Department of Genetics and Bioengineering, Istanbul Bilgi University, Istanbul, Turkey.
PLoS One. 2014 Jan 9;9(1):e85233. doi: 10.1371/journal.pone.0085233. eCollection 2014.
Although whole human genome sequencing can be done with readily available technical and financial resources, the need for detailed analyses of genomes of certain populations still exists. Here we present, for the first time, sequencing and analysis of a Turkish human genome. We have performed 35x coverage using paired-end sequencing, where over 95% of sequencing reads are mapped to the reference genome covering more than 99% of the bases. The assembly of unmapped reads rendered 11,654 contigs, 2,168 of which did not reveal any homology to known sequences, resulting in ∼1 Mbp of unmapped sequence. Single nucleotide polymorphism (SNP) discovery resulted in 3,537,794 SNP calls with 29,184 SNPs identified in coding regions, where 106 were nonsense and 259 were categorized as having a high-impact effect. The homo/hetero zygosity (1,415,123∶2,122,671 or 1∶1.5) and transition/transversion ratios (2,383,204∶1,154,590 or 2.06∶1) were within expected limits. Of the identified SNPs, 480,396 were potentially novel with 2,925 in coding regions, including 48 nonsense and 95 high-impact SNPs. Functional analysis of novel high-impact SNPs revealed various interaction networks, notably involving hereditary and neurological disorders or diseases. Assembly results indicated 713,640 indels (1∶1.09 insertion/deletion ratio), ranging from -52 bp to 34 bp in length and causing about 180 codon insertion/deletions and 246 frame shifts. Using paired-end- and read-depth-based methods, we discovered 9,109 structural variants and compared our variant findings with other populations. Our results suggest that whole genome sequencing is a valuable tool for understanding variations in the human genome across different populations. Detailed analyses of genomes of diverse origins greatly benefits research in genetics and medicine and should be conducted on a larger scale.
虽然利用现有的技术和财务资源可以进行全人类基因组测序，但仍然需要对某些人群的基因组进行详细分析。在这里，我们首次展示了对土耳其人类基因组的测序和分析。我们使用配对末端测序进行了 35x 覆盖，其中超过 95%的测序读数被映射到参考基因组上，覆盖了超过 99%的碱基。未映射读取的组装产生了 11654 个连续序列，其中 2168 个没有显示出与已知序列的同源性，导致约 1 Mbp 的未映射序列。单核苷酸多态性（SNP）的发现导致了 3537794 个 SNP 调用，其中 29184 个 SNP 位于编码区域，其中 106 个是无义突变，259 个被归类为具有高影响效应。同/杂合性（1415123∶2122671 或 1∶1.5）和转换/颠换比（2383204∶1154590 或 2.06∶1）在预期范围内。在鉴定的 SNP 中，480396 个可能是新的 SNP，其中 2925 个位于编码区域，包括 48 个无义突变和 95 个高影响 SNP。对新的高影响 SNP 的功能分析揭示了各种相互作用网络，特别是涉及遗传性和神经紊乱或疾病。组装结果表明，713640 个插入/缺失（1∶1.09 插入/缺失比），长度从-52bp 到 34bp，导致约 180 个密码子插入/缺失和 246 个移码突变。使用配对末端和读深方法，我们发现了 9109 个结构变体，并将我们的变体发现与其他人群进行了比较。我们的结果表明，全基因组测序是了解不同人群中人类基因组变异的一种有价值的工具。对不同来源的基因组进行详细分析极大地促进了遗传学和医学的研究，应该在更大的范围内进行。
