Examining ENCODE Elements on a per individual basis in the Normal and Cancer GenomePanel A shows the breakdown of variants in a single genome (NA12878) by both frequency (common or rare (i.e., variants not present in the low-coverage sequencing of 179 individuals in the pilot 1 European panel of the 1000 Genomes project55) and by ENCODE annotation, including protein-coding gene and non-coding elements (GENCODE annotations for protein-coding genes, pseudogenes, and other ncRNAs, as well as TF-binding sites from ChIP-seq datasets, excluding broad annotations such as histone modifications, segmentations, and RNA-seq). Annotation status is further subdivided by predicted functional effect, being non-synonymous and missense mutations for protein-coding regions and variants overlapping bound TF motifs for non-coding element annotations. A substantial proportion of variants are annotated as having predicted functional effects in the non-coding category. Panel B shows one of several relatively rare occurrences, where alignment to an individual genome sequence (paternal and maternal panels) shows a different readout from the reference genome. In this case, a paternal haplotype-specific CTCF peak is identified. Panel C shows the relative level of somatic variants from whole-genome melanoma sample that occur in DHSs unique to different cell lines. The coloured bars show cases that are significantly enriched or supressed in somatic mutations. Details of ENCODE cell types can be found at http://encodeproject.org/ENCODE/cellTypes.html.
