Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data
复制标题
从单倍型数据中识别和估计倒位多态性
DOI：
10.1007/978-3-642-02008-7_30
复制
发表时间：
2009
期刊：
影响因子：
--
通讯作者：
Benjamin J. Raphael
中科院分区：
文献类型：
--
作者：
Suzanne S. Sindi;Benjamin J. Raphael
结构重排，包括拷贝数改变和倒置，越来越被认为是导致人类遗传变异的重要因素。拷贝数变异很容易通过基于阵列的技术来测量，如比较基因组杂交，但如果没有全基因组测序，诸如倒位多态等拷贝中性变异仍然很难识别。我们介绍了一种使用现成的单核苷酸多态(SNP)数据来识别倒位多态并估计其在人群中频率的方法。我们的方法使用概率模型将种群描述为正反向染色体的混合物，并通过反转断点附近单倍型频率的特征差异来识别假定的反转。在模拟数据上，我们的方法准确地预测了人群中频率低至25%的倒置，并在很大范围内可靠地估计了倒置频率。在人类HapMap阶段2数据上，我们预测了88到142个倒位多态，频率从20%到81%不等。其中许多对应于已知的倒置，或有其他证据支持它们，预测的倒置频率与目前可用的有限信息基本一致。
Structural rearrangements, including copy-number alterations and inversions, are increasingly recognized as an important contributor to human genetic variation. Copy number variants are readily measured via array-based techniques like comparative genomic hybridization, but copy-neutral variants such as inversion polymorphisms remain difficult to identify without whole genome sequencing. We introduce a method to identify inversion polymorphisms and estimate their frequency in a population using readily available single nucleotide polymorphism (SNP) data. Our method uses a probabilistic model to describe a population as a mixture of forward and inverted chromosomes and identifies putative inversions by characteristic differences in haplotype frequencies around inversion breakpoints. On simulated data, our method accurately predicts inversions with frequencies as low as 25% in the population and reliably estimates inversion frequencies over a wide range. On the human HapMap Phase 2 data, we predict between 88 and 142 inversion polymorphisms with frequency ranging from 20 to 81 percent. Many of these correspond to known inversions or have other evidence supporting them, and the predicted inversion frequencies largely agree with the limited information presently available.
影响因子：
9.8
作者：
Anderson, EC;Novembre, J
通讯作者：
Novembre, J
影响因子：
9.8
作者：
Perry, George H.;Ben-Dor, Amir;Lee, Charles
通讯作者：
Lee, Charles
使用多位点基因型数据推断群体结构：连锁位点和相关等位基因频率。
影响因子：
3.3
作者：
Falush,Daniel;Stephens,Matthew;Pritchard,JonathanK
通讯作者：
Pritchard,JonathanK