Breakdance Simulator: A 3D Model of a Breakdance Ride with Amazing Graphics and Sound Effects
We use BreakDancer to identify SVs on ploidy matched brain tumor and normal samples. We focus on aneuploid brain tumors (PD4218, PD4188, PD4145, PD2187, PD2189), whose aneuploidy is characterized by a high percentage of trisomies. Each tissue has multiple trisomies with different genetic compositions, suggesting the possibility of multiple subclonal mutations. Our goal is to focus on SVs that may be present in the normal from which the tumor originates. In the tumor tissues, we call SV using BreakDancer on normal and tumor samples independently and identify a total of 81 candidate SVs, of which 23 (28%) overlap previously reported aneuploid-specific regions (see Additional file 5 : Table S4). We then run Breakdown on the predicted deletions, and find 21 deletions that are observed in both the normal and tumor. The only SVs of potential functional impact are one deletion at chr20p11.23 (1.7 Mb, see Figure 5A ) and one deletion at chr2q33.2 (1.9 Mb, see Figure 5B ). Both of them are likely homozygous deletions because their VAFs in the tumor samples are larger than 0.95. A recent study characterized copy number variations (CNVs) by tissue-specific loss of heterozygosity using chromosomal microarrays, with the results differing between the tumor (cortical oligodendroglioma) and adjacent normal cortex [ 44 ]. We further confirmed the CNV at chr2q33.2 by calling CNVs in a second set of samples that also had the normal tissue, as well as in the atlas of Mendelian diseases (OMIM) reference genome, which we obtained from ftp://ftp.1000genomes.ebi.ac.uk. There are 75 CNV variants overlapping the chr2q33.2 region, 32 of which are biallelic and three are homozygous. Of the 32 homozygous variants, one is likely homozygous deletion. The homozygous CNV at chr2q33.2 is inherited, and is a previously reported variant in OMIM. The heterozygous CNV at chr2q33.2 is inherited, and has not been previously reported.
breakdancer no 1 simulation download