适用于降解样本的201个遗传标记检测体系的构建和验证

doi:10.16288/j.yczz.23-253

遗传 ›› 2024, Vol. 46 ›› Issue (4): 306-318.doi: 10.16288/j.yczz.23-253

适用于降解样本的201个遗传标记检测体系的构建和验证

韩伟(), 张庆珍, 杨静(), 周喆()

军事科学院军事医学研究院生物信息中心，北京 100850

收稿日期:2023-12-05 修回日期:2024-01-30 出版日期:2024-04-20 发布日期:2024-01-31
通讯作者: 杨静,周喆 E-mail:651430459@qq.com;jingyang0511@163.com;zhouzhe@bmi.ac.cn
作者简介:韩伟，硕士研究生，专业方向：公共卫生。E-mail: 651430459@qq.com

A DNA typing panel of 201 genetic markers for degraded samples: development and validation

Wei Han(), Qingzhen Zhang, Jing Yang(), Zhe Zhou()

Bioinformatics Center of Academy of Military Medical Sciences, Beijing 100850, China

Received:2023-12-05 Revised:2024-01-30 Published:2024-04-20 Online:2024-01-31
Contact: Jing Yang, Zhe Zhou E-mail:651430459@qq.com;jingyang0511@163.com;zhouzhe@bmi.ac.cn

摘要/Abstract

摘要：

近年来，法医实践中复杂案件数量逐渐增多，需要联合使用短串联重复序列(short tandem repeat, STR)、单核苷酸多态性(single nucleotide polymorphisms, SNP)、插入缺失多态性(insertion/deletion polymorphism, InDel)、微单倍型(microhaplotype, MH)等不同类型的遗传标记，为案件提供更多的参考信息。本研究筛选了24个常染色体STR(autosomes STR, A-STR)、24个Y染色体STR(Y-STR)、110个A-SNP、24个Y-SNP、9个A-InDel、1个Y-InDel、8个MH和Amelogenin共201个遗传标记，建立二代测序检测体系HID_AM Panel v1.0。根据DNA 分析方法科学工作组(Scientific Working Group on DNA Analysis Methods，SWGDAM)的验证指南，对该体系的重复性、准确性、灵敏度、对降解样本的适用性、物种特异性、抗抑制性等指标进行评估。本体系分型结果与基于毛细管电泳方法检测的48个STR和Amelogenin结果完全一致，与ForenSeq™ DNA Signature Prep Kit重合的79个SNP分型结果完全一致；当DNA加入量不低于200 pg时可获得全部等位基因分型结果；当检测降解指数大于15.87的模拟降解样本时，检出成功率明显高于GlobalFiler^TM PCR扩增试剂盒；当体系内血红素浓度不高于40 µmol/L、靛蓝浓度不高于2 mmol/L、或腐殖酸浓度不高于15 ng/µL时，扩增无明显抑制；鸭、鼠、牛、兔、鸡的DNA特异性扩增较少；常规样本中STR检出率达99.74%，SNP、InDel、MH全部检出。综上所述，本研究建立的检测体系具有较高的准确性、灵敏度、物种特异性和抗抑制性，适用于降解样本的个体识别。

关键词: 二代测序, 多类型, 遗传标记, 降解样本

Abstract:

With the increasing number of complex forensic cases in recent years, it’s more important to combine the different types of genetic markers such as short tandem repeats (STRs), single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (InDels), and microhaplotypes (MHs) to provide more genetic information. In this study, we selected totally 201 genetic markers, including 24 autosomes STRs (A-STRs), 24 Y chromosome STRs (Y-STRs), 110 A-SNPs, 24 Y-SNPs, 9 A-InDels, 1 Y-InDel, 8 MHs, and Amelogenin to establish the HID_AM Panel v1.0, a Next-Generation Sequencing (NGS) detection system. According to the validation guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), the repeatability, accuracy, sensitivity, suitability for degraded samples, species specificity, and inhibitor resistance of this system were assessed. The typing results on 48 STRs and Amelogenin of this system were completely consistent with those obtained using capillary electrophoresis. This system accurately detected 79 SNPs as parallelly confirmed by a FGx sequencer with the ForenSeq™ DNA Signature Prep Kit. Complete allele typing results could be obtained with a DNA input of no less than 200 pg. The detection success rate of this system was significantly higher than that of the GlobalFiler™ kit when the degradation index of mock degraded sample was greater than 15.87. When the concentration of hematin in the amplification system was ≤40 µmol/L, indigo blue was ≤2 mmol/L, or humic acid was ≤15 ng/µL, amplification was not significantly inhibited. The system barely amplified the DNA extract from duck, mouse, cow, rabbit, and chick. The detection rate of STRs on routine samples of this panel is 99.74%, while all the SNPs, InDels, and MHs were successfully detected. In summary, we setup a NGS individual typing panel including 201 genetic markers with the high accuracy, sensitivity, species specificity, and inhibitors resistance, which is applicable for individual identification of degraded samples.

