法庭科学核心STR基因座的序列特征

doi:10.16288/j.yczz.25-021

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Hereditas(Beijing) ›› 2025, Vol. 47 ›› Issue (11): 1214-1230.doi: 10.16288/j.yczz.25-021

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Sequence features of forensic core short tandem repeat loci

Lei Miao¹^,²(), Kelai Kang¹(), Chi Zhang¹, Shuang Liu¹, Ruilian Jiao¹, Li Yuan²(), Le Wang¹()

1. Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
2. Collaborative Innovation Center of Judicial Civilization, Key Laboratory of Evidence Science, Ministry of Education, China University of Political Science and Law, Beijing 100088, China

Received:2025-03-15 Revised:2025-05-22 Online:2025-05-23 Published:2025-05-23
Contact: Li Yuan, Le Wang E-mail:947676188@qq.com;kang_kl@yeah.net;yuanliwcy@126.com;wangle_02@163.com
Supported by:
National Key R&D Program of China(2022YFC3341001);Ministry of Public Security of China(2023JC15);Institute of Forensic Science, Ministry of Public Security of China(2024JB027);Institute of Forensic Science, Ministry of Public Security of China(2024JB044);Institute of Forensic Science, Ministry of Public Security of China(2024JB046)

Abstract

Abstract:

Short tandem repeat (STR) is a significant genetic marker for the identification of forensic DNA. DNA databases worldwide, including those in China, are established based on STR markers. Length- and sequence-based polymorphism are two features of STR markers. Sequence-based polymorphism includes polymorphisms in both repeat and flanking regions. Traditional capillary electrophoresis-based STR genotyping method can only profile length-based genotypes. However, a deep understanding of the sequence polymorphism of core STR loci is crucial for primer design and DNA identification. Firstly, single nucleotide polymorphisms and insertions/deletions in STR primer binding regions may reduce the affinity between primers and DNA templates, leading to allele dropout or poor interlocus balance, thereby impacting the accuracy of DNA identification. Secondly, sequence-based polymorphism can be unveiled by next-generation sequencing technology, which could significantly enhance the detectable polymorphic information of core STR loci and improve the efficiency of individual identification and kinship analysis. Thirdly, different populations exhibit distinct STR sequence characteristics. Over the past decade, studies on sequence-based polymorphisms of STR loci have increased alongside the application of next-generation sequencing technology, and sequence-based polymorphisms from multiple populations were reported. However, previously studied populations and data were scattered, and different formats of repeat region sequences were used in various studies. These limitations result in the absence of a systematic summary and analysis of sequence polymorphism for core STR loci, hindering its further application in forensic practices. A comprehensive understanding of core STR loci sequence characteristics is crucial for individual identification from trace DNA, deconvolution of mixed samples, and determination of mutation origins in paternity testing. In this review, we focus on 19 autosomal core STRs and systematically review the sequence polymorphisms of these loci based on population data reported in the literature. We summarize variations in repeat regions, analyze variation patterns, present high-frequency variations in flanking regions within the Chinese population, and discuss potential challenges encountered in STR sequence analyses, with the aim to provide a reference for the analyses and application of STR sequence, the identification of rare alleles in criminal case testing, and the development of STR genotyping panel.

Key words: forensic genetics, autosomal chromosome, short tandem repeat, sequence-based polymorphism

Lei Miao, Kelai Kang, Chi Zhang, Shuang Liu, Ruilian Jiao, Li Yuan, Le Wang. Sequence features of forensic core short tandem repeat loci[J]. Hereditas(Beijing), 2025, 47(11): 1214-1230.

Figures/Tables 6

Fig. 1

Table 1

Table 2

Table 3

Table 4

High-frequency variations on flanking regions (within 200 bp of the repeat regions) of 19 class A STR loci among the Chinese population (f≥0.01)"

