中国汉族人群66个InDel基因座的遗传多态性

doi:10.16288/j.yczz.22-006

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Hereditas(Beijing) ›› 2022, Vol. 44 ›› Issue (4): 335-345.doi: 10.16288/j.yczz.22-006

• Research Article • Previous Articles Next Articles

Genetic polymorphisms of 66 InDel loci in the Chinese Han population

Xueqian Wang^1,²(), Qingzhen Zhang², Peng Cheng², Tingting Dong², Weiguo Li¹(), Zhe Zhou²(), Shengqi Wang²()

1. College of Life Sciences, Henan Normal University, Xinxiang 453007, China
2. Beijing institute of Radiation Medicine, Academy of Military Medical Sciences, Beijing 100850, China

Received:2022-01-06 Revised:2022-03-15 Online:2022-04-20 Published:2022-03-24
Contact: Li Weiguo,Zhou Zhe,Wang Shengqi E-mail:Wangxqer0122@163.com;liwg0618@htu.edu.cn;zhouzhe@bmi.ac.cn;sqwang@bmi.ac.cn

Abstract

Abstract:

Insertion/deletion polymorphism (InDel) genetic markers refer to insertion or deletion of DNA fragments into genomic DNA, which have advantages in the identification of degraded samples. In this study, we independently screened 66 highly polymorphic InDel markers from the dbSNP database to establish a multiplex PCR system for forensic DNA identification using next-generation sequencing system (66-plex InDels). We assessed the population genetic data among 251 Chinese Han population using this system and evaluated their potential forensic application. The results showed that all 66 InDel loci conformed to the Hardy-Weinberg equilibrium (P>0.000 758), and all the pairwise InDel loci were in linkage equilibrium after Bonferroni correction. The mean observed heterozygosity (Ho) was 0.482, the mean expected heterozygosity (He) was 0.483,the mean discrimination power (DP) was 0.612, the mean polymorphism information content (PIC) was 0.365, the total discrimination power (TDP) reached 0.999 999 999 999 999 999 999 999 999 428 18. The cumulative power of exclusion for 66 InDel loci was 0.999 739 in duo cases (CPE_duo) and was 0.999 999 999 417 in trios cases (CPE_trio). The results show that the 66 InDel loci have high genetic polymorphisms in the Chinese Han population and can be used independently for forensic DNA identification and paternity testing.

Key words: insertion/delationpolymorphism (InDel), Chinese Han population, DNA identification, paternity testing

Xueqian Wang, Qingzhen Zhang, Peng Cheng, Tingting Dong, Weiguo Li, Zhe Zhou, Shengqi Wang. Genetic polymorphisms of 66 InDel loci in the Chinese Han population[J]. Hereditas(Beijing), 2022, 44(4): 335-345.

Figures/Tables 5

Table 1

The genetic information of 66 InDel loci and the genotyping result of positive control DNA sample"

