Resolving the full spectrum of human genome variation using Linked-Reads
Resolving the full spectrum of human genome variation using Linked-Reads
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DOI：
10.1101/gr.234443.118
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发表时间：
2019-04-01
期刊：
影响因子：
7
通讯作者：
Church, Deanna M.
中科院分区：
文献类型：
--
作者：
Marks, Patrick;Garcia, Sarah;Church, Deanna M.
大规模的人口分析加上技术的进步表明，人类基因组比原来想象的更加多样化。到目前为止，这种多样性在很大程度上是使用短读全基因组测序发现的。然而，这些短读方法无法给出基因组的完整图片。他们很难识别结构事件，无法访问重复区域，并且无法将人类基因组解析为单倍型。在这里，我们描述了一种方法，保留长范围的信息，同时保持短读的优势。从近似1 ng的高分子量DNA开始，我们产生条形码化的短读段文库。新的信息学方法允许条形码化的短读段与其原始长分子相关联，产生称为“连接读段”的新数据类型。这种方法允许从单个文库中同时检测小的和大的变体。在本文中，我们展示了Linked-Reads在基于参考的分析中优于标准短阅读方法的优势。Linked-Reads允许映射到短读段无法访问的38 Mb序列，在423个难以测序的基因中添加序列，包括疾病相关基因STRC，SMN 1和SMN 2。Linked-Read全基因组测序和全外显子组测序均可识别复杂的结构变异，包括平衡事件和单外显子缺失和重复。此外，Linked-Reads将高置信度调用的区域扩展了68.9 Mb。这里提供的数据表明，Linked-Reads为综合基因组分析提供了一种可扩展的方法，而这是单独使用短读段无法实现的。
Large-scale population analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short-read whole-genome sequencing. However, these short-read approaches fail to give a complete picture of a genome. They struggle to identify structural events, cannot access repetitive regions, and fail to resolve the human genome into haplotypes. Here, we describe an approach that retains long range information while maintaining the advantages of short reads. Starting from similar to 1 ng of high molecular weight DNA, we produce barcoded short-read libraries. Novel informatic approaches allow for the barcoded short reads to be associated with their original long molecules producing a novel data type known as "Linked-Reads". This approach allows for simultaneous detection of small and large variants from a single library. In this manuscript, we show the advantages of Linked-Reads over standard short-read approaches for reference-based analysis. Linked-Reads allow mapping to 38 Mb of sequence not accessible to short reads, adding sequence in 423 difficult-to-sequence genes including disease-relevant genes STRC, SMN1, and SMN2. Both Linked-Read whole-genome and whole-exome sequencing identify complex structural variations, including balanced events and single exon deletions and duplications. Further, Linked-Reads extend the region of high-confidence calls by 68.9 Mb. The data presented here show that Linked-Reads provide a scalable approach for comprehensive genome analysis that is not possible using short reads alone.