Fig. 8

FuSpot Visualization of THRB-AZIN2 False Positive Fusion Junction Using Extracted STAR Supporting Reads. FuSpot’s alternative visualization of the putative THRB-AZIN2 fusion gene claimed by FusionMap when given the BEERS data set [25]. Each read seen here was extracted from either the normal or chimeric output file produced by aligning the BEERS [25] data set with STAR. All reads were extracted using the FuSpot extraction tool available on the FuSpot website. STAR’s chimeric file yielded no reads that aligned near the breakpoint with at least a 95/100 score percentage. However, STAR’s normal alignment file contained many non-fusion reads (Group 1) which together form an even distribution across the AZIN2 gene. Four reads (Group 2) align such that the first mate spans the fusion breakpoint with a small anchor on the 5′ end and the second mate aligns entirely in the 3′ end of the AZIN2 reference. Below these are five reads (Group 3) that align such that the first mate aligns fully in the 5′ end of the AZIN2 reference and the second mate aligns such that its first few bases align to the 5′ end of the THRB reference and the remaining bases align to the 3′ end of the AZIN2 reference. These “nonsense alignments” in Group 3 suggest that there is homology between the sequence at the terminus of the 5′ end of the THRB reference and the sequence at the terminus of the 5′ end of the AZIN2 reference. This homology is confirmed in Fig. 9 by aligning Groups 2 and 3 to only AZIN2 references