rs#¹⁾	物理位置²⁾	突变基因座信息³⁾(参考基因Ref/突变基因Alt)		目的片段长度(bp)	9947A	9948
rs56113354	chr1:45018875~45018876	-/ATTA		176	1,2	1,2
rs66493016	chr1:62247127~62247132	GCTTTC/-		155	1,2	2,2
rs34947838	chr1:84607676~84607677	TT/-		165	1,1	1,2
rs10562732	chr1:112154318~112154321	TACA/-		168	1,1	1,2
rs10555133	chr1:160678978~160678979	AA/-		161	1,1	2,2
rs3028599	chr1:175158983~175158984	-/GAGAGA		172	2,2	1,2
rs34105738	chr1:200039007~200039008	-/AT		151	2,2	2,2
rs10541877	chr2:51510007~51510008	CT/-		161	1,2	2,2
rs3030108	chr2:207819130~207819131	-/AA		176	1,2	1,2
rs10535391	chr2:234910112~234910114	ATT/-		174	2,2	1,2
rs142380122	chr3:830142~830149	TATTTTTA/-		179	1,2	1,2
rs5849187	chr3:57111346~57111347	-/AG		152	1,2	1,1
rs59715790	chr3:125227757~125227758	-/AG		178	1,2	1,2
rs139940865	chr3:151246716~151246717	-/CT		168	1,2	2,2
rs35052276	chr4:56498033~56498034	AT/-		155	1,1	1,2
rs10562881	chr4:90225051~90225052	AT/-	180		1,1	1,1
rs59027185	chr4:107185571~107185581	CTCACAAAAGT/-	157		2,2	2,2
rs35908330	chr4:154092802~154092804	ATA/-	180		1,2	1,1
rs70954609	chr5:19843605~19843609	AAGTT/-	171		2,2	1,2
rs147779273	chr5:118725106~118725107	AG/-	179		2,2	2,2
rs35829610	chr5:131823862~131823863	-/TG	171		1,1	1,2
rs60570384	chr5:170837222~170837223	-/AG	178		1,2	1,2
rs146109101	chr6:25420796~25420798	CGA/-	180		1,2	1,2
rs151142037	chr6:62835920~62835930	GCAGGGTAGAG/-	165		1,2	1,2
rs59258861	chr6:82184508~82184509	AC/-	174		2,2	1,1
rs4053254	chr6:127484851~127484852	-/AT	180		2,2	1,1
rs145041883	chr6:156295757~156295759	ATG/-	170		1,2	1,1
rs56012194	chr7:34013472~34013473	TT/-	169		1,2	1,2
rs3074767	chr7:106542693~106542694	TT/-	167		1,2	2,2
rs36119043	chr7:137772061~137772062	CT/-	169		1,1	1,2
rs34812419	chr7:151669590~151669591	-/TT	165		1,1	2,2
rs144650377	chr8:605792~605793	TC/-	150		1,2	1,2
rs33928328	chr8:33345203~33345205	GTG/-	164		2,2	2,2
rs4009127	chr8:69001469~69001470	TT/-	153		1,2	1,2
rs372779701	chr8:87918722~87918723	AT/-	179		1,1	2,2
rs79444593	chr8:108392362~108392363	-/CT	152		1,1	1,1
rs56110100	chr9:94516336~94516338	GAC/-	154		1,2	1,2
rs142281120	chr9:115167202~115167203	AG/-	156		1,2	1,2
rs34822234	chr10:3177604~3177605	CA/-	150		1,1	1,1
rs367897009	chr10:27693664~27693665	-/TGACCTCA	172		2,2	1,2
rs145635184	chr10:45607159~45607160	-/GG	176		2,2	1,1
rs6143946	chr10:63754553~63754554	-/TGATATAAGCACAGAATT	158		2,2	1,2
rs76989317	chr10:114144063~114144064	TT/-	163		2,2	2,2
rs34825333	chr11:3889423~3889424	AA/-	170		1,2	2,2
rs34399561	chr11:72500114~72500115	AC/-	160		1,2	1,1
rs10667259	chr11:94222748~94222749	-/AA	166		1,1	1,2
rs139101426	chr11:129108689~129108695	CATAATT/-	153		1,2	1,1
rs3061475	chr12:21597614~21597616	AGG/-	153		1,2	1,2
rs200055056	chr12:49463362~49463374	CCTCCACTCTTCC/-	155		1,2	1,2
rs34564973	chr12:63157978~63157979	-/CAG	160		2,2	2,2
rs144581522	chr12:104293761~104293762	CT/-	169		1,1	1,2
rs10656522	chr12:119567037~119567038	-/AA	151		1,2	1,2
rs10623704	chr12:129659763~129659764	-/AA	165		1,1	1,2
rs58303500	chr13:25442008~25442010	CAT/-	154		1,2	1,2
rs71102499	chr13:64606780~64606781	-/AA	180		1,2	1,2
rs2307807	chr13:77083474~77083477	TGTT/-	162		2,2	1,2
rs56053760	chr13:95418135~95418144	GCAATCAACT/-		156	1,1	1,1
rs33955557	chr14:55227708~55227717	TGAAAGTGTT/-		164	1,2	1,1
rs59306401	chr14:69752162~69752163	AT/-		156	1,2	1,1
rs139530962	chr14:85881796~85881797	AG/-		176	1,2	1,1
rs10544053	chr15:33782138~33782141	CTTA/-		174	1,2	1,1
rs35615387	chr15:81105775~81105776	CT/-		175	1,2	1,2
rs71843136	chr17:2917277~2917278	AG/-		177	1,2	2,2
rs34339565	chr18:1326066~1326067	-/AT		177	1,2	1,2
rs61149315	chr20:35053964~35053965	-/AT		172	1,2	1,2
rs11471707	chr20:51686268~51686269	-/AA		168	2,2	1,2

