Albert Einstein College of Medicine, Department of Genetics, New York, NY 10461, United States.
Mutat Res. 2012 Jan 3;729(1-2):1-15. doi: 10.1016/j.mrfmmm.2011.10.001. Epub 2011 Oct 12.
DNA mutations are the source of genetic variation within populations. The majority of mutations with observable effects are deleterious. In humans mutations in the germ line can cause genetic disease. In somatic cells multiple rounds of mutations and selection lead to cancer. The study of genetic variation has progressed rapidly since the completion of the draft sequence of the human genome. Recent advances in sequencing technology, most importantly the introduction of massively parallel sequencing (MPS), have resulted in more than a hundred-fold reduction in the time and cost required for sequencing nucleic acids. These improvements have greatly expanded the use of sequencing as a practical tool for mutation analysis. While in the past the high cost of sequencing limited mutation analysis to selectable markers or small forward mutation targets assumed to be representative for the genome overall, current platforms allow whole genome sequencing for less than $5000. This has already given rise to direct estimates of germline mutation rates in multiple organisms including humans by comparing whole genome sequences between parents and offspring. Here we present a brief history of the field of mutation research, with a focus on classical tools for the measurement of mutation rates. We then review MPS, how it is currently applied and the new insight into human and animal mutation frequencies and spectra that has been obtained from whole genome sequencing. While great progress has been made, we note that the single most important limitation of current MPS approaches for mutation analysis is the inability to address low-abundance mutations that turn somatic tissues into mosaics of cells. Such mutations are at the basis of intra-tumor heterogeneity, with important implications for clinical diagnosis, and could also contribute to somatic diseases other than cancer, including aging. Some possible approaches to gain access to low-abundance mutations are discussed, with a brief overview of new sequencing platforms that are currently waiting in the wings to advance this exploding field even further.
DNA 突变是种群内遗传变异的来源。大多数具有可观察效应的突变都是有害的。在人类中，生殖细胞中的突变会导致遗传疾病。在体细胞中，多次突变和选择导致癌症。自人类基因组草图完成以来，遗传变异的研究进展迅速。测序技术的最新进展，尤其是大规模并行测序（MPS）的引入，使得核酸测序的时间和成本减少了 100 多倍。这些改进极大地扩展了测序作为突变分析实用工具的用途。虽然过去测序的高成本将突变分析限制在可选择的标记或假设代表整个基因组的小正向突变靶标上，但目前的平台允许对整个基因组进行测序，费用不到 5000 美元。这已经通过比较父母和后代之间的全基因组序列，直接估计了包括人类在内的多个生物体的生殖系突变率。在这里，我们简要介绍了突变研究领域的历史，重点介绍了用于测量突变率的经典工具。然后我们回顾了 MPS，它的当前应用以及通过全基因组测序获得的对人类和动物突变频率和谱的新认识。虽然已经取得了巨大的进展，但我们注意到，当前 MPS 方法在突变分析中最关键的限制是无法解决使体细胞成为细胞马赛克的低丰度突变。这些突变是肿瘤内异质性的基础，对临床诊断具有重要意义，也可能导致除癌症以外的其他体细胞疾病，包括衰老。讨论了一些获得低丰度突变的可能方法，并简要概述了目前正在等待进一步推进这一快速发展领域的新测序平台。
