Discovery and genotyping of structural variation from long-read haploid genome sequence data.
Discovery and genotyping of structural variation from long-read haploid genome sequence data.
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DOI：
10.1101/gr.214007.116
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发表时间：
2017-05
期刊：
影响因子：
7
通讯作者：
Eichler EE
中科院分区：
文献类型：
--
作者：
Huddleston J;Chaisson MJP;Steinberg KM;Warren W;Hoekzema K;Gordon D;Graves-Lindsay TA;Munson KM;Kronenberg ZN;Vives L;Peluso P;Boitano M;Chin CS;Korlach J;Wilson RK;Eichler EE
为了更充分地了解人类遗传变异的全部范围，我们使用基于组装的方法（SMRT-SV）产生了深层的单分子，实时（SMRT）测序数据。系统地评估了每个基因组的结构变体（SV），并在461,553个遗传变异的序列结构中从2 bp到28 kbp。即使在调整了更常见的变体之后，变体也被遗漏了1000个基因组项目的一部分（MAF> 1％）。与短读序列数据相比，长期读取的数据对遗传变异的敏感性增加了五倍，范围从7 bp到1 kbp。一旦替代等位基因是序列分解的，我们就无法通过短阅读方法检测到变体，我们表明可以在高度准确性的情况下以短读序列数据集进行基因分型。当我们通过合并两个单倍体的伪造基因组重复SV检测时，这错过了人口中的共同变异。 SMRT-SV不再检测到59％的杂合SV。
In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF > 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.