Genetic polymorphisms of 22 autosomal STR loci in Chinese Han population

J.N. Li; H.B. Luo; F. Song; Y.P. Hou

doi:10.1016/j.fsigss.2015.09.018

Research Article| Volume 5, e45-e47, December 2015

Genetic polymorphisms of 22 autosomal STR loci in Chinese Han population

J.N. Li ¹
Author Footnotes
1 Both authors contributed equally to this work.
J.N. Li
Footnotes
1 Both authors contributed equally to this work.
Affiliations
Institute of Forensic Medicine, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
Search for articles by this author
H.B. Luo ¹
Author Footnotes
1 Both authors contributed equally to this work.
H.B. Luo
Footnotes
1 Both authors contributed equally to this work.
Affiliations
Institute of Forensic Medicine, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
Search for articles by this author
F. Song
F. Song
Affiliations
Institute of Forensic Medicine, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
Search for articles by this author
Y.P. Hou
Y.P. Hou
Correspondence
Corresponding author. Fax: +86 28 85501550.
Affiliations
Institute of Forensic Medicine, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
Search for articles by this author
Show footnotesHide footnotes
Author Footnotes
1 Both authors contributed equally to this work.

Published:September 09, 2015DOI:https://doi.org/10.1016/j.fsigss.2015.09.018

Abstract

Microreader™ 23sp ID system was a new STR multiplex system developed for forensic application, but there was a lack of population data in the Chinese Han population. This kit contained 21 non-CODIS STR loci (D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D7S3048, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D12S391, D2S1338, D17S1290, D5S2500), one CODIS STR locus (D16S539) and the amelogenin locus. In this study, a population sample in Chengdu Han population was analyzed with the kit. Forensic genetic parameters and probability values of the Hardy–Weinberg equilibrium (HWE) were calculated with software PowerStats v1.2 and Arlequin v3.5. Allele frequencies of the 22 STR loci and further forensic genetic parameters were obtained. The results suggested that Microreader™ 23sp ID system can provide informative polymorphic data for identification and parentage testing in Chinese Han population.

Keywords

1. Introduction

STRs was widely used in paternity test, individual identification and biological anthropology because they can be easily amplified by the polymerase chain reaction (PCR) [

[1]

Butler J.M.
Hill C.R.

Biology and genetics of new autosomal STR loci useful for forensic DNA analysis.

Google Scholar

], and its diversity and genetic differentiation of human populations. Nevertheless, there was an absence of genetic information for some countries or areas. In this study, 22 autosomal STR loci in the Chengdu Han population were investigated using the Microreader™ 23sp ID system, to obtain the data of population genetics and determine the genetic variability.

2. Materials and methods

Blood samples were collected from 152 unrelated individuals (109 males and 43 females) of the Han population living in Chengdu, northwest China after informed consent. Genomic DNA was isolated by the salting out extraction method and quantified by the NanoDrop1000 Spectrophotometer (Nano-Drop Technologies, Wilmington, DE, USA). The samples were amplified using the Microreader™ 23sp ID system (Suzhou Microread Genetics, Suzhou, Jiangsu, China), PCR amplification was carried out on a Mastercycler^® pro (Eppendorf, Germany) following the manufacturer’s instructions, and amplified products were separated by capillary electrophoresis on a 3130 DNA Genetic Analyzer (Applied Biosystems, USA). Electrophoresis results were analyzed using GeneMapper ID 3.2 software (Applied Biosystems). The experimental procedures were guided in keeping with laboratory internal control standards and kit controls. Forensic statistical parameters were calculated by PowerStats v1.2 software [

[2]

Tereba A.

Tools for analysis of population statistics.

Google Scholar

], observed heterozygosity, expected heterozygosity and the chi-square test of Hardy–Weinberg equilibrium (HWE) were analyzed with ARLEQUIN version 3.5 software [

[3]

Excoffier L.
Lischer H.E.L.

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.

].

3. Results and discussion

Allele frequencies and forensic parameters were listed in Table 1. The observed heterozygosity (Ho) ranged from 0.7171 (D10S1435) to 0.8684 (D2S1338) while the expected heterozygosity (He) ranged from 0.7294 (D10S1435) to 0.8733 (D7S3048). The power of discrimination (PD) ranged from 0.8831 (D10S1435) to 0.9627 (D11S2368) and the probability of excluding paternity (PE) ranged from 0.4552 (D10S1435) to 0.7315 (D2S1338). The combined power of discrimination (CPD) in the 22 STR loci was 0.999999999999999999999999996806 and combined probability of matching (CPE) was 3.1943 × 10⁻²⁷. The value of combined probability of exclusion was 0.99999999975. All of 22 STR loci showed no statistically significant deviation from Hardy–Weinberg equilibrium (HWE). Except D10S1435 (PIC = 0.6860) rest of the 21 STR loci presented high polymorphism (PIC > 0.7), and the most informative locus was D7S3048 (PIC = 0.8566).

