Long range mate-pair genome sequence data for the CEPH 1463 family

We sequenced a family trio using long range mate-pair data that combined with existing short insert genome datasets will allow improved the sensitivity to detect insertions, deletions and translocations. The mate pair libraries were prepared using the Nextera mate pair gel-free sample preparation protocol starting with 1 µg of genomic DNA and were sequenced on a HiSeq 2000 platform, for 2 x 100 bp. PF yields are NA12877, 87.83Gb, NA12878, 129.91Gb, NA12882, 108.36Gb. These data have a physical insert size of ~2000bp and compared with a normal paired end data that spans ~300bp, for the same total sequence depth this mate pair data will contain almost 7x the number of read pairs that cross any specific break point. The addition of more read pairs crossing a break point will improve sensitivity and allow improved detection of SVs in highly repetitive regions.

我们利用长距离伴侣配对（long range mate-pair）测序数据对一个家系三人组完成测序，该数据结合已有的短插入片段基因组数据集，可提升插入、缺失与染色体易位的检测灵敏度。本研究采用Nextera无凝胶样本制备流程构建伴侣配对文库，以1微克基因组DNA为起始原料，随后在HiSeq 2000测序平台上开展双端100碱基对测序。各样本的测序产出分别为：NA12877为87.83Gb，NA12878为129.91Gb，NA12882为108.36Gb。该数据的物理插入片段长度约为2000bp，相较于插入片段长度约为300bp的常规双端测序数据，在总测序深度相同的情况下，该伴侣配对测序数据中跨越任意特定断裂点的读对数量几乎是常规双端数据的7倍。增加跨越断裂点的读对数量可提升检测灵敏度，进而实现对高度重复区域内结构变异（Structural Variants, SVs）的更精准检测。