De novo and inherited variants in coding and regulatory regions in genetic cardiomyopathies

Figures

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  Fig. 1. Proband demographics and phenotype in trio analysis. A Ethnicities recorded of participants. B, Age distribution of participants at present time and type of diagnosis made. B Top 20 Human Phenotype Ontology (HPO) terms for participants recruited

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  Fig. 2. Noncoding de novo variant filtering criteria. DCM = dilated cardiomyopathy; ARVC = arrhythmogenic right ventricular cardiomyopathy; LVNC = left ventricular non-compaction cardiomyopathy; and HCM = hypertrophic cardiomyopathy

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  Fig. 3. Chromatin interaction map of chr20:44,116,250 locus. A One-to-all interaction plots are shown for the lead variant chr20:44,116,250 A > G shown in blue as bait. Y-axes on the left and the right measure bias-removed interaction frequency (blue bar graph) and distance-normalised interaction frequency (magenta dots), respectively. The arc representation of significant interactions for distance-normalised interaction frequencies ≥ 2 is displayed relative to the Refseq-annotated genes in the locus. The DNV physically interacts with the JPH2 enhancer by long-range chromatin interaction. B Close-up of region containing JPH2. The ABC model independently predicted the DNV (red triangle) is within the JPH2 enhancer. CM = cardiomyocyte

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  Fig. 4. An integrative genomics approach for prioritising noncoding variants. A We performed a rare-variant association study in cardiomyocyte-specific regulatory regions of genes associated with cardiomyopathy. These variants should be tested for deleteriousness or transcriptional activity, and, by inference, for causality. B MPRAs allow for thousands of short DNA sequences to be assayed simultaneously by first synthesising DNA oligos on an array, integrating them into plasmids and inserting into cells. Both input DNA and RNA libraries are sequenced to assess the tag counts associated with the test sequences. Barcode abundance thus scales quantitatively with the regulatory activity of a given tested sequence (figure adapted from Ajore et al. [63]). This technique can be used in future studies to screen all prioritised cardiomyocyte-specific regulatory variants in cardiomyopathy cases