转录组分析在血液样本时间和供体特征刻画中的应用研究

doi:10.16288/j.yczz.22-293

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Hereditas(Beijing) ›› 2023, Vol. 45 ›› Issue (1): 52-66.doi: 10.16288/j.yczz.22-293

• Research Article • Previous Articles Next Articles

Application of transcriptome in time analysis and donor characterization in blood samples

Jin Zhang^1,²(), Kaihui Liu², Ying Zhang², Jinping Hao², Guangfeng Zhang², Xiaoyu Xu², Jingjing Chang², Xingpeng Liu³, Xueying Yang²(), Jian Ye^1,²()

1. People's Public Security University of China, Beijing 100038, China
2. Institute of Forensic Science Ministry of Public Security, Beijing 100038, China
3. Ruijin Public Security Bureau, Ruijin 342500, China

Received:2022-10-31 Revised:2022-11-29 Online:2023-01-20 Published:2022-12-09
Contact: Yang Xueying,Ye Jian E-mail:zhangjin1101@126.com;yxystyhhp@163.com;yejian77@126.com
Supported by:
the Science and Technology Development Programs of Ministry of Public Security P.R.C(2017JSYJC22);the Public Security Scientific and Technological Achievements Promotion and Guidance Programs of Ministry of Public Security P.R.C(2020TGYDBGAES25);the Basic research Funds for Public Welfare Research Institutes of the Central Government(2020JB008)

Abstract

Abstract:

As an effective supplement to the current forensic DNA typing and one of the research hotpots in forensic science, the in-depth mining and characterization of biological evidence can provide rich and reliable clues for case investigation. In this study, the time-dependent variations of transcriptome were confirmed in in vitro blood samples within 0-168 days and a random forest model was established to realize the classification of blood samples with different TSD (time since deposition). Meanwhile, significant differences were observed in the transcripts of blood samples with different smoking habits and genders within a certain time period. HLA-DRB1, HLA-DQB1 and HLA-DQA2 were identified as markers for smoking habit identification, while the transcripts for RPS4Y1 and EIF1AY from the non-recombining region of the Y chromosome (NRY) were identified as markers for male sex identification. Thus, this study provides a theoretical foundation and experimental strategy for establishing a transcriptome-based method for characterizing blood sample retention time and donor characteristics in the field of forensic investigation.

Key words: forensic science, blood, time since deposition, smoking habit, gender

Jin Zhang, Kaihui Liu, Ying Zhang, Jinping Hao, Guangfeng Zhang, Xiaoyu Xu, Jingjing Chang, Xingpeng Liu, Xueying Yang, Jian Ye. Application of transcriptome in time analysis and donor characterization in blood samples[J]. Hereditas(Beijing), 2023, 45(1): 52-66.

Figures/Tables 13

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References 57

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物证特征	分组	样本数量	离体时间D (天)	取样时间点
吸烟	吸烟组(smoker)	56	0≤D≤168	D0、D0.5、D1、D2、D4、D7、D14、D21、D28、D56、D84、D112、D140、D168
吸烟	对照组(control)	70	0≤D≤168	D0、D0.5、D1、D2、D4、D7、D14、D21、D28、D56、D84、D112、D140、D168
性别	男性组(male)	140	0≤D≤168	D0、D0.5、D1、D2、D4、D7、D14、D21、D28、D56、D84、D112、D140、D168
性别	女性组(female)	138	0≤D≤168	D0、D0.5、D1、D2、D4、D7、D14、D21、D28、D56、D84、D112、D140、D168
离体时间	D0~2组	80	0≤D≤2	D0、D0.5、D1、D2
	D4~14组	58	2<D≤14	D4、D7、D14
	D21~56组	60	14<D≤56	D21、D28、D56
	D84~168组	80	56<D≤168	D84、D112、D140、D168

分组	Raw reads (Mean ± SD)	Clean reads (Mean ± SD)	错误率 (%) (Mean ± SD)	Q20 (%) (Mean ± SD)	Q30 (%) (Mean ± SD)	GC含量 (%) (Mean ± SD)
吸烟组 (n = 56)	57928613.071±11306086.212	56796377.250±11069341.242	0.022 ± 0.004	98.226 ± 0.254	94.867 ± 0.574	56.115 ± 1.985
对照组 (n = 70)	59559976.829±12657910.627	58188050.543±12252512.979	0.021 ± 0.003	98.272 ± 0.229	94.965 ± 0.508	57.314 ± 2.118
男性组 (n = 140)	58822285.871±12184267.688	57535769.014±11852506.630	0.021 ± 0.003	98.258 ± 0.239	94.933 ± 0.534	56.736 ± 2.117
女性组 (n = 138)	56861638.043±13407561.979	55739764.043±13003300.979	0.022 ± 0.004	98.168 ± 0.272	94.716 ± 0.581	55.667 ± 2.543
D0~2组 (n = 80)	69324109.250±9861979.513	67804445.700±9697013.881	0.021 ± 0.003	98.220 ± 0.190	94.877 ± 0.437	53.855 ± 1.214
D4~14组 (n = 58)	64783625.207±10637521.112	63346337.621±10173427.925	0.022 ± 0.004	98.204 ± 0.291	94.837 ± 0.672	56.134 ± 1.580
D21~56组 (n = 60)	50664396.800±7061084.292	49725835.000±6685845.152	0.021 ± 0.002	98.321 ± 0.193	95.032 ± 0.447	59.043 ± 1.099
D84~168组 (n = 80)	46734790.775±5268303.017	45813772.025±5235594.729	0.023 ± 0.005	98.132 ± 0.307	94.610 ± 0.612	56.480 ± 2.041