基因座	在GRCh38上的位置	相对重复区的位置	dbSNP数据库中Rs编号	变异类型	突变型在3个中国人群数据库中的频率
TPOX	Chr.2:1489832	+148 bp	rs13413321	G>T	0.5025^[53]、0.5164^[54]、0.5219^[55]
D5S818	Chr.5:123775552	-4 bp	rs73801920	C>A	0.048^[55]
	Chr.5:123775612	+13 bp	rs25768	A>G	0.943^[53]、0.935^[54]、0.930^[55]
	Chr.5:123775724	+125 bp	rs3909331	T>C	0.058^[53]、0.036^[54]、0.054^[55]
D6S1043	Chr.6:91740418	+146 bp	rs2325399	G>C	0.4256^[53]、0.4308^[54]、0.4335^[55]
D7S820	Chr.7:84160110	-116 bp	rs59186128	C>T	0.026^[53]、0.023^[54]、0.025^[55]
	Chr.7:84160161	-65 bp	rs7786079	A>C	0.0431^[53]、0.041^[54]、0.044^[55]
	Chr.7:84160204	-22 bp	rs7789995	T>A	0.944^[54]、0.906^[55]
	Chr.7:84160286	+9 bp	rs16887642	G>A	0.182^[54]、0.174^[55]
TH01	Chr.11:2171219	+104 bp	rs369097987	C>T	0.017^[54]、0.032^[55]
D13S317	Chr.13:82148069	+1 bp	rs9546005	A>T	0.186^[55]
	Chr.13:82148073	+5 bp	rs202043589	A>T	0.036^[54]、0.044^[55]
	Chr.13:82148183	+115 bp	rs9531308	A>C	0.485^[53]、0.511^[54]、0.517^[55]
Penta E	Chr.15:96831162	+123 bp	rs8036258	C>T	0.948^[53]、0.949^[54]、0.948^[55]
D16S539	Chr.16:86352607	-95 bp	rs1728369	A>C	0.244^[53]、0.236^[54]、0.237^[55]
D16S539	Chr.16:86352761	+16 bp	rs11642858	A>C	0.410^[53]、0.417^[54]、0.421^[55]
D2S1338	Chr.2:218014824	-35 bp	rs6736691	C>A	0.0894^[54]、0.1042^[55]
D2S1338	Chr.2:218015082	+132 bp	rs72951992	T>G	0.4081^[53]、0.3970^[54]、0.3988^[55]
vWA	Chr.12:5983882	-95 bp	rs216870	T>A	0.6820^[54]、0.6754^[55]
	Chr.12:5983970	-7 bp	rs75219269	A>G	0.2449^[54]、0.2428^[55]
	Chr.12:5984116	+72 bp	rs11063969	A>T	0.2638^[53]、0.2300^[54]、0.2434^[55]
	Chr.12:5984121	+77 bp	rs11063970	C>T	0.2641^[53]、0.2300^[54]、0.2434^[55]
	Chr.12:5984134	+90 bp	rs11063971	T>C	0.2638^[53]、0.2303^[54]、0.2434^[55]
D12S391	Chr.12:12296827	-193 bp	rs7962284	T>C	0.2938^[53]、0.2687^[54]、0.2622^[55]

Table 4

Fig. 2

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基因座	中国^[3]	ENFSI (1999)/ 国际刑警组织^[9]	ENFSI (2009)^[10]	德国^[2]	美国(1997)^[11]	美国(2017)^[13]
D1S1656			√			√
TPOX	√				√	√
D2S441			√			√
D2S1338	√					√
D3S1358	√	√	√	√	√	√
FGA	√	√	√	√	√	√
D5S818	√				√	√
CSF1PO	√				√	√
D6S1043	√
SE33				√
D7S820	√				√	√
D8S1179	√	√	√	√	√	√
D10S1248			√			√
TH01	√	√	√	√	√	√
vWA	√	√	√	√	√	√
D12S391	√		√			√
D13S317	√				√	√
Penta E	√
D16S539	√				√	√
D18S51	√	√	√	√	√	√
D19S433	√					√
D21S11	√	√	√	√	√	√
Penta D	√
D22S1045			√			√

基因座	染色体	GRCh38上物理位置	重复结构^[15]	常见的重复区序列^[6,14,16~52]
TPOX^#	2	1489653~1489684	[AATG]_a	[AATG]_4~14
D5S818^#	5	123775556~123775599	[ATCT]_a	[ATCT]_6~16
CSF1PO^#	5	150076324~150076375	[ATCT]_a	[ATCT]_5~16
D6S1043^#	6	91740225~91740272	[ATCT]_a	(1)[ATCT]_8~20(2)[ATCT]_3~6ATAG[ATCT]_8~17
D7S820^#	7	84160226~84160277	[TATC]_a	[TATC]_6~15
TH01^#	11	2171088~2171115	[AATG]_a	[AATG]_3~12
D13S317^#	13	82148025~82148068	[TATC]_a	[TATC]_5~16
Penta E^#	15	96831015~96831039	[TCTTT]_a	[TCTTT]_5~32
D16S539^#	16	86352702~86352745	[GATA]_a	[GATA]_5~16
D18S51^#	18	63281667~63281738	[AGAA]_a	[AGAA]_8~40
Penta D^#	21	43636205~43636269	[AAAGA]_a	[AAAGA]_5~19
D2S1338^*	2	218014859~218014950	[GGAA]_a[GGCA]_b	[GGAA]_5~19[GGCA]_2~9
D3S1358^*	3	45540739~45540802	[TCTA]_a[TCTG]_b[TCTA]_c	[TCTA][TCTG]_1~4[TCTA]_7~19
D8S1179^*	8	124894865~124894916	[TCTA]_a[TCTG]_b[TCTA]_c	(1)[TCTA]_7~16 (2)[TCTA]_1~2[TCTG]_1~3[TCTA]_7~16
vWA^*	12	5983977~5984044	[TAGA]_a[CAGA]_bTAGA	[TAGA]_7~17[CAGA]_3~6TAGA
D12S391^*	12	12297020~12297095	[AGAT]_a[AGAC]_b[AGAT]_c	(1)[AGAT]_6~18[AGAC]_4~13[AGAT] (2)[AGAT]_8~18[AGAC]_6~13
FGA^†	4	154587736~154587823	[GGAA]_aGGAG[AAAG]_bAGAAAAAA[GAAA]_c	[GGAA]₂GGAG[AAAG]_5~21AGAAAAAA[GAAA]₃
D19S433^†	19	29926235~29926298	[CCTT]_aCCTA[CCTT]_bCTTT[CCTT]_c	[CCTT]_2~16CCTA[CCTT]CTTT[CCTT]
D21S11^†	21	19181973~19182099	[TCTA]_a[TCTG]_b[TCTA]_cTA[TCTA]_dTCA[TCTA]_eTCCATA[TCTA]_f	[TCTA]_4~13[TCTG]_3~8[TCTA]_2~3TA[TCTA]_2~3TCA[TCTA]₂TCCATA[TCTA]_6~15

