Optimization of primer design for the detection of variable genomic lesions in cancer
Optimization of primer design for the detection of variable genomic lesions in cancer
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DOI：
10.1093/bioinformatics/btm390
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发表时间：
2007-11-01
期刊：
影响因子：
5.8
通讯作者：
Bafna, Vineet
中科院分区：
文献类型：
--
作者：
Bashir, Ali;Liu, Yu-Tsueng;Bafna, Vineet
引物近似多重PCR（Primer Approximation Multiple PCR，PAMP）是一种高效检测基因组结构变异的新方法。PAMP特别适合于癌症基因组，其中改变的精确断点（例如缺失或易位）在患者之间变化。用于PAMP的PCR引物组的设计是具有挑战性的，因为需要大量的引物对来检测癌症中可能发生的数百种酶范围内的改变。这些引物组必须实现感兴趣区域的高覆盖度，同时避免引物二聚体并满足良好PCR引物的物理化学约束。我们描述了一个自然制定这些约束作为一个组合优化问题。我们证明了PAMP引物设计问题是NP难的，并设计了基于模拟退火和整数规划的算法，在实践中为这个问题提供了很好的解决方案，这些算法被应用于已知CDKN2A缺失周围的测试区域，即使在突变：野生型细胞的1：49混合物中也显示出优异的结果。我们使用这些测试结果来帮助设置更大问题的设计参数。我们可以在接近1 Mb的区域实现接近最佳的设计。
Primer approximation multiplex PCR (PAMP) is a new experimental protocol for efficiently assaying structural variation in genomes. PAMP is particularly suited to cancer genomes where the precise breakpoints of alterations such as deletions or translocations vary between patients. The design of PCR primer sets for PAMP is challenging because a large number of primer pairs are required to detect alterations in the hundreds of kilobases range that can occur in cancer. These sets of primers must achieve high coverage of the region of interest, while avoiding primer dimers and satisfying the physico-chemical constraints of good PCR primers. We describe a natural formulation of these constraints as a combinatorial optimization problem. We show that the PAMP primer design problem is NP-hard, and design algorithms based on simulated annealing and integer programming, that provide good solutions to this problem in practice.The algorithms are applied to a test region around the known CDKN2A deletion, which show excellent results even in a 1:49 mixture of mutated:wild-type cells. We use these test results to help set design parameters for larger problems. We can achieve near-optimal designs for regions close to 1 Mb.