program for the analysis of allelic data, Version 1.0, < html> 30. Edwards A, Civitello A, Hammond HA, Caskey CT. D- NA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet 1991;49: Puers C, Hammond HA, Jin L, Caskey CT, Schumm JW. Identification of repeat sequence heterogeneity at the polymorphic short tandem repeat locus HUMTH01 [AATG]n and reassignment of alleles in population analysis by using a locus-specific allelic ladder. Am J Hum Genet 1993;53: Chakraborty R, Stivers DN, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond hyman i- dentification: Implications for development of new DNA typing systems. Electrophoresis 1999;20: D13S317, D5S818) 33. Walsh PS, Fildes NJ, Reynolds R. Sequence analysis and. 1999;23: characterization of shutter products at the tetranucleotide repeat locus vwa. Nucleic Acids Rsearch 1996; 18.,,,,,. STRs 24: ;20: Weber JL. Informativeness of human (dc-da)n-(dg-dt)n 19.,,,. 4 STRs polymorphisms. Genomics 1990;7: ; 35. Gill P, Urquhart A, Millican ES, et al. A new method of 21: STR interpretation using inferential logic-development 20.,. STR CSF1PO, STR TPOX, STR TH01 of criminal intelligence database. Int J Legal Med 1996;. 109: ;22: Grattapaglia D, Schmidt AB, Costa e Silva C, Stringher 21.,,,,,. C, Fernandes AP, Ferreira ME. Brazilian population D16S539. database for the 13 STR loci of the AmplSTR Profiler 2000;25: Plus TM and COfiler TM multiplex kits. Forensic Sci Int 22. International Society for Forensic Haemogenetics. DNA 2001;118: recommendations Further report of the DNA 37. Budowle B, Moretti TR, Baumstark AL, Defenbaugh Commission of the ISFH regarding the use of short tandem repeat systems. Int J Legal Med 1997;100: core short tandem repeat loci in African Americans, U.S. DA, Keys KM. Population data on the thirteen CODIS 23. Tereba A. Tools for analysis of population statistics. Caucasians, Hispanics, Bahamians, Jamaicans, and Profiles in DNA 1999;2: Trinidadians. J Forensic Sci 1999;44: ,,, : STR 38. Bagdonavicius A, Turbett GR, Buckleton JS, Walsh SJ., 1998;22: Western Austrailian sub-population data for the thirteen 25. Nei M, Roychoudhury AK. Sampling variance of heterozygosity and genetic distance. Genetics 1974;76:379- Forensic Sci 2002;47: AMPFlSTR Profiler PlusTM and COfilerTM STR loci. J Borys S, Vanstone H, Carmody G, Fourney R. Allele frequencies for the COfiler STR loci in the Canadian 26. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Forensic Sci 2000;45: Caucasian and Canadian First Nations population. J Genet 1980;32: Sanz P, Prieto V, Flores I, Torres Y, Lopez-Soto M, 81

18 Farfan MJ. Population data of 13 STRs in southern Spain (Andalusia). Forensic Sci Int 2001;119: Farfan MJ, Prieto V, Torres Y, Lopez-Soto M, Sanz P. STR data for the AmplSTR Profiler Plus and COfiler loci from the Maghreb (North Africa). Forensic Sci Int 2001; 121: Gehrig C, Hochmeister M, Dirnhofer R, Budowle B. Swiss Caucasian population data for 13 STR loci using AmplSTR Profiler Plus and COfiler PCR amplification k- its. J Forensic Sci 1999;44: Budowle B, Chidambaram A, Strickland L, Beheim CW, Taft GM, Chakraborty R. Population studies on three Native Alaska population groups using STR loci. Forensic Sci Int 2002;129: Lee JCI, Chen CH, Tsai LC, Linacre A, Chang JG. The screening of 13 short tandem repeat loci in the Chinese population. Forensic Sci Int 1997;87: Huang NE, Schumm J, Budowle B. Chinese population data on three tetrameric short tandem repeat loci-- HUMTHO1, TPOX, and CSF1PO--derived using multiplex PCR and manual typing. Forensic Sci Int 1995;71:

한수지 50(6), , 2017 Original Article Korean J Fish Aquat Sci 50(6), ,2017 해삼 (Stichopus japonicus) 의 microsatellite 유전자형분석을위한 multiplex PCR

한수지 50(6), , 2017 Original Article Korean J Fish Aquat Sci 50(6), ,2017 해삼 (Stichopus japonicus) 의 microsatellite 유전자형분석을위한 multiplex PCR 한수지 50(6), 806-811, 2017 Original Article Korean J Fish Aquat Sci 50(6),806-811,2017 해삼 (Stichopus japonicus) 의 microsatellite 유전자형분석을위한 multiplex PCR 시스템개발 심용택 * 이철상 1 * midna 유전체연구소, 1 군산대학교생물학과 Development