Abstract
Allele frequencies for 15 short tandem repeat (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were obtained from 7,636 unrelated individuals of Chinese Han population living in Qinghai and Chongqing, China. Totally 206 alleles were observed, with the corresponding allele frequencies ranging from 0.0001–0.4982. Chi-square test showed that all of the STR loci agreed with the Hardy-Weinberg equilibrium. We also compared our data with previously published population data of other ethnics or areas. The results are valuable for human identification and paternity testing in Chinese Han population.
Key words: forensic science, DNA typing, population genetic analysis, short tandem repeats, Chinese Han population
Introduction
Short tandem repeat (STR) loci have been widely used as human identification markers in forensic sciences. In this study we obtained and analyzed allele frequencies for 15 STR loci in Chinese Han population from West China, with the aim of setting up a primary forensic DNA database and acquiring more reliable statistic data for human identification and paternity testing.
Results and Discussion
Allele frequencies and statistical parameters regarding the 15 STR loci in Chinese Han population were shown in Table 1. A total of 206 alleles and 930 genotypes of the 15 STR loci were detected, with the corresponding allele frequencies ranging from 0.0001–0.4982. The combined probability of exclusion (Pe), power of discrimination (PD), and probability of match (Pm) for all the 15 STR loci were 0.999999, 0.9999999999, and 5.85×10−11, respectively. The observed and expected genotype frequencies were evaluated by χ2 test and the heredity of all STR loci followed the Hardy-Weinberg equilibrium (P>0.05).
Table 1.
Allele frequencies and statistical parameters for the 15 STR loci in Chinese Han population
| Allele | D8S1179 | D21S11 | D7S820 | CSF1PO | D3S1358 | TH01 | D13S317 | D16S539 | D2S1338 | DS19S433 | vWA | TPOX | D18S51 | D5S818 | FGA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5 | – | – | – | – | – | 0.0001 | – | – | – | – | – | 0.0001 | – | – | – |
| 5.3 | – | – | – | – | – | 0.0001 | – | – | – | – | – | – | – | – | – |
| 6 | – | – | – | – | – | 0.0940 | – | 0.0001 | – | – | – | 0.0002 | – | 0.0001 | – |
| 6.3 | – | – | – | – | – | 0.0001 | – | – | – | – | – | – | – | – | – |
| 7 | – | – | 0.0016 | 0.0037 | – | 0.2786 | 0.0013 | 0.0001 | – | – | – | 0.0007 | – | 0.0203 | – |
| 8 | 0.0012 | – | 0.1602 | 0.0020 | – | 0.0563 | 0.2692 | 0.0095 | – | – | – | 0.5270 | 0.0001 | 0.0024 | – |
| 8.3 | – | – | – | – | – | 0.0002 | – | – | – | – | – | – | – | – | – |
| 9 | 0.0004 | – | 0.0678 | 0.0522 | – | 0.4982 | 0.1360 | 0.2765 | – | 0.0002 | – | 0.1271 | 0.0003 | 0.0726 | – |
| 9.2 | – | – | – | – | – | – | – | – | – | 0.0001 | – | – | – | – | – |
| 9.3 | – | – | – | – | – | 0.0435 | – | – | – | – | – | – | – | – | – |
| 10 | 0.1127 | – | 0.1644 | 0.2368 | – | 0.0286 | 0.1465 | 0.1239 | – | 0.0001 | 0.0001 | 0.0221 | 0.0010 | 0.1958 | – |
| 10.2 | – | – | – | – | – | – | – | – | – | 0.0001 | – | – | – | – | – |
| 11 | 0.0768 | – | 0.3379 | 0.2420 | 0.0001 | 0.0005 | 0.2319 | 0.2544 | – | 0.0033 | – | 0.2950 | 0.0039 | 0.3296 | – |
| 11.2 | – | – | – | – | – | – | – | – | – | 0.0006 | – | – | – | – | – |
| 12 | 0.1261 | – | 0.2268 | 0.3760 | 0.0007 | – | 0.1659 | 0.2205 | – | 0.0393 | 0.0003 | 0.0256 | 0.0364 | 0.2316 | – |
| 12.2 | – | – | – | – | – | – | – | – | – | 0.0058 | – | – | – | – | – |
| 13 | 0.2290 | – | 0.0364 | 0.0760 | 0.0014 | – | 0.0395 | 0.1001 | – | 0.2735 | 0.0020 | 0.0021 | 0.1971 | 0.1363 | – |
| 13.2 | – | – | – | – | – | – | – | – | – | 0.0484 | – | – | – | – | – |
| 14 | 0.1946 | – | 0.0047 | 0.0101 | 0.0430 | – | 0.0097 | 0.0142 | 0.0001 | 0.2441 | 0.2367 | 0.0003 | 0.2143 | 0.0098 | – |
| 14.2 | – | – | – | – | – | – | – | – | – | 0.1120 | – | – | – | – | – |
| 15 | 0.1703 | – | 0.0002 | 0.0013 | 0.3566 | – | 0.0001 | 0.0008 | 0.0001 | 0.0740 | 0.0296 | – | 0.1708 | 0.0013 | – |
| 15.2 | – | – | – | – | – | – | – | – | – | 0.1434 | – | – | – | – | – |