Table 1Allele frequencies of the 22 autosomal STR loci and forensic parameters of Chengdu Han population in China (N = 152).

Allele	D6S477	D18S535	D19S253	D15S659	D11S2368	D20S470	D1S1656	D22-GATA198B05	D16S539	D7S3048	D8S1132
6						0.0033
7			0.1743
8			0.0428	0.0033					0.0033
9		0.1809				0.0066			0.2401
10	0.0066	0.0559	0.0263	0.0099		0.1118			0.1513
10.3				0.0033
11	0.0066	0.0197	0.1349	0.1776		0.0329	0.0592		0.2401
11.3				0.0033
12	0.0493	0.0987	0.3454	0.2270		0.0559	0.0395		0.2566
12.1
12.3
13	0.2138	0.2500	0.2072	0.1053		0.1283	0.0954		0.1020
13.3
14	0.2204	0.2895	0.0559	0.0329	0.0033	0.1382	0.1250	0.0033	0.0066
15	0.2895	0.0954	0.0132	0.1250	0.0099	0.1941	0.3125	0.0099			0.0033
15.3
16	0.1941	0.0099		0.1678	0.0461	0.1908	0.2007	0.0888			0.0164
16.2
16.3							0.0033
17	0.0197			0.1086	0.1645	0.0921	0.0658	0.1447		0.0033	0.1250
17.3							0.0658
18				0.0329	0.1184	0.0428	0.0066	0.0592		0.0789	0.2303
18.3							0.0197
19				0.0033	0.1414	0.0033	0.0033	0.0855		0.0987	0.1743
19.3							0.0033
20					0.1447			0.1151		0.1776	0.1349
21					0.1908			0.2993		0.1151	0.1480
22					0.1184			0.1546		0.0789	0.0954
23					0.0493			0.0329		0.1875	0.0559
24					0.0099			0.0066		0.1118	0.0099
25										0.1184	0.0066
26					0.0033					0.0296
27

Ho	0.7632	0.8092	0.7895	0.8553	0.8618	0.8487	0.8487	0.8026	0.7763	0.8618	0.8158
He	0.7839	0.8012	0.7859	0.8508	0.8656	0.8661	0.8259	0.8351	0.7881	0.8733	0.8510
MP	0.0839	0.0771	0.0794	0.0490	0.0373	0.0389	0.0583	0.0519	0.0850	0.0387	0.0441
PD	0.9161	0.9229	0.9206	0.9510	0.9627	0.9611	0.9417	0.9481	0.9150	0.9613	0.9559
PIC	0.7464	0.7701	0.7538	0.8298	0.8472	0.8482	0.8034	0.8136	0.7511	0.8566	0.8301
PE	0.5325	0.6162	0.5797	0.7053	0.7183	0.6923	0.6923	0.6039	0.5558	0.7183	0.6287
TPI	2.1111	2.6207	2.3750	3.4545	3.6190	3.3043	3.3043	2.5333	2.2353	3.6190	2.7143
p	0.4313	0.3724	0.9053	0.2697	0.8935	0.3871	0.4230	0.3281	0.5685	0.1719	0.3943
Allele	D4S2366	D21S1270	D13S325	D9S925	D3S3045	D14S608	D10S1435	D12S391	D2S1338	D17S1290	D5S2500
6						0.0855
7						0.2204
8						0.0132	0.0164
9	0.2928				0.3388	0.1118	0.0033				0.0066
10	0.0822	0.2862			0.0362	0.2467	0.0197			0.0428	0.0329
10.3
11	0.3684	0.0625			0.0296	0.2138	0.1414			0.0559	0.3026
11.3
12	0.1250	0.0493			0.1283	0.0855	0.4145			0.0132	0.1382
12.1		0.0033
12.3		0.1020
13	0.0625	0.1086		0.0099	0.2500	0.0164	0.2336			0.0132	0.0592
13.3		0.0329
14	0.0658	0.2336		0.1217	0.1842	0.0066	0.1612			0.0329	0.0691
15	0.0033	0.0987		0.2237	0.0296		0.0066	0.0132		0.1974	0.2829
15.3		0.0099		0.0033
16		0.0132		0.3289	0.0033		0.0033		0.0132	0.2533	0.0954
16.2										0.0033
16.3				0.0263
17			0.0066	0.2039				0.0658	0.0822	0.1776	0.0132
17.3				0.0066
18			0.0428	0.0724				0.2336	0.1118	0.1151
18.3
19			0.2368	0.0033				0.2204	0.1711	0.0691
19.3
20			0.2763					0.1809	0.1020	0.0230
21			0.2204					0.1184	0.0263	0.0033
22			0.1546					0.0789	0.0395
23			0.0428					0.0395	0.1908
24			0.0164					0.0164	0.1908
25			0.0033					0.0164	0.0625
26								0.0099	0.0099
27								0.0066

