Figure 2: Confirmation of predictions in the catalogue.

(a) Our computational pipeline recovered the known TAL1-proximal insertion in the MOLT4 and Jurkat T-ALL genomes. The insertions CG[GT]TA in MOLT4, and CG[GTTAGGAAACGG]TA noted in red, upstream of the TAL1 gene are bound by H3K27 acetylated histones. This region was immunoprecipitated in ChIP-Seq experiments targeting acetylated H3K27, and sequence reads from this experiment contain the insertion and surrounding genomic context. (b) Left: Example enhancer-associated insertion in MOLT4 T-ALL cells that was confirmed by high-throughput sequencing pooled PCR products. Number of H3K27ac ChIP-Seq reads in bins at the USP39/SFTPB/GNLY locus is represented in purple. Annotated RefSeq genes are noted below. Representative contigs detected in the high-throughput sequencing that contain reference sequence and the predicted insertion, suggesting this insertion is heterozygous. The insertion is noted in red. Note that scaffolds were aligned to the negative strand, so insertion predicted was GCG but insertion in scaffold is GCG. Right: Pie chart summarizing numbers of predicted insertions detected using this approach. (c) Left: Example enhancer-associated insertion in Jurkat T-ALL cells that was confirmed by Sanger sequencing of PCR products. Number of H3K27ac ChIP-Seq reads in bins at the AUH locus is represented in purple. Annotated RefSeq genes are noted below. Chromatograms of Sanger sequencing of this locus are below. Chromatograms show the signal from each of four possible nucleotides at a position. Sequences of the insertions are indicated with a grey box. Right: Pie chart summarizing numbers of predicted insertions detected using this approach. (d) Left: Example enhancer-associated insertion in GM12878 B lymphoblastoid cells that was confirmed by the Illumina Platinum genome of these cells. Number of H3K27ac ChIP-Seq reads in bins at the CLLU1 locus is represented in purple. The predicted insertion in genomic context is noted below in red. The Illumina-identified variant is below. Right: Pie chart summarizing numbers of predicted insertions detected using this approach.