Marsden Carolyn G, Dragon Julie A, Wallace Susan S, Sweasy Joann B
The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT, United States.
The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT, United States; Yale University School of Medicine, New Haven, CT, United States.
Methods Enzymol. 2017;591:119-157. doi: 10.1016/bs.mie.2017.03.003. Epub 2017 May 5.
Base excision repair (BER) is a key genome maintenance pathway that removes endogenously damaged DNA bases that arise in cells at very high levels on a daily basis. Failure to remove these damaged DNA bases leads to increased levels of mutagenesis and chromosomal instability, which have the potential to drive carcinogenesis. Next-generation sequencing of the germline and tumor genomes of thousands of individuals has uncovered many rare mutations in BER genes. Given that BER is critical for genome maintenance, it is important to determine whether BER genomic variants have functional phenotypes. In this chapter, we present our in silico methods for the identification and prioritization of BER variants for further study. We also provide detailed instructions and commentary on the initial cellular assays we employ to dissect potentially important phenotypes of human BER variants and highlight the strengths and weaknesses of our approaches. BER variants possessing interesting functional phenotypes can then be studied in more detail to provide important mechanistic insights regarding the role of aberrant BER in carcinogenesis.
碱基切除修复（BER）是一种关键的基因组维护途径，它能去除内源性损伤的DNA碱基，这些碱基在细胞中每天都会以非常高的水平出现。未能去除这些受损的DNA碱基会导致诱变水平增加和染色体不稳定，这有可能推动癌症的发生。对数千人的种系和肿瘤基因组进行的下一代测序发现了BER基因中的许多罕见突变。鉴于BER对基因组维护至关重要，确定BER基因组变异是否具有功能表型非常重要。在本章中，我们介绍了用于识别和优先选择BER变异以进行进一步研究的计算机方法。我们还提供了关于我们用于剖析人类BER变异潜在重要表型的初始细胞检测的详细说明和评论，并突出了我们方法的优缺点。然后可以更详细地研究具有有趣功能表型的BER变异，以提供关于异常BER在致癌作用中作用的重要机制见解。
