Copy number variation of individual cattle genomes using next-generation sequencing
Copy number variation of individual cattle genomes using next-generation sequencing
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DOI：
10.1101/gr.133967.111
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发表时间：
2012-04-01
期刊：
影响因子：
7
通讯作者：
Liu, George E.
中科院分区：
文献类型：
--
作者：
Bickhart, Derek M.;Hou, Yali;Liu, George E.
拷贝数变异（CNVs）影响广泛的表型性状，然而，在或接近节段性重复区域的CNVs往往是棘手的。使用基于下一代测序的读取深度方法，我们检查了5头牛磺酸（3头安格斯、1头荷斯坦和1头赫里福德）和1头indicine（Nelore）牛之间的全基因组拷贝数差异。在绘制的染色体序列中，我们确定了1265个CNV区域，包括类似于55.6-Mbp的序列-其中476个（类似于38%）以前没有报道过。我们用阵列比较基因组杂交（aCGH）、定量PCR（qPCR）和荧光原位杂交（FISH）验证了这种基于序列的CNV调用集，验证率为82%，假阳性率为8%。我们进一步估计了每个个体中基因组片段和注释基因的绝对拷贝数。对前25个最可变基因的调查显示，Nelore个体在13例中具有最低的拷贝数（类似于52%，卡方检验; P值
Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value