基因座	重复区单碱基替换^[6,14,16~52]	重复区内插入/缺失^[6,14,16~52]
TPOX	[AATG]> TATG/AAT T	—
D5S818	[ATCT]> GTCT/A GCT/AT GT/AT TT	A插入
CSF1PO	[ATCT]> GTCT/ CTCT/A CCT/AT AT	A/ATC插入
D6S1043	[ATCT]>AT AT/AT GT	C/AT/ATC/ACT插入
D7S820	[TATC]> CATC/T GTC/TA CC/TAT T	T/TAC插入
TH01	[AATG]>A GTG/AA CG/AAT T/AAT A	ATG插入
D13S317	[TATC]> AATC/T GTC/TA AC/TAT T	ATC/AATCAATCATCTATCTATCTTTCTGTCTGTCTTTTTGGGCTGCCTA插入
Penta E	[TCTTT]> CCTTT/T ATTT/TC CTT	TTTT/CTTT/TCTT插入
D16S539	[GATA]> TATA/ CATA/ AATA/G GTA/GA CA/GAT T	GAT插入
D18S51	[AGAA]> GGAA/A TAA/AG CA/AGA T	AG/AAAGAGAGAGGAA插入
Penta D	[AAAGA]>A GAGA/AA CGA/AAA TA/AAAG G	AAAG/AAGA插入
D2S1338	[GGAA]> AGAA/G TAA/G AAA/GGA C([GGAA]_a) [GGCA]>G ACA/GG AA([GGCA]_b)	GAA插入([GGAA]_a)
D3S1358	1. [TCTA]>TCT G([TCTA]_a)2. [TCTA]>T GTA/TCT G([TCTA]_c)	A/TC插入
D8S1179	[TCTA]> CCTA/T GTA/TC CA([TCTA]_c)	T插入([TCTA]_c)
vWA	1. [TAGA]> CAGA/T GGA/TA AA/TAG G([TAGA]_a) 2. [CAGA]> TAGA/C TGA([CAGA]_b) 3. TAGA> CAGA/ GAGA/TAG T(非重复序列TAGA)	T/TA/TGA插入([TAGA]_a)
D12S391	1. [AGAT]>A AAT/AG GT/AGA C([AGAT]_a) 2. [AGAC]> GGAC/AG GC/AGA A([AGAC]_b)	T/AT/GAT插入([AGAT]_a)
FGA	1. GGAG>G AAG(非重复序列GGAG) 2. [AAAG]>A GAG/AA GG/AAA C([AAAG]_b) 3. AGAAAAAA> GGAAAAAA(非重复序列AGAAAAAA) 4. [GAAA]> AAAA/G CAA([GAAA]_c)	1. A/AG/AAG插入([AAAG]_b) 2. AA/AG插入、AG缺失(非重复序列AGAAAAAA)
D19S433	1. [CCTT]> TCTT/C TTT/C ATT/CC CT([CCTT]_a) 2. CCTA>CCT G/CCT T(非重复序列CCTA)	1. T/CTT/TTTTT插入([CCTT]_a) 2. CT缺失(非重复序列CTTT)
D21S11	1. [TCTA]>T TTA/T ATA([TCTA]_a) 2. [TCTG]>TC GG/TC AG([TCTG]_b) 3. [TCTA]>T TTA/T GTA/TCT G([TCTA]_d) 4. [TCTA]>TC GA([TCTA]_e) 5. [TCTA]>T GTA([TCTA]_f)	A/TA/TCA插入([TCTA]_f)

Sequence features of forensic core short tandem repeat loci

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