Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing
Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing
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DOI：
10.1093/bioinformatics/btt481
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发表时间：
2013-11
期刊：
影响因子：
5.8
通讯作者：
Caihong Zheng;Xuexia Miao;Yanen Li;Ying Huang;Jue Ruan;Xi Ma;Li Wang;Chung-I Wu;Jun Cai
中科院分区：
文献类型：
--
作者：
Caihong Zheng;Xuexia Miao;Yanen Li;Ying Huang;Jue Ruan;Xi Ma;Li Wang;Chung-I Wu;Jun Cai
动机拷贝数缩写（CNA）是一种基因组畸变，通常由基因组不稳定引起，并与癌症等疾病有关。确定全基因组的CNA谱是确定潜在突变机制的重要步骤。基于下一代测序技术的基因组数据特别适合于确定高质量的CNA图谱。现在是重新评估测序技术在CNA分析中的应用的重要时期，特别是随着不同的靶向基因组和全基因组测序策略的快速发展。在这项研究中，我们提供了一种重测序策略的比较，关于它们的效用，适用于相同的肝细胞癌样本的拷贝数测定。这些策略包括全基因组、外显子组和限制性位点相关DNA （RAD）测序。最后一种策略是靶向测序技术，它涉及到用限制性内切酶切割基因组并分离目标序列。我们的数据表明，RAD测序是一种高效和全面的策略，可以经济有效地确定CNAs。对RAD测序数据的进一步研究发现，由于两个原因，精确测量等位基因频率将有助于补充CNA分析的读取深度。首先，对等位基因频率的了解有助于解决等位基因特异性拷贝数的精确计算，进而确定在亲本等位基因的自然选择下功能重要的CNAs。其次，这种知识使复杂基因组区域的CNA模式反卷积成为可能。
MOTIVATION Copy number abbreviation (CNA) is one type of genomic aberration that is often induced by genome instability and is associated with diseases such as cancer. Determination of the genome-wide CNA profile is an important step in identifying the underlying mutation mechanisms. Genomic data based on next-generation sequencing technology are particularly suitable for determination of high-quality CNA profile. Now is an important time to reevaluate the use of sequencing techniques for CNA analysis, especially with the rapid growth of the different targeted genome and whole-genome sequencing strategies. RESULTS In this study, we provide a comparison of resequencing strategies, with regard to their utility, applied to the same hepatocellular carcinoma sample for copy number determination. These strategies include whole-genome, exome and restriction site-associated DNA (RAD) sequencing. The last of these strategies is a targeted sequencing technique that involves cutting the genome with a restriction enzyme and isolating the targeted sequences. Our data demonstrate that RAD sequencing is an efficient and comprehensive strategy that allows the cost-effective determination of CNAs. Further investigation of RAD sequencing data led to the finding that a precise measurement of the allele frequency would be a helpful complement to the read depth for CNA analysis for two reasons. First, knowledge of the allele frequency helps to resolve refined calculations of allele-specific copy numbers, which, in turn, identify the functionally important CNAs that are under natural selection on the parental alleles. Second, this knowledge enables deconvolution of CNA patterns in complex genomic regions.