Key words: next generation sequencing, multiple types, genetic markers, degraded samples

韩伟, 张庆珍, 杨静, 周喆. 适用于降解样本的201个遗传标记检测体系的构建和验证[J]. 遗传, 2024, 46(4): 306-318.

Wei Han, Qingzhen Zhang, Jing Yang, Zhe Zhou. A DNA typing panel of 201 genetic markers for degraded samples: development and validation[J]. Hereditas(Beijing), 2024, 46(4): 306-318.

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样本名称	大片段(pg/μL)	小片段(pg/μL)	Y片段(pg/μL)	降解指数 DI	STR分型成功率(%)	SNP+InDel分型成功率(%)	MH分型成功率(%)	全部遗传标记分型成功率(%)
D1	0.44	0.80	1.32	1.84	98.51	99.11	100	98.97
D2	0.24	0.71	1.18	2.93	98.51	100	100	99.66
D3	0.14	0.70	1.03	4.84	97.01	99.11	100	98.63
D4	0.31	0.86	1.29	2.72	97.01	99.11	100	98.63
D5	0.07	0.69	0.94	10.45	95.52	98.22	100	97.6
D6	0.04	0.65	0.99	15.78	92.54	97.33	100	96.23
D7	0.02	0.40	0.74	16.66	97.01	100	100	99.32
D8	0.03	0.51	0.80	20.35	97.01	99.11	100	98.63
D9	0.01	0.41	0.69	37.61	97.01	98.67	100	98.29
D10	0.01	0.54	0.66	82.78	91.04	98.22	100	96.58
D11	0.00	0.49	0.62	401.02	83.58	95.56	87.5	92.12

样品名	分型错误STR	分型错误SNP	分型错误InDel	分型错误MH
血红素-空白	/	/	/	/
血红素-5 µmol/L	CSF1PO	/	/	/
血红素-10 µmol/L	CSF1PO 、D7S820、D9S1122、DYS437、DYS392、DYS448、DYS438	/	rs3032356	/
血红素-20 µmol/L	/	/	/	/
血红素-40 µmol/L	D17S974、D19S433、D3S1358、D7S820、DYS481、DYS19、DYS643、Y_GATA_H4、DYS389II	/	/	/
血红素-80 µmol/L	×	×	×	×
靛蓝-空白	/	/	/	/
靛蓝-2 mmol/L	D18S51、Penta D、FGA、DYS458、DYS518、DYS389II	rs1413212、rs2399332、rs717302、rs159606、rs12174864、rs1336071、rs826472、rs3780962、rs2107612、rs1295330、rs2096458、rs914165、rs747718394	rs35771136、rs2307805、rs16660	mh13KK-213
靛蓝-4 mmol/L	×	×	×	×
腐殖酸-空白	/	/	/	/
腐殖酸-1 ng/µL	/	/	/	/
腐殖酸-5 ng/µL	CSF1PO、D7S820、DYS393、DYS389I	rs1295330	/	/
腐殖酸-10 ng/µL	DYS389II	rs1295330	/	/
腐殖酸-15 ng/µL	D18S51、D21S11、Penta D、DYS518、DYS389II	rs1295330、rs2096458	/	/
腐殖酸-50 ng/µL	×	×	×	×

适用于降解样本的201个遗传标记检测体系的构建和验证

A DNA typing panel of 201 genetic markers for degraded samples: development and validation

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