Systematic biases in DNA copy number originate from isolation procedures.
Systematic biases in DNA copy number originate from isolation procedures.
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DOI：
10.1186/gb-2013-14-4-r33
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发表时间：
2013-04-24
期刊：
影响因子：
12.3
通讯作者：
Guryev V
中科院分区：
文献类型：
--
作者：
van Heesch S;Mokry M;Boskova V;Junker W;Mehon R;Toonen P;de Bruijn E;Shull JD;Aitman TJ;Cuppen E;Guryev V
以灵敏和定量的方式准确检测DNA拷贝数变异的能力在许多研究领域中是重要的。然而，全基因组DNA拷贝数分析由于检测信号的变化而变得复杂。虽然GC含量已被用来纠正这一点，在这里，我们表明，覆盖偏差是组织特异性和独立的检测方法所证明的下一代测序和阵列CGH。此外，我们表明，DNA分离严格性影响等摩尔覆盖的程度，所观察到的偏差与染色质的特征，如基因表达，基因组isochore，和复制时间相吻合。这些结果表明，染色质组织是差异DNA检索的主要决定因素。这些发现与生殖系和体细胞DNA拷贝数变异分析高度相关。
The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal. While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing. These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.
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