Sequence determinants of human microsatellite variability.
Sequence determinants of human microsatellite variability.
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DOI：
10.1186/1471-2164-10-612
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发表时间：
2009-12-16
期刊：
影响因子：
4.4
通讯作者：
Rosenberg NA
中科院分区：
文献类型：
--
作者：
Pemberton TJ;Sandefur CI;Jakobsson M;Rosenberg NA
微卫星座位经常用于DNA序列重复序列的基因组研究和遗传变异的群体研究。为了研究微卫星的序列特性对其变异性水平的影响，我们分析了来自HGDP-CEPH细胞系的1048个全球个体的627个微卫星基因座的基因类型，以及人类RefSeq数据库中这些微卫星的DNA序列。通过使用RefSeq序列校准单个基因型中的PCR片段长度，使我们能够推断HGDP-CEPH数据集中的重复数并计算平均重复数(与平均PCR片段长度相反)，前提是PCR片段长度的差异反映了嵌入的重复序列中重复数的差异。我们发现个体间的平均重复数和最大重复数与杂合性呈正相关。微卫星重复单位的大小和组成也是预测杂合性的重要因素，G/C含量高的四核苷酸重复单位导致更高的杂合性。最后，我们发现包含更多独立重复基序集的微卫星通常具有更高的杂合度。这些结果表明，微卫星的序列特性对确定人类微卫星的变异性特征具有重要影响。
Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length), under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.
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影响因子：
64.8
作者：
Dib, C;Faure, S;Weissenbach, J
通讯作者：
Weissenbach, J
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BOWCOCK, AM;RUIZLINARES, A;CAVALLISFORZA, LL
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