Merlin-rapid analysis of dense genetic maps using sparse gene flow trees
Merlin-rapid analysis of dense genetic maps using sparse gene flow trees
复制标题
DOI：
10.1038/ng786
复制
发表时间：
2002-01-01
期刊：
影响因子：
30.8
通讯作者：
Cardon, LR
中科院分区：
文献类型：
--
作者：
Abecasis, GR;Cherny, SS;Cardon, LR
使用高密度单核苷酸多态性（SNP）图谱寻找疾病基因的努力将产生超出当前计算工具限制的数据集。在这里，我们描述了一种新的，有效的方法，用于分析密集的遗传图谱的系谱数据，提供了非常快速的解决方案，如等位基因共享分析和单倍型分析的常见问题。我们表明，稀疏二叉树表示模式的基因流一般系谱在一个吝啬的方式，并推导出一个家庭的系谱遍历的相关算法。利用这些树，可以有效地对单个标记或多个连锁标记进行精确的似然计算。使用忽略大量重组体的不太可能性的近似多点计算进一步提高了速度，并在具有数千个标记的密集图谱中提供了准确的解决方案。我们的多点快速似然推理引擎（Merlin）是一种计算机程序，它使用稀疏遗传树进行系谱分析; 2它进行快速单体型分析、基因型错误检测和受影响的配对连锁分析，并且可以处理比其他系谱分析软件包更多的标记。
Efforts to find disease genes using high-density single-nucleotide polymorphism (SNP) maps will produce data sets that exceed the limitations of current computational tools. Here we describe a new, efficient method for the analysis of dense genetic maps in pedigree data that provides extremely fast solutions to common problems such as allele-sharing analyses and haplotyping. We show that sparse binary trees represent patterns of gene flow in general pedigrees in a parsimonious manner, and derive a family of related algorithms for pedigree traversal. With these trees, exact likelihood calculations can be carried out efficiently for single markers or for multiple linked markers. Using an approximate multipoint calculation that ignores the unlikely possibility of a large number of recombinants further improves speed and provides accurate solutions in dense maps with thousands of markers. our multipoint engine for rapid likelihood inference (Merlin) is a computer program that uses sparse inheritance trees for pedigree analysis; it performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.