EA-YPredictor:基于Y-STR数据的家系特异性单倍群归属判别分析软件

目的Y染色体为男性所特有,其遗传标记蕴含着丰富的生物地理信息,故可溯源家系,在嫌疑人排查和追踪中发挥作用。Y-STR突变率较高,而Y-SNP突变率极低,几乎不会发生回复突变,所以后代男性群体携带祖先特有的Y-SNP。本研究期望通过现在我国Y库建设中通用的17个Y-STR的单倍型数据预测Y-SNP单倍群细支。方法基于前期观察,选取千人基因组计划III期中的513例东亚人群(中国及周边区域)作为基础数据集,在Java平台和Microsoft Excel软件框架下,以遗传距离计算和Y染色体进化树构建手段相联合研发Y-STR数据的家系特异性单倍群归属判别分析软件:EA-YPredictor。结果本研究揭示了15个单倍群大支下的核心单倍型。通过随机选取70个公开数据库样本,EA-YPredictor软件预测准确性达到92.8%(95%置信区间:[84.1%,97.6%])。结论在Y-SNP复合扩增检测尚无定论的情况下,本软件可基于二代测序样本对Y-STR数据库样本进行单倍群细支的准确预测,能适用于辅助家系单倍群判断。随着测序技术的不断换代和优化,更多高通量的Y-STR和Y-SNP数据补充将会使本软件进一步优化。此外,本软件对于Y数据库中Y-SNP遗传标记的筛查建库有一定指向作用。

EA-YPredictor:One New Software Developed to Predict Pedigree Haplogroup Based on Y-STR Haplotypes

Y chromosome,male specifi c,carres the genetic markers that could indicate the bio-geographic information of unknown male individuals,therefore playing vital and unique roles in pedigree searching and individuals tracking.Y-SNPs,the genetic markers hardly occurring of reverse mutation,harbor extreme low mutation rate compared to Y-STRs.Thus,male individuals of the same lineages always carry the specifi c Y-SNPs of their identical ancestors.However,Y-SNP typing is time-and cost-consuming,making it not an ideal tool for investigation.To target suspects’pedigree for investigation purpose,Y-SNP haplogroups were here tentatively predicted from the current 17 Y-STR haplotypes that are commonly used for Y-database construction.With re-evaluation of previous research results and analysis of the open East-Asian datasets from 1000-Genome Project(Phase III),one new Y-STR-based pedigree-specific haplogroup prediction software,EAYPredictor,was developed through calculation of genetic distance and Y chromosomal phylogenetic tree reconstruction,hence successfully having screened the 15 Y-SNP major haplogroups out from the core 17 Y-STR haplotypes on the adaptable Java platform or Microsoft Excel formulation.Randomly selected of 70 new samples,EA-YPredictor was tested of its prediction accuracy(92.8%,95%CI:[84.1%,97.6%]),revealing the exact Y haplogroup affi liation to the males of East Asian ancestry,thereby demonstrating its validity to predict the Y-SNP haplogroup of samples in existing Y chromosome database.Following the next-generation sequencing technology to confirm the location and annotation of more Y-STRs and Y-SNPs,EAYPredictor will be defi nitely optimized further so that more indications would be provided on screening which set of Y-SNP markers from Y chromosome databases.