Efficient multipoint linkage analysis through reduction of inheritance space
Efficient multipoint linkage analysis through reduction of inheritance space
复制标题
通过缩小遗传空间实现高效的多点联系分析
DOI：
10.1086/319507
复制
发表时间：
2001-04-01
影响因子：
9.8
通讯作者：
Kruglyak, L
中科院分区：
文献类型：
--
作者：
Markianos, K;Daly, MJ;Kruglyak, L
目前，计算限制限制了对中等规模谱系的精确多点连锁分析。我们引入了新的算法，可以通过减少计算的时间和内存需求来分析更大的谱系。我们使用观察到的谱系基因型来减少需要考虑的遗传模式的数量。这些算法在软件包 GENEHUNTER 的新版本（版本 2.1）中实现。性能增益取决于标记杂合性和可用于基因分型的谱系成员数量，但与之前版本（版本 2.0）的性能相比，通常为 10-1,000 倍。因此，已经分析了最多具有 30 位遗传信息的家庭，并且进一步增加家庭规模是可行的。除了连锁统计计算和单倍型测定之外，GENEHUNTER 还可以进行单基因座和多基因座传递/不平衡测试。我们描述并实施了一组排列测试，允许在标记位点之间存在连锁不平衡的情况下确定经验显着性水平。
Computational constraints currently limit exact multipoint linkage analysis to pedigrees of moderate size. We introduce new algorithms that allow analysis of larger pedigrees by reducing the time and memory requirements of the computation. We use the observed pedigree genotypes to reduce the number of inheritance patterns that need to be considered. The algorithms are implemented in a new version (version 2.1) of the software package GENEHUNTER. Performance gains depend on marker heterozygosity and on the number of pedigree members available for genotyping, but typically are 10-1,000-fold, compared with the performance of the previous release (version 2.0). As a result, families with up to 30 bits of inheritance information have been analyzed, and further increases in family size are feasible. In addition to computation of linkage statistics and haplotype determination, GENEHUNTER can also perform single-locus and multilocus transmission/disequilibrium tests. We describe and implement a set of permutation tests that allow determination of empirical significance levels in the presence of linkage disequilibrium among marker loci.