断裂-融合-桥接机制的组合学
Combinatorics of the breakage-fusion-bridge mechanism.
作者信息
Kinsella Marcus, Bafna Vineet
机构信息
Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA.
出版信息
J Comput Biol. 2012 Jun;19(6):662-78. doi: 10.1089/cmb.2012.0020. Epub 2012 Apr 16.
Abstract
The breakage-fusion-bridge (BFB) mechanism was proposed over seven decades ago and is a source of genomic variability and gene amplification in cancer. Here we formally model and analyze the BFB mechanism, to our knowledge the first time this has been undertaken. We show that BFB can be modeled as successive inverted prefix duplications of a string. Using this model, we show that BFB can achieve a surprisingly broad range of amplification patterns. We find that a sequence of BFB operations can be found that nearly fits most patterns of copy number increases along a chromosome. We conclude that this limits the usefulness of methods like array CGH for detecting BFB.
摘要
断裂-融合-桥接（BFB）机制是七十多年前提出的，是癌症中基因组变异和基因扩增的一个来源。在此，我们首次对BFB机制进行了正式建模和分析。我们表明，BFB可以建模为一个字符串的连续反向前缀重复。利用这个模型，我们表明BFB可以实现一系列令人惊讶的广泛扩增模式。我们发现，可以找到一系列BFB操作，几乎能匹配沿染色体的大多数拷贝数增加模式。我们得出结论，这限制了像阵列比较基因组杂交（array CGH）这样的方法用于检测BFB的有效性。
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