Figure 1.

LINX schematic and visualizations

(A) The LINX algorithm works in four steps to annotate, cluster, chain, and determine the functional impact of an integrated copy number. The Circos on the left represents the input of LINX and shows three structural variants (purple lines) affecting two chromosomes (outer track in green and blue) with consistent copy number breakpoints (middle track showing green for gain and red for loss). The Circos on the right shows example output of LINX, including the chaining of the variants into two continuous predicted derivative chromosomes (lines in brown and purple) and a canonical TMPRSS2_ERG fusion (genes depicted in blue and light brown on second outer circle with fused exons showing darker shading) on one of the two predicted chromosomes.

(B) A detailed guide to the visualizations produced by LINX.