Optimal sequencing strategies for surveying molecular genetic diversity.
Optimal sequencing strategies for surveying molecular genetic diversity.
复制标题
用于调查分子遗传多样性的最佳测序策略。
DOI：
10.1093/genetics/144.3.1247
复制
发表时间：
1996
期刊：
影响因子：
3.3
通讯作者：
Donnelly,P
中科院分区：
文献类型：
--
作者：
Pluzhnikov,A;Donnelly,P
种内DNA序列数据的遗传多样性的两个常用措施是基于，分别是分离位点的数量，和成对核苷酸差异的平均数。表达式推导出它们的方差在基因内重组的存在下，为一个panmictic人口的固定大小，是在中性平衡的区域测序。我们发现，在缓慢减少的方差随着样本量的增加，如果重组率是非零的，渐近速率的方差随着序列长度的增加，对于固定的样本量，是相当迅速的减少。特别是，它接近于通过对独立染色体区域进行测序而获得的结果。还研究了相关区域的多样性措施之间的相关性。对于在特定区域中测序的给定碱基总数，导出最佳测序策略。这些通常涉及对该区域的相对较少（3至10个）长拷贝进行测序。在最优策略下，对于所考虑的大多数参数值，这两个度量的方差非常相似。关于最佳测序策略的结果将是敏感的，从根本上的假设，如人口瓶颈，选择性扫描，大量的人口子结构的总偏离。
Two commonly used measures of genetic diversity for intraspecies DNA sequence data are based, respectively, on the number of segregating sites, and on the average number of pairwise nucleotide differences. Expressions are derived for their variance in the presence of intragenic recombination for a panmictic population of fixed size that is at neutral equilibrium at the region sequenced. We show that, in contrast to the slow decrease in variance with increasing sample size, if the recombination rate is nonzero, the asymptotic rate of decrease of variance with increasing sequence length, for fixed sample size, is quite rapid. In particular, it is close to that which would be obtained by sequencing independent chromosome regions. The correlation between measures of diversity from linked regions is also examined. For a given total number of bases sequenced in a particular region, optimal sequencing strategies are derived. These typically involve sequencing relatively few (three to 10) long copies of the region. Under optimal strategies, the variances of the two measures are very similar for most parameter values considered. Results concerning optimal sequencing strategies will be sensitive to gross departures from the underlying assumptions, such as population bottlenecks, selective sweeps, and substantial population substructure.
登录
查看更多内容
影响因子：
2.9
作者：
Santos-Garcia MO;Karia CT;Resende RM;Chiari L;Vieira ML;Zucchi MI;Souza AP
通讯作者：
Souza AP
杂合度与不同频率类别等位基因数量的相关性
影响因子：
1.4
作者：
R. Chakraborty;R. Griffiths
通讯作者：
R. Griffiths
影响因子：
3.3
作者：
K. Simonsen;G. Churchill;C. Aquadro
通讯作者：
K. Simonsen;G. Churchill;C. Aquadro
影响因子：
1.9
作者：
ETHIER, SN;GRIFFITHS, RC
通讯作者：
GRIFFITHS, RC
影响因子：
1.4
作者：
GRIFFITHS, RC
通讯作者：
GRIFFITHS, RC