Ho	0.7434	0.8355	0.7895	0.7763	0.7895	0.8355	0.7171	0.8618	0.8684	0.8421	0.8026
He	0.7504	0.8267	0.7937	0.7818	0.7718	0.8199	0.7294	0.8399	0.8647	0.8432	0.7932
MP	0.1090	0.0530	0.0770	0.0842	0.0934	0.0675	0.1169	0.0519	0.0380	0.0480	0.0764
PD	0.8910	0.9470	0.9230	0.9158	0.9066	0.9325	0.8831	0.9481	0.9620	0.9520	0.9236
PIC	0.7105	0.8030	0.7594	0.7467	0.7345	0.7922	0.6860	0.8173	0.8466	0.8217	0.7621
PE	0.4986	0.6665	0.5797	0.5558	0.5797	0.6665	0.4552	0.7183	0.7315	0.6794	0.6039
TPI	1.9487	3.0400	2.3750	2.2353	2.3750	3.0400	1.7674	3.6190	3.8000	3.1667	2.5333
p	0.4769	0.9715	0.7945	0.5742	0.5399	0.1329	0.5679	0.3961	0.4703	0.2522	0.3368

Ho: observed heterozygosity, He: expected heterozygosity, MP: matching probability, PD: power of discrimination, PIC: polymorphism information content, PE: probability of excluding paternity, TPI: Typical Patemity Index, p: p values of the exact test for the Hardy–Weinberg equilibrium.

Open table in a new tab

4. Conclusion

Our results showed that Microreader™ 23sp ID system could amplify 22 autosomal STR loci (contained 21 non-CODIS STR loci) and one sex-determining locus in a single reaction and it presented extremely high CPD and CPE value in the Chengdu Han population. Based on these we suggest that Microreader™ 23sp ID system could provide informative polymorphic data for identification and parentage testing in Chinese Han population, especially for deficiency cases of paternity test and the presence of STR mutation.

Conflict of interest

None.

Acknowledgements

The authors would like to thank all volunteers who donated samples. This work was supported by the National Natural Science Foundation of China (81273349, 81330073).

References

- Butler J.M.
- Hill C.R.
Biology and genetics of new autosomal STR loci useful for forensic DNA analysis.
For. Sci. Rev. 2012; 24: 15
View in Article
- Google Scholar
- Tereba A.
Tools for analysis of population statistics.
Profiles DNA. 1999; 3: 14-16
View in Article
- Google Scholar
- Excoffier L.
- Lischer H.E.L.
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
Mol. Ecol. Resour. 2010; 10: 564-567
View in Article

Article info

Publication history

Published online: September 09, 2015

Accepted: September 7, 2015

Received: August 18, 2015

Identification

DOI: https://doi.org/10.1016/j.fsigss.2015.09.018

Copyright

ScienceDirect

Access this article on ScienceDirect

Toggle Thumbstrip

Property	Value
Status
Version
Ad File
Disable Ads Flag
Environment
Moat Init
Moat Ready
Contextual Ready
Contextual URL
Contextual Initial Segments
Contextual Used Segments
AdUnit
SubAdUnit
Custom Targeting
Ad Events
Invalid Ad Sizes

Genetic polymorphisms of 22 autosomal STR loci in Chinese Han population

Abstract

Keywords

1. Introduction

2. Materials and methods

3. Results and discussion

4. Conclusion

Conflict of interest

Acknowledgements

References

Article info

Publication history

Identification

Copyright

ScienceDirect

Related Articles