Characterization of tandem RNA chimeras.

<p>Barplot representing the frequency of the predicted structural classes for all tandem RNA chimeras. The most prevalent observed class is a promoter swap event.</p

The most significant SNPs associated with RNA chimeras formation.

<p>The most significant SNPs associated with RNA chimeras formation.</p

Intron length density plots.

<p>Density plots showing the distributions of the fusion 5′ and 3′ introns length versus the length of the rest of the introns comprising the fusion partner genes. Observed is a notable higher proportion of larger introns at the breakpoint.</p

Tandem RNA chimeras frequency plots in five human populations.

<p>All populations show similar patterns with most of the chimeric transcripts found only in a few individuals.</p

Exon exclusion pattern.

<p>Plot showing the proportions of the exon exclusion patterns in the tandem RNA chimeras. The numbers of the exons for the 5′ partner gene are counted from last to first, while the numbers of the exons for the 3′ partner gene are counted from first to last. The most abundant exon exclusion pattern involves the exclusion of the terminal exon of the 5′ partner gene and the first exon of the 3′ partner gene.</p

Venn diagrams.

<p>Venn diagrams displaying the relations between tandem RNA chimeras in five human populations (A); intrachromosomal chimeras located on different strands (B); and interchromosomal chimeras (C).</p

Empirical False Positive Rate estimates.

<p>Percent of SNPs showing <i>p</i>-values below 0.01, after randomly assigning AI to 5, 10, 15, 20 and 29 individuals out of the 54 considered (based on the set of Ge et al.). Based on 20 whole genome scans for 10, 15 and 20 AI individuals and on 20 scans of chromosomes 1 to 4 for 5 and 29 AI individuals.</p

Distances between chimeric partner genes.

<p>Shown are distances between the tandem RNA chimeric partner genes in Mb. The majority of the distances are in the range between 5 kb and 170 kb.</p

Four possible mutational pathways creating three distinct sets of three haplotypes.

<p>Depending on the sequence of mutations starting with the ancestral haplotype on the left, we obtain three sets of haplotypes, referred to as below, parallel and above to reflect the position of the <i>A</i>-site vs. <i>R</i>-site mutation on the genealogy shown on the right. These genealogical positions can be modified by recombination. We assume no recurrent mutations.</p

Sets of possible genotypes under complete and incomplete linkage disequilibrium.

<p>Under complete LD for genealogical positions below (<b>A</b>), parallel (<b>B</b>) and above (<b>C</b>), there are always two genotypes characterizing AI-individuals and only one type of A-site homozygote present (AA or aa). Under equilibrium or incomplete linkage disequilibrium (<b>D</b>) all four haplotypes involving R and A sites are present and thus potentially all ten resulting genotypes as well.</p