| 16 | 0.0735 | – | 0.0001 | – | 0.3223 | – | – | 0.0001 | 0.0084 | 0.0167 | 0.1870 | – | 0.1270 | 0.0001 | 0.0006 |
| 16.2 | – | – | – | – | – | – | – | – | – | 0.0322 | – | – | – | – | – |
| 17 | 0.0136 | – | – | – | 0.2010 | – | – | – | 0.0640 | 0.0017 | 0.2492 | – | 0.0771 | 0.0001 | 0.0011 |
| 17.2 | – | – | – | – | – | – | – | – | – | 0.0039 | – | – | – | – | 0.0001 |
| 18 | 0.0018 | – | – | – | 0.0692 | – | – | – | 0.1113 | 0.0001 | 0.1887 | – | 0.0475 | – | 0.0251 |
| 18.2 | – | – | – | – | – | – | – | – | – | 0.0005 | – | – | – | – | – |
| 19 | – | – | – | – | 0.0054 | – | – | – | 0.1837 | – | 0.0884 | – | 0.0461 | – | 0.0479 |
| 20 | – | – | – | – | 0.0003 | – | – | – | 0.1192 | – | 0.0167 | – | 0.0336 | – | 0.0490 |
| 21 | – | – | – | – | – | – | – | – | 0.0304 | – | 0.0011 | – | 0.0207 | – | 0.1047 |
| 21.2 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 0.0031 |
| 22 | – | – | – | – | – | – | – | – | 0.0491 | – | 0.0001 | – | 0.0136 | – | 0.1738 |
| 22.2 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 0.0067 |
| 23 | – | – | – | – | – | – | – | – | 0.2003 | – | – | – | 0.0063 | – | 0.2191 |
| 23.2 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 0.0093 |
| 24 | – | – | – | – | – | – | – | – | 0.1560 | – | – | – | 0.0027 | – | 0.1835 |
| 24.2 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 0.0095 |
| 25 | – | – | – | – | – | – | – | – | 0.0620 | – | – | – | 0.0011 | – | 0.1053 |
| 25.2 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 0.0039 |
| 26 | – | 0.0003 | – | – | – | – | – | – | 0.0123 | – | – | – | 0.0004 | – | 0.0426 |
| 26.2 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 0.0014 |
| 27 | – | 0.0027 | – | – | – | – | – | – | 0.0025 | – | – | – | 0.0001 | – | 0.0097 |
| 27.2 | – | 0.0001 | – | – | – | – | – | – | 0.0006 | – | – | – | – | – | 0.0002 |
| 28 | – | 0.0450 | – | – | – | – | – | – | 0.0001 | – | – | – | – | – | 0.0026 |
| 28.2 | – | 0.0093 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 29 | – | 0.2636 | – | – | – | – | – | – | – | – | – | – | – | – | 0.0007 |
| 29.2 | – | 0.0016 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 30 | – | 0.2805 | – | – | – | – | – | – | – | – | – | – | – | – | 0.0001 |
| 30.2 | – | 0.0132 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 31 | – | 0.1019 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 31.2 | – | 0.0764 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 32 | – | 0.0261 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 32.2 | – | 0.1266 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 33 | – | 0.0030 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 33.2 | – | 0.0436 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 34 | – | 0.0005 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 34.2 | – | 0.0052 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 35 | – | 0.0001 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 35.2 | – | 0.0002 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 36 | – | 0.0001 | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Ho | 0.1653 | 0.1868 | 0.2453 | 0.2612 | 0.2859 | 0.3556 | 0.2077 | 0.2274 | 0.1385 | 0.1852 | 0.2027 | 0.3833 | 0.1460 | 0.2219 | 0.1469 |
| He | 0.8347 | 0.8132 | 0.7547 | 0.7388 | 0.7141 | 0.6444 | 0.7923 | 0.7726 | 0.8615 | 0.8148 | 0.7973 | 0.6167 | 0.8540 | 0.7781 | 0.8531 |
| PIC | 0.8207 | 0.7917 | 0.7426 | 0.6920 | 0.6732 | 0.5571 | 0.7762 | 0.7509 | 0.8489 | 0.7797 | 0.7728 | 0.5571 | 0.8407 | 0.7410 | 0.8432 |
| PD | 0.8406 | 0.8147 | 0.7758 | 0.7354 | 0.7141 | 0.6180 | 0.7923 | 0.7846 | 0.8639 | 0.8218 | 0.8023 | 0.6180 | 0.8565 | 0.7751 | 0.8586 |
| Pe | 0.6951 | 0.6582 | 0.5896 | 0.5271 | 0.5045 | 0.3845 | 0.6320 | 0.5984 | 0.7378 | 0.6684 | 0.6272 | 0.3845 | 0.7265 | 0.5871 | 0.7302 |
| P | 0.1668 | 0.2037 | 0.5809 | 0.3765 | 0.3050 | 0.2019 | 0.6789 | 0.6275 | 0.1471 | 0.1994 | 0.2026 | 0.8353 | 0.1686 | 0.4018 | 0.1772 |
Ho, observed heterozygosity; He, expected heterozygosity; PIC, polymorphism information content; PD, power of discrimination; Pe, probability of exclusion; P, probability values of the exact tests for Hardy-Weinberg equilibrium.
