Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons
Figure 2
(A) PET mapping overlap scheme based on the same number of PETs. 10 kb library dPETs have a higher chance than 1 kb library dPETs to cross the same breakpoints. (B) One common deletion identified in K562 by 1 kb, 10 kb and 20 kb libraries. Red track represents the coverage of the cPETs. The dPET cluster count in each library was 6, 51 and 95, respectively. The genomic PCR and Sanger sequencing confirmed the presence of the deletion and located the breakpoint positions to chr10:126,631,456 and chr10:126,720,709 (hg18). The differences between breakpoint position predicted by DNA-PET and PCR were 387 bp and 238 bp for the 1 kb library; 333 bp and 36 bp for the 10 kb library, and 482 bp and 37 bp in 20 kb library. (C) Cluster count correlation of the same set of SVs identified by both 1 kb and 10 kb libraries in the three genomes (left panel), and 10 kb and 20 kb libraries in K562 (right panel). The black line represents the trendline. The rearrangement between chromosomes 9 and 22 creating the CML causing BCR-ABL1 fusion gene [23] was identified by the largest clusters of 692 dPETs in the 10 kb library and 2,106 dPETs in the 20 kb library (red arrow head). (D) Length distribution of 5′ and 3′ anchor regions (regions in which the tags of dPET clusters are mapping) in 1 kb, 10 kb and 20 kb libraries of K562. The 10 kb library showed a more even length distribution of 5′ and 3′ anchor regions which suggested more balanced mapping characteristics around breakpoints for 10 kb libraries.