利用二代测序数据判定SNP基因型

发布时间：2018-06-20 11:27

  本文选题：单核苷酸多态性(SNP) + 二代测序　； 参考：《东华大学学报(自然科学版)》2017年03期

【摘要】：通过将二代测序数据与连接酶检测反应(ligase detection reaction,LDR)对单核苷酸多态性(single nucleotide polymorphism,SNP)基因分型的结果进行比对,确定二代测序数据判定SNP基因型的经验性阈值.利用多重聚合酶链式反应(multiplex polymerase chain reaction,multiplex PCR)对91个样本进行19个SNP位点的扩增,扩增的产物混匀纯化后在Ion torrent PGM仪器上进行二代测序.利用LDR技术对相应的SNP位点进行检测,将其分型结果作为二代测序数据判定SNP基因型的标准,确定了二代测序数据判定SNP基因型的阈值:测序深度≥6X,等位基因比率在15%~85%的位点为杂合子,在范围之外的为纯合子,该阈值准确度达到99.6%;针对等位基因频率分布在阈值边缘的数据,结合聚类分析可将正确率提升至100%.研究结果为利用二代测序数据判定SNP基因型提供了一个准确、快捷和经验性的阈值与方案.
[Abstract]:The results of single nucleotide polymorphisms single nucleotide polymorphismSNPs genotyping were compared with ligase detection reactionation (LDRs) of the second generation sequencing data, and the empirical threshold for determining the genotypes of SNPs was determined by sequencing data of the second generation. Nineteen SNPs of 91 samples were amplified by multiplex polymerase chain reaction multiplex PCR. The amplified products were mixed and purified and sequenced by second generation on Ion torrent PGM instrument. The corresponding SNP loci were detected by using LDR technique, and the typing results were used as the criteria for judging the SNP genotypes by the second-generation sequencing data. The threshold for determining SNP genotypes by second-generation sequencing data was determined: the sequencing depth 鈮，

本文编号：2044103