Genome‐wide Screen for Individual Identification SNPs (IISNPs) and the Confirmation of Six of Them in Han Chinese with Pyrosequencing Technology*

Abstract: Single nucleotide polymorphisms (SNPs) offer promise to forensic DNA analysts, but it remains uncertain whether a panel of individual identification SNPs can be as informative as the Combined DNA Index System short tandem repeats. Based on the highly accurate and publicly available HapMap SNP database (r21a) and a minor allele frequency cutoff of ≥0.45, we completed a genome‐wide screen through 3,905,819 SNPs with internally modified computer programs and identified 1439 SNPs with high heterozygosity and low F_st values among four populations (Utah Caucasian, Han Chinese, Tokyo Japanese, and Nigerian Yoruba). Using pyrosequencing technology, we studied six loci in a relatively large group of samples to determine whether these loci were as informative as the HapMap data suggest. These SNPs performed as expected in the Han Chinese in terms of heterozygosity and F_st. The 1439 identified SNPs should provide a comprehensive and reliable set of loci for identity and relationship testing.     

华东汉族人群乙醇代谢酶相关SNP位点的多态性

目的对ADH2、ADH3、ALDH2和CYP2E1基因的40个SNP位点进行群体遗传学分析,得到多态性信息。方法利用PCR和质谱技术平台对SNP位点进行分型检测,通过对中国华东地区汉族人群199个无关个体的调查,统计分析40个SNP位点的等位基因分布频率。结果 40个SNP位点中,rs698、rs2241894（ADH3基因座）,rs13306164、rs671（ALDH2基因座）和rs28371746、rs2515641（CYP2E1基因座）的小等位基因分布频率（MAF）均大于1%,其它SNP位点的MAF均小于1%。结论 ADH2、ADH3、ALDH2和CYP2E1基因的40个SNP位点中,6个位点（rs698、rs2241894、rs13306164、rs671、rs28371746和rs2515641）在华东汉族人群中具有多态性。     

Testing the performance of mtSNP minisequencing in forensic samples

There is a growing interest among forensic geneticists in developing efficient protocols for genotyping coding region mitochondrial DNA (mtDNA) SNPs (mtSNPs). Minisequencing is becoming a popular method for SNP genotyping, but it is still used by few forensic laboratories. In part, this is due to the lack of studies testing its efficiency and reproducibility when applied to real and complex forensic samples. Here we tested a minisequencing design that consists of 71 mtSNPs (in three multiplexes) that are diagnostic of known branches of the R0 phylogeny, in real forensic samples, including degraded bones and teeth, hair shafts, and serial dilutions. The fact that amplicons are short coupled with the natural efficiency of the minisequencing technique allow these assays to perform well with all the samples tested either degraded and/or those containing low DNA amount. We did not observe phylogenetic inconsistencies in the 71 mtSNP haplotypes generated, indicating that the technique is robust against potential artefacts that could arise from unintended contamination and/or spurious amplification of nuclear mtDNA pseudogenes (NUMTs).     

Scotland’s Faltering Green Industrial Revolution

Renewable energy has long been central to SNP policy making and Scottish independence. During the 2014 referendum, green electricity generation was presented as a means for Scotland to achieve ‘reindustrialisation’. Despite a world‐leading transition in electricity supply, the Scottish government has struggled to develop renewables manufacturing. Scotland’s largest offshore engineering company, BiFab, entered administration in 2020. This article explains the faltering of Scotland’s green industrial revolution. First, it assesses renewables’ privileged place in SNP perspectives, underlining its deep roots in North Sea oil and criticisms of British governments’ mismanagement of offshore opportunities. Second, the failure of market‐led policy making to provide the anticipated industrial benefits from offshore wind developments is explained through the domineering role of foreign state‐owned enterprises and global supply chains in the UK’s renewables sector. The conclusion argues that older nationalist perspectives offer remedies, but these require a more active industrial policy that diverges from the current approach of the Scottish Government.     

Y染色体法医DNA检验策略

法医DNA检验在实际工作中发挥了重要作用,其中针对Y染色体进行的DNA检验,可以开展家系排查和辅助父系亲缘鉴定,为案件侦查提供重要线索。本文针对Y染色体DNA检验,讨论完整利用染色体具有的信息,制定整体检验策略,以期为相关研究和试剂盒开发研制提供参考。     

单核苷酸多态性及其检测方法

单核苷酸多态性(single nucleotide polymorphisms,SNPs),作为第三代遗传标记,已经广泛应用于基因作图、遗传性和遗传相关性疾病的诊断、群体遗传学、药学研究和法医学等领域。SNP的检测方法多种多样,本文简要介绍SNP的特点和几种检测方法。     

Y染色体3个SNP基因座及其单倍型的遗传多态性和群体差异

目的 探讨人类Y染色体3个SNP基因座及其单倍型的遗传多态性和群体差异。方法 应用PCR-RFLPs结合DNA序列分析技术,对140例来自中国藏族、日本、南非黑人及南非白人男性的Y染色体M4、M9和M122基因座的等位基因进行分析。结果 全部样品M4基因座的等位基因均为野生型M4A,未发现多态性。共检出3种单倍型,黑人个体均为野生型单倍型M4A/M9C/M122T。白人个体有8例单倍型为M4A/M9G/M122T,未检出等位基因M122C。日本及中国藏族群体以单倍型M4A/M9C/M122T为主,频率分别为0.50和0.65,未检出单倍型M4A/M9C/M122C,个人识别机率与父权排除率分别为0.6191和0.4994。单倍型频率分布在中国藏族和日本群体之间存在显著性差异(P<0.01)。结论 单倍型M4A/M9G/M122C为亚洲人特征,M9和M122基因座在中国藏族和日本群体中具有较高的遗传多态性,并显示出明显的人种和群体差异。     

特征表型信息SNP在法医学分析中的研究进展

以DNA为基础的STR和SNP遗传标记的检验,已广泛应用于各种个人识别、亲子鉴定和人口失踪案件。但现场DNA样本分型不能与相关个体匹配时,利用特征表型信息SNP则可能为侦查提供有价值线索。本文综述了近年来特征表型信息SNP在法医学应用中的研究进展,并简述其发展方向,旨在为相关研究和应用提供参考和借鉴。     

法医SNP复合检测体系的构建及应用

目的构建48-SNP位点复合检测体系,用于个体识别、性别鉴定、ABO基因分型。方法采集225份无关个体样本(血斑及口腔拭子),18份案例样本(不同组织及体液斑),选择43个常染色体位点、4个ABO基因位点和1个性别鉴定位点,根据单碱基延伸技术通过GenomeLabTMSNPstream基因分型系统进行SNP分型;并检测体系灵敏度、同一个体不同组织同一性及模拟腐败检材。结果 48-SNP体系分型结果与测序结果的一致性为100%,最小DNA检出量为0.25ng,不同组织来源样本检测同一性很好;利用该体系检测225名无关汉族个体,所有位点均符合Hardy-Weinberg平衡,整个系统的随机匹配概率为9.4×10-18,累积非父排除率(CEP)为0.999 788,累积个体识别率大于0.999 999 999 999 999 99。结论本文48-SNP体系能同时进行个体识别、ABO基因分型和性别鉴定,可以作为现有STR检验体系的补充。