We also compared these data with previous population data observed at the same 15 STR loci by using the method of χ2 test after Bonferroni’s correction of SPSS 11.5 (www.spss.com). As a result, no significant differences were observed between our data and the Chinese Han population living in Guangdong Province (1), Hui (2) and Uigur (3) ethnic groups of China, Korean population (4), and Kosovo population (5). However, we found that there were significant differences between our data and the Chinese Miao population (6) at locus vWA (P=0.027), Maghreb population (7) at locus D13S317 (P<0.001), Polish population (8) at loci D8S1179 (P=0.043) and D7S820 (P=0.001), and Otomi population (9) at loci vWA, D7S820, CSF1PO, FGA, and D8S1179 (P<0.001), respectively. The results of the present study are valuable for human identification and paternity testing in Chinese Han population.
Materials and Methods
Blood-stained samples were obtained with informed consent from 7,636 unrelated individuals of Chinese Han population living in Qinghai Province and Chongqing Municipality in West China. Genomic DNA was extracted using the Chelex-100 method (10). Fifteen STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were amplified in five fluorescence-based multiplex polymerase chain reactions (PCRs) using the AmpFLSTR™ Identifiler kit (Applied Biosystems, Foster City, USA). The amplification reactions in a total volume of 10 µL contained 2.0 µL primer set, 0.2 µL AmpliTaq Gold DNA Polymerase (5 U/µL), 2.9 µL deionized water, 4.0 µL dNTP, and 0.9 µL genomic DNA. Thermal cycling was conducted with the following conditions: 95°C for 11 min; 28 cycles of 94°C for 1 min, 59°C for 1 min, 72°C for 1 min; and a final extension of 60°C for 45 min using the GeneAmp PCR system 9700 (Applied Biosystems). Detection and genotyping of all the PCR products were accomplished using the ABI 3130xl DNA Genetic Analyzer (Applied Biosystems). Allele designation was performed using GeneMapper ID Software v3.2 (Applied Biosystems). Quality control was adhered to laboratory internal control standards and kit controls. Allele and genotype frequencies were estimated by direct counting.
The complete dataset is available from the corresponding author via e-mail requests.
Authors’ contributions
XGY, HFM, YQH, XTS, and WMS carried out the DNA typing. YZL performed the statistical analysis. YJD and JWY conceived of the study, participated in its design and coordination, and drafted the manuscript. All authors read and approved the final manuscript.
Competing interests
The authors have declared that no competing interests exist.
Acknowledgements
We thank Mr. Chuan-Hai Wang for his hard work on collecting blood samples.
References
- 1.Zhu J. Population data of 15 STR in Chinese Han population from north of Guangdong. J. Forensic Sci. 2005;50:1510–1511. [PubMed] [Google Scholar]
- 2.Wang Z. Genetic polymorphisms of 15 STR loci in Chinese Hui population. J. Forensic Sci. 2005;50:1508–1509. [PubMed] [Google Scholar]
- 3.Zhu B. Genetic analysis of 15 STR loci of Chinese Uigur ethnic population. J. Forensic Sci. 2005;50:1235–1236. [PubMed] [Google Scholar]
- 4.Kim Y.L. Allele frequencies of 15 STR loci using AmpFLSTR Identifiler kit in a Korean population. Forensic Sci. Int. 2003;136:92–95. doi: 10.1016/s0379-0738(03)00255-x. [DOI] [PubMed] [Google Scholar]
- 5.Kubat M. Population genetics of the 15 AmpFlSTR identifiler loci in Kosovo Albanians. Int. J. Legal Med. 2004;118:115–118. doi: 10.1007/s00414-004-0430-y. [DOI] [PubMed] [Google Scholar]
- 6.Liu C. Genetic studies of 15 STR loci in Guangxi Miao population. J. Forensic Med. 2003;19:204–206. [PubMed] [Google Scholar]
- 7.Farfan M.J. STR data for the AmpFlSTR Profiler Plus and COfiler loci from the Maghreb (North Africa) Forensic Sci Int. 2001;121:199–200. doi: 10.1016/s0379-0738(01)00393-0. [DOI] [PubMed] [Google Scholar]
- 8.Szczerkowska Z. Northern Polish population data and forensic usefulness of 15 autosomal STR loci. Forensic Sci. Int. 2004;144:69–71. doi: 10.1016/j.forsciint.2004.02.020. [DOI] [PubMed] [Google Scholar]
- 9.Barrot C. Characterisation of three Amerindian populations from Hidalgo State (Mexico) by 15 STR-PCR polymorphisms. Int. J. Legal Med. 2005;119:111–115. doi: 10.1007/s00414-004-0488-6. [DOI] [PubMed] [Google Scholar]
- 10.Walsh P.S. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques. 1991;10:506–513. [PubMed] [Google Scholar]