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Scanning for Genomic Regions Subject to Selective Sweeps Using SNP-MaP Strategy
  • ISSN号:1672-0229
  • 期刊名称:Genomics Proteomics Bioinformatics
  • 时间:0
  • 页码:256-261
  • 语言:英文
  • 分类:Q75[生物学—分子生物学] S513[农业科学—作物学]
  • 作者机构:[1]Faculty of Basic Medical Science, Nanchang University, Nanchang 330006, China, [2]Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China, [3]The Institute of Translational Medicine, Nanchang University, Nanchang 330006, China, [4]Graduate University of Chinese Academy of Sciences, Beijing 100049, China
  • 相关基金:supported by the National Natural Science Foundation of China (No. 30871348 and 30700470); Educational Department of Jiangxi Province (No. GJJ10303); National Key Laboratory Specific Fund (No. 2060204)
  • 相关项目:正选择在人群分化及中国人特异遗传背景形成中作用的研究
中文摘要:

人口 genomic 途径,利用高产量的 genotyping,还是强大的扫描为的昂贵的方法选择扫。因为它是大规模单个 genotyping 的一种划算的选择,分享 DNA 策略广泛地为协会研究被使用了。这里,我们执行了 SNP 地图(单个核苷酸多型性 microarrays 并且分享) 使用的分析从欧亚大陆取样评估为选择在染色体宽的扫描分享策略的效率。由进行 allelotype 数据的模拟,我们首先证明有平均杂合现象(HET ) 的 boxplot 是一个有希望的方法检测强壮选择与分享错误的中等水平扫。基于这,我们使用了 HET 的滑动窗户分析通常认为地检测大连续区域(LCR ) 在下面选择从欧亚大陆数据集扫。这调查在一张欧洲人口识别了 63 LCR。这些信号被综合 haplotype 分数(iHS ) 进一步支持测试使用 HapMap II 数据。我们也证实从几的积极选择的欧洲人特定的签名以前识别了基因(KEL, TRPV5, TRPV6, EPHB6 ) 。在摘要,我们的结果不仅在扫描为揭示了 SNP 地图策略的高可靠选择扫,而且提供了卓见进人口区别。

英文摘要:

Population genomic approaches, which take advantages of high-throughput genotyping, are powerful yet costly methods to scan for selective sweeps. DNA-pooling strategies have been widely used for association studies because it is a cost-effective alternative to large-scale individual genotyping. Here, we performed an SNP-MaP (single nucleotide polymorphism microarrays and pooling) analysis using samples from Eurasia to evaluate the efficiency of pooling strategy in genome-wide scans for selection. By conducting simulations of allelotype data, we first demonstrated that the boxplot with average heterozygosity (HET) is a promising method to detect strong selective sweeps with a moderate level of pooling error. Based on this, we used a sliding window analysis of HET to detect the large contiguous regions (LCRs) putatively under selective sweeps from Eurasia datasets. This survey identified 63 LCRs in a European population. These signals were further supported by the integrated haplotype score (iHS) test using HapMap II data. We also confirmed the European-specific signatures of positive selection from several previously identified genes (KEL, TRPV5, TRPV6, EPHB6). In summary, our results not only revealed the high credibility of SNP-MaP strategy in scanning for selective sweeps, but also provided an insight into the population differentiation.

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期刊信息
  • 《基因组蛋白质组与生物信息学报:英文版》
  • 主管单位:中国科学院
  • 主办单位:中科院北京基因组研究所
  • 主编:
  • 地址:北京市朝阳区北土城西路7号中科院北京基因组研究所
  • 邮编:100029
  • 邮箱:editor@big.ac.cn
  • 电话:010-82995372
  • 国际标准刊号:ISSN:1672-0229
  • 国内统一刊号:ISSN:11-4926/Q
  • 邮发代号:82-557
  • 获奖情况:
  • 国内外数据库收录:
  • 俄罗斯文摘杂志,美国化学文摘(网络版),波兰哥白尼索引,荷兰文摘与引文数据库,荷兰医学文摘,美国生物医学检索系统,美国剑桥科学文摘,美国生物科学数据库
  • 被引量:52