Dissection of mitochondrial superhaplogroup H using coding region SNPs
Dissection of mitochondrial superhaplogroup H using coding region SNPs
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DOI：
10.1002/elps.200500772
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发表时间：
2006-07-01
期刊：
影响因子：
2.9
通讯作者：
Parson, Walther
中科院分区：
文献类型：
--
作者：
Brandstatter, Anita;Salas, Antonio;Parson, Walther
单倍型群H（hg H）包括迄今为止研究的西欧亚线粒体DNA（mtDNA）样品的约40-50%。为了提高这一单倍型群内的歧视，我们选择了45个编码区的SNP，允许归因于样本的主要系统发育分支的超级Hg HV（包括Hg H），特别是H亚系与更精细的分辨率比以前的研究。SNP选择使用最新的群体和法医遗传学文献进行，并通过完整或编码区基因组（> 430）和控制区序列的系统发育分析进行扩展。对hg H的发生进行了细致的研究，使我们观察到了hg H的各种各样但没有特征的亚支。选择的SNP在两个PCR多重反应中扩增，随后在三个单碱基延伸多重反应中靶向。共对2214份西欧亚人群进行了hg H特异位点2706和7028的筛选，其中859份为hg H，并进一步进行了亚单倍型群分型。我们总共观察到35个不同的单倍型亚群，其中33个亚群的频率低于5%。该检测可用作法医案例中的预筛选工具，用于快速区分不同的谱系（对于高容量犯罪案件非常有效）或作为歧视性检测，当通过控制区测序获得相同的hg H单倍型时。
Haplogroup H (hg H) includes about 40-50% of the West Eurasian mitochondrial DNA (mtDNA) samples investigated so far. In order to enhance discrimination within this haplogroup we selected 45 coding region SNPs that allow to ascribe samples to the main phylogenetic branches of super hg HV (that embraces hg H) and, in particular, to H sublineages with a much finer resolution than previous studies. SNP selection was carried out using the most up-to-date available literature on population and forensic genetics and extended by means of phylogenetic analysis of complete or coding region genomes (> 430) and control region sequences. A meticulous inspection of the H phylogeny led us to the observation of various but uncharacterized subclades of hg H. The selected SNPs were amplified in two PCR-multiplex reactions and subsequently targeted in three single-base extension multiplex reactions. A total of 2214 West Eurasian samples were screened for hg H specific loci 2706 and 7028, of which 859 fell in hg H and were further subjected to subhaplogroup typing. We observed 35 different subhaplogroups in total, 33 of which were found at frequencies below 5%. This assay can be used as a prescreening tool in forensic casework for rapid discrimination between divergent lineages (very effective for high-volume crime cases) or as discriminatory assay, when identical hg H haplotypes were obtained by control region sequencing.