利用经典代数统计揭示染色体区域的邻近性
Uncovering Proximity of Chromosome Territories using Classical Algebraic Statistics
摘要：
交换型染色体畸变（Exchange type chromosome aberrations，ETCA）是指染色体断裂后产生的片段与来自其他染色体的其他片段重新连接时发生的基因组重排。ETCA通常在癌细胞和暴露于辐射的细胞中观察到。这些染色体重排的频率与它们的空间接近性相关，因此它可以用来推断基因组的三维结构。由于数据的稀疏性，从癌症和辐射数据中提取空间邻近度的统计意义仍然有些难以捉摸。我们在这里提出了一种新的方法来研究的三维组织的基因组使用代数统计。我们测试我们的方法上公布的数据集的照射人血淋巴细胞。我们提供了一个严格的方法来测试基因组的整体组织，并在协议与以前的结果，我们发现一个随机的相对定位的染色体与染色体对\{1，22\}和\{13，14\}，有一个显着更大的ETCA的数量比其余的染色体对，这表明他们的空间接近。我们的结论是，代数方法可以成功地用于分析遗传数据，并有潜在的应用到更大，更复杂的数据集。
英文摘要：
Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with other fragments from other chromosomes. ETCAs are commonly observed in cancer cells and in cells exposed to radiation. The frequency of these chromosome rearrangements is correlated with their spatial proximity, therefore it can be used to infer the three dimensional organization of the genome. Extracting statistical significance of spatial proximity from cancer and radiation data has remained somewhat elusive because of the sparsity of the data. We here propose a new approach to study the three dimensional organization of the genome using algebraic statistics. We test our method on a published data set of irradiated human blood lymphocyte cells. We provide a rigorous method for testing the overall organization of the genome, and in agreement with previous results we find a random relative positioning of chromosomes with the exception of the chromosome pairs \{1,22\} and \{13,14\} that have a significantly larger number of ETCAs than the rest of the chromosome pairs suggesting their spatial proximity. We conclude that algebraic methods can successfully be used to analyze genetic data and have potential applications to larger and more complex data sets.
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