上调转录本			下调转录本
序号	基因 ID	基因名称	序号	基因 ID	基因名称
1	ENSG00000196126	HLA-DRB1	1	ENSG00000237541	HLA-DQA2
2	ENSG00000019169	MARCO	2	ENSG00000276345	AC004556.1
3	ENSG00000196735	HLA-DQA1	3	ENSG00000284690	CD300H
4	ENSG00000103355	PRSS33	4	ENSG00000060709	RIMBP2
5	ENSG00000105205	CLC	5	ENSG00000174171	-
6	ENSG00000276085	CCL3L1	6	ENSG00000229391	-
7	ENSG00000214026	MRPL23	7	ENSG00000211821	TRDV2
8	ENSG00000179344	HLA-DQB1	8	ENSG00000204345	CD300LD
9	ENSG00000189068	VSTM1	9	ENSG00000211638	IGLV8-61
10	ENSG00000105366	SIGLEC8	10	ENSG00000022556	NLRP2
11	ENSG00000172322	CLEC12A	11	ENSG00000211666	IGLV2-14
12	ENSG00000205927	OLIG2
13	ENSG00000277632	CCL3
14	ENSG00000092067	CEBPE

序号	基因 ID	基因名称
1	ENSG00000114374	USP9Y
2	ENSG00000129824	RPS4Y1
3	ENSG00000183878	UTY
4	ENSG00000198692	EIF1AY
5	ENSG00000067646	ZFY
6	ENSG00000154620	TMSB4Y
7	ENSG00000280969	RPS4Y2

序号	基因 ID	基因名称	MDA
1	ENSG00000078747	ITCH	2.1454
2	ENSG00000128585	MKLN1	2.1290
3	ENSG00000215421	ZNF407	2.1264
4	ENSG00000126945	HNRNPH2	2.0812
5	ENSG00000143751	SDE2	2.0780
6	ENSG00000127954	STEAP4	2.0617
7	ENSG00000113580	NR3C1	1.9407
8	ENSG00000112096	SOD2	1.9382
9	ENSG00000198105	ZNF248	1.9331
10	ENSG00000125304	TM9SF2	1.9190
11	ENSG00000103994	ZNF106	1.9133

Application of transcriptome in time analysis and donor characterization in blood samples

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性别特征刻画			吸烟特征刻画
判别标志	男性	女性	判别标志	吸烟	不吸烟
RPS4Y1	FPKM≥1	FPKM<1	HLA-DRB1/ACTB	RER_HLA-DRB1_/_ACTB≥0.04099	RER_HLA-DRB1_/_ACTB≤0.02322
EIF1AY	FPKM≥1	FPKM<1	HLA-DRB1/GAPDH	RER_HLA-DRB1_/_GAPDH≥0.67420	RER_HLA-DRB1_/_GAPDH≤0.3564
			HLA-DQB1/ACTB	RER _HLA-DQB1_/_ACTB≥0.00651	RER _HLA-DQB1_/_ACTB≤0.00269
			HLA-DQA2/ACTB	RER _HLA-DQA2_/_ACTB≤0.00026	RER _HLA-DQA2_/_ACTB≥0.00193
			HLA-DQA2/GAPDH	RER_HLA-DQA2_/_GAPDH≤0.00397	RER_HLA-DQA2_/_GAPDH≥0.02989

时间信息/供体特征	判别标志	交叉验证组别	随机抽取样本数	样本判断正确率	平均正确率
离体时间	-	D0~2	26	92.31%	91.03%
		D4~14	14	85.71%
		D21~56	13	76.92%
		D84~168	25	100%
吸烟习惯	HLA-DRB1/ACTB	1	13	92.31%	76.92%
		2	13	76.92%
		3	13	46.15%
		4	13	84.62%
		5	13	84.62%
	HLA-DRB1/GAPDH	1	13	69.23%	73.85%
		2	13	76.92%
		3	13	53.85%
		4	13	84.62%
		5	13	84.62%
	HLA-DQB1/ACTB	1	13	92.31%	72.31%
		2	13	61.54%
		3	13	61.54%
		4	13	76.92%
		5	13	69.23%
	HLA-DQA2/ACTB	1	13	69.23%	55.39%
		2	13	53.85%
		3	13	46.15%
		4	13	53.85%
		5	13	53.85%
	HLA-DQA2/GAPDH	1	13	69.23%	58.46%
		2	13	61.54%
		3	13	46.15%
		4	13	69.23%
		5	13	46.15%
性别	RPS4Y1	1	28	100%	100%
		2	28	100%
		3	28	100%
		4	28	100%
		5	28	100%
	EIF1AY	1	28	100%	100%
		2	28	100%
		3	28	100%
		4	28	100%
		5	28	100%

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