Table 1

Fig. 1

Table 2

The forensic parameters of 66 InDel loci (n=251)"

rs#	Ref	Alt	P_HWE	Ho	He	DP	PIC	TPI
rs56113354	0.508	0.492	0.871	0.506	0.500	0.622	0.375	1.012
rs66493016	0.398	0.602	0.233	0.518	0.479	0.595	0.364	1.037
rs34947838	0.596	0.404	0.985	0.482	0.482	0.615	0.366	0.965
rs10562732	0.462	0.538	0.897	0.494	0.497	0.625	0.374	0.988
rs10555133	0.546	0.454	0.930	0.494	0.496	0.624	0.373	0.988
rs3028599	0.610	0.390	0.971	0.478	0.476	0.611	0.363	0.958
rs34105738	0.540	0.460	0.205	0.538	0.497	0.601	0.373	1.082
rs10541877	0.566	0.434	0.481	0.470	0.491	0.630	0.371	0.944
rs3030108	0.596	0.404	0.214	0.522	0.482	0.595	0.366	1.046
rs10535391	0.468	0.532	0.635	0.514	0.498	0.616	0.374	1.029
rs142380122	0.376	0.624	0.381	0.498	0.469	0.595	0.359	0.996
rs5849187	0.540	0.460	0.078	0.442	0.497	0.646	0.373	0.896
rs59715790	0.635	0.365	0.754	0.474	0.463	0.600	0.356	0.951
rs139940865	0.460	0.540	0.805	0.490	0.497	0.627	0.373	0.980
rs35052276	0.655	0.345	0.667	0.466	0.452	0.592	0.350	0.937
rs10562881	0.556	0.444	0.364	0.466	0.494	0.634	0.372	0.937
rs59027185	0.357	0.643	0.224	0.498	0.459	0.585	0.354	0.996
rs35908330	0.564	0.436	0.154	0.538	0.492	0.596	0.371	1.082
rs70954609	0.500	0.500	0.549	0.482	0.500	0.633	0.375	0.965
rs147779273	0.490	0.510	0.071	0.558	0.500	0.591	0.375	1.131
rs35829610	0.713	0.287	0.513	0.430	0.409	0.562	0.325	0.878
rs60570384	0.365	0.635	0.952	0.466	0.463	0.604	0.356	0.937
rs146109101	0.526	0.474	0.028	0.430	0.499	0.651	0.374	0.878
rs151142037	0.514	0.486	0.965	0.502	0.500	0.624	0.375	1.004
rs59258861	0.580	0.420	0.144	0.442	0.487	0.636	0.369	0.896
rs4053254	0.490	0.510	0.970	0.502	0.500	0.624	0.375	1.004
rs145041883	0.626	0.375	0.435	0.494	0.469	0.596	0.359	0.988
rs56012194	0.414	0.586	0.204	0.446	0.485	0.633	0.368	0.903
rs3074767	0.548	0.452	0.649	0.482	0.495	0.629	0.373	0.965
rs36119043	0.576	0.424	0.074	0.546	0.489	0.587	0.369	1.101
rs34812419	0.588	0.412	0.911	0.482	0.485	0.618	0.367	0.965
rs144650377	0.512	0.488	0.153	0.546	0.500	0.599	0.375	1.101
rs33928328	0.486	0.514	0.835	0.494	0.500	0.628	0.375	0.988
rs4009127	0.568	0.432	0.955	0.490	0.491	0.621	0.370	0.980
rs372779701	0.532	0.468	0.122	0.450	0.498	0.644	0.374	0.909
rs79444593	0.902	0.098	0.123	0.139	0.176	0.286	0.161	0.581
rs56110100	0.490	0.510	0.772	0.510	0.500	0.620	0.375	1.020
rs142281120	0.492	0.508	0.871	0.506	0.500	0.622	0.375	1.012
rs34822234	0.635	0.365	0.228	0.426	0.463	0.617	0.356	0.872
rs367897009	0.520	0.480	0.747	0.490	0.499	0.629	0.375	0.980
rs145635184	0.522	0.478	0.413	0.526	0.499	0.610	0.375	1.055
rs6143946	0.464	0.536	0.811	0.506	0.497	0.619	0.374	1.012
rs76989317	0.496	0.504	0.874	0.506	0.500	0.622	0.375	1.012
rs34825333	0.394	0.606	0.626	0.494	0.478	0.606	0.364	0.988
rs34399561	0.416	0.584	0.244	0.450	0.486	0.632	0.368	0.909
rs10667259	0.488	0.512	0.868	0.506	0.500	0.622	0.375	1.012
rs139101426	0.500	0.500	0.508	0.522	0.500	0.613	0.375	1.046
rs3061475	0.566	0.434	0.001	0.390	0.491	0.653	0.371	0.820
rs200055056	0.651	0.349	0.094	0.402	0.454	0.614	0.351	0.837
rs34564973	0.438	0.562	0.081	0.438	0.492	0.643	0.371	0.890
rs144581522	0.446	0.554	0.588	0.478	0.494	0.629	0.372	0.958
rs10656522	0.398	0.602	0.407	0.454	0.479	0.624	0.364	0.916
rs10623704	0.410	0.590	0.971	0.486	0.484	0.616	0.367	0.973
rs58303500	0.570	0.430	0.503	0.470	0.490	0.629	0.370	0.944
rs71102499	0.580	0.420	0.087	0.434	0.487	0.639	0.369	0.884
rs2307807	0.472	0.528	0.048	0.562	0.498	0.587	0.374	1.141
rs56053760	0.510	0.490	0.640	0.486	0.500	0.631	0.375	0.973
rs33955557	0.530	0.470	0.677	0.486	0.498	0.630	0.374	0.973
rs59306401	0.540	0.460	0.310	0.530	0.497	0.606	0.373	1.064
rs139530962	0.520	0.480	0.663	0.514	0.499	0.617	0.375	1.029
rs10544053	0.414	0.586	0.453	0.510	0.485	0.605	0.368	1.020
rs35615387	0.566	0.434	0.842	0.486	0.491	0.623	0.371	0.973
rs71843136	0.448	0.552	0.940	0.498	0.495	0.621	0.372	0.996
rs34339565	0.582	0.418	0.479	0.510	0.487	0.607	0.368	1.020
rs61149315	0.534	0.466	0.172	0.542	0.498	0.599	0.374	1.091
rs11471707	0.643	0.357	0.287	0.426	0.459	0.613	0.354	0.872
TDP	0.999 999 999 999 999 999 999 999 999 428 18

