Samples investigated in the study.

1<p>All 38 investigated fusion genes are ranked based on the likelihood of being the correct fusion gene in the particular sample. Lower numbers indicate higher likelihood.</p>2<p>Information about RT-PCR protocols for fusion gene detection. In house: protocol not previously published. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070649#s2" target="_blank">Materials and Methods</a> for more details. NK: Normal karyotype.</p

Top ranked fusion genes in two sarcoma samples.

<p>A. <i>EWSR1</i>-<i>NR4A3</i> in the 168/97 sample. B. <i>SS18</i>-<i>SSX1</i> in the 9972 sample. I) Intensity heat map of chimeric oligos. Each square represents one possible exon-exon boundary between the two gene partners. One square is highly expressed (A: 13-3, B: 10-6) and reflects the presence of chimeric RNA covering the corresponding exon-exon boundary. This fusion breakpoint corresponds with a shift in relative expression measured by intragenic oligos covering both the upstream (II) and downstream (III) fusion gene partners. Blue and red colours represent the two possible chimeric transcripts generated from the fusion gene.</p