BAM

Variants: Clinvar VCF, Custom MYC variants

BigWig

BigWig, stranded coverage

JSON BED

Tumor-normal allelic imbalance

ChromHMM + gene expression, aka PGV

FusionEditor

Differential gene expression as MA and Volcano plots, with RNA-seq coverage

Hi-C

Splice junction

Single-cell RNAseq tSNE

GenomePaint

• Illustrating multiple mechanisms for oncogene TAL1 activation in Cohort View.
• Matrix View reviews mutual-exclusive or co-mutation pattern, for association with patient outcome.
• Visualize multi-omics data with dynamic range in Sample View.
• Sample View of interchromsomal rearrangement leading to MYC dysregulation by enhancer-hijacking.
• Assessing aberrant splicing in CREBBP caused by somatic splice site variants.
• MYC dysregulation by enhancer duplications in pediatric cancers.
• Cohort View shows different mutation mechanisms causing loss-of-function in tumor suppressors.
• Cohort View enables associating mutation or expression data with patient outcomes.
• B-ALL shows diverse alterations targeting CREBBP RING domain.
• Previously unreported cases of likely MYC enhancer duplication/amplification in pediatric tumors and cell line.
• In-situ Hi-C shows MYC interaction with duplicated enhancers in NALM6 and NALM16.
• Phased sequencing coverage in NALM6.
• DUX4 but not NOTCH1 likely binds at N-ME in NALM6.
• CDKN2A/2B focal deletion and sequence mutations from adult diffuse large B-cell lymphoma (DLBC)
• TERT sequence mutations in adult cutaneous melanoma (SKCM).
• RNA-seq tSNE plot of the pan-BALL study