Table 2

Table 3

Table 4

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rs#	PE_duo	PE_trio	rs#	PE_duo	PE_trio	rs#	PE_duo	PE_trio
rs56113354	0.125	0.281	rs146109101	0.124	0.281	rs34399561	0.118	0.277
rs66493016	0.115	0.275	rs151142037	0.125	0.281	rs10667259	0.125	0.281
rs34947838	0.116	0.276	rs59258861	0.119	0.277	rs139101426	0.125	0.281
rs10562732	0.124	0.280	rs4053254	0.125	0.281	rs3061475	0.121	0.279
rs10555133	0.123	0.280	rs145041883	0.110	0.271	rs200055056	0.103	0.267
rs3028599	0.113	0.274	rs56012194	0.118	0.277	rs34564973	0.121	0.279
rs34105738	0.123	0.280	rs3074767	0.123	0.280	rs144581522	0.122	0.279
rs10541877	0.121	0.279	rs36119043	0.119	0.278	rs10656522	0.115	0.275
rs3030108	0.116	0.276	rs34812419	0.117	0.276	rs10623704	0.117	0.276
rs10535391	0.124	0.281	rs144650377	0.125	0.281	rs58303500	0.120	0.278
rs142380122	0.110	0.272	rs33928328	0.125	0.281	rs71102499	0.119	0.277
rs5849187	0.123	0.280	rs4009127	0.121	0.278	rs2307807	0.124	0.281
rs59715790	0.107	0.270	rs372779701	0.124	0.281	rs56053760	0.125	0.281
rs139940865	0.123	0.280	rs79444593	0.016	0.142	rs33955557	0.124	0.281
rs35052276	0.102	0.266	rs56110100	0.125	0.281	rs59306401	0.123	0.280
rs10562881	0.122	0.279	rs142281120	0.125	0.281	rs139530962	0.125	0.281
rs59027185	0.105	0.268	rs34822234	0.107	0.270	rs10544053	0.118	0.277
rs35908330	0.121	0.279	rs367897009	0.125	0.281	rs35615387	0.121	0.279
rs70954609	0.125	0.281	rs145635184	0.125	0.281	rs71843136	0.122	0.280
rs147779273	0.125	0.281	rs6143946	0.124	0.280	rs34339565	0.118	0.277
rs35829610	0.084	0.251	rs76989317	0.125	0.281	rs61149315	0.124	0.281
rs60570384	0.107	0.270	rs34825333	0.114	0.274	rs11471707	0.105	0.268
CPE_duo	0.999 739
CPE_trio	0.999 999 999 417

体系	TDP	CPE_(trio)
66-plex InDels	0.999 999 999 999 999 999 999 999 999 428 18	0.999 999 999 417
Investigator^® DIPplex^[19]	0.999 999 926 31	0.997 806 392
AGCU InDel 50^[2]	0.999 999 999 999 999 999 8	0.999 732 16
DNA Typer 21^™[20]	0.999 999 999 999 999 999 999 998 85	0.999 999 996

Genetic polymorphisms of 66 InDel loci in the Chinese Han population

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