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Ultrarare noncoding variants enhance arrhythmia risk (A) Noncoding regulatory regions of CMAR and epilepsy genes were identified by overlaying ATAC sequencing and Hi-C data from the heart and brain. Variants within these regions were analyzed. (B) Ultrarare variants (defined as not observed in gnomAD and a combined cohort AF <0.01) were enriched in cases compared to controls (permutation test, ∗∗∗∗ p < 1e−4, mean per individual ±SEM). (C) Enrichment of ultrarare regulatory variant target genes in cases compared to controls, with probability of loss of function intolerance (pLI). y axis is −log10 p value (χ2 test, Bonferroni corrected). Color is the ratio of variants per mapped gene (dots indicate genes with p < 0.05). (D) Motif enrichment in the 20-bp surrounding ultra-rare variants in cases. (E) Example noncoding regions with ultrarare case variants in transcription factor-binding motifs. Tracks shown in hg38 with human <t>cardiomyocyte</t> (CM) ATAC-seq tracks (top) and engineered heart tissue ATAC-seq tracks (below). Hi-C promoter contacts with ATAC-seq peaks also shown. Regulatory elements highlighted in yellow and promoters in pink. Within each peak sits a variant predicted to alter transcription factor binding. Motif and base pair change shown below in blue. (F) Regulatory variant score boxplots within-cohort. Scores derived from a linear model that incorporates ultrarare and rare (gnomAD AF<0.001) variants in the regulatory intervals (Wilcoxon rank-sum test, boxplot: median, IQR, and 1.5 IQR). (G) Log2 OR of being a case is shown across the regulatory variant score quintiles within-cohort (# indicates an OR 95% CI lower bound ≥1; dashed line indicating the null hypothesis, OR = 1, and untransformed ORs to the right.).
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Ultrarare noncoding variants enhance arrhythmia risk (A) Noncoding regulatory regions of CMAR and epilepsy genes were identified by overlaying ATAC sequencing and Hi-C data from the heart and brain. Variants within these regions were analyzed. (B) Ultrarare variants (defined as not observed in gnomAD and a combined cohort AF <0.01) were enriched in cases compared to controls (permutation test, ∗∗∗∗ p < 1e−4, mean per individual ±SEM). (C) Enrichment of ultrarare regulatory variant target genes in cases compared to controls, with probability of loss of function intolerance (pLI). y axis is −log10 p value (χ2 test, Bonferroni corrected). Color is the ratio of variants per mapped gene (dots indicate genes with p < 0.05). (D) Motif enrichment in the 20-bp surrounding ultra-rare variants in cases. (E) Example noncoding regions with ultrarare case variants in transcription factor-binding motifs. Tracks shown in hg38 with human cardiomyocyte (CM) ATAC-seq tracks (top) and engineered heart tissue ATAC-seq tracks (below). Hi-C promoter contacts with ATAC-seq peaks also shown. Regulatory elements highlighted in yellow and promoters in pink. Within each peak sits a variant predicted to alter transcription factor binding. Motif and base pair change shown below in blue. (F) Regulatory variant score boxplots within-cohort. Scores derived from a linear model that incorporates ultrarare and rare (gnomAD AF<0.001) variants in the regulatory intervals (Wilcoxon rank-sum test, boxplot: median, IQR, and 1.5 IQR). (G) Log2 OR of being a case is shown across the regulatory variant score quintiles within-cohort (# indicates an OR 95% CI lower bound ≥1; dashed line indicating the null hypothesis, OR = 1, and untransformed ORs to the right.).

Journal: Cell Reports Medicine

Article Title: A combined genomic arrhythmia propensity score delineates cumulative risk

doi: 10.1016/j.xcrm.2025.102455

Figure Lengend Snippet: Ultrarare noncoding variants enhance arrhythmia risk (A) Noncoding regulatory regions of CMAR and epilepsy genes were identified by overlaying ATAC sequencing and Hi-C data from the heart and brain. Variants within these regions were analyzed. (B) Ultrarare variants (defined as not observed in gnomAD and a combined cohort AF <0.01) were enriched in cases compared to controls (permutation test, ∗∗∗∗ p < 1e−4, mean per individual ±SEM). (C) Enrichment of ultrarare regulatory variant target genes in cases compared to controls, with probability of loss of function intolerance (pLI). y axis is −log10 p value (χ2 test, Bonferroni corrected). Color is the ratio of variants per mapped gene (dots indicate genes with p < 0.05). (D) Motif enrichment in the 20-bp surrounding ultra-rare variants in cases. (E) Example noncoding regions with ultrarare case variants in transcription factor-binding motifs. Tracks shown in hg38 with human cardiomyocyte (CM) ATAC-seq tracks (top) and engineered heart tissue ATAC-seq tracks (below). Hi-C promoter contacts with ATAC-seq peaks also shown. Regulatory elements highlighted in yellow and promoters in pink. Within each peak sits a variant predicted to alter transcription factor binding. Motif and base pair change shown below in blue. (F) Regulatory variant score boxplots within-cohort. Scores derived from a linear model that incorporates ultrarare and rare (gnomAD AF<0.001) variants in the regulatory intervals (Wilcoxon rank-sum test, boxplot: median, IQR, and 1.5 IQR). (G) Log2 OR of being a case is shown across the regulatory variant score quintiles within-cohort (# indicates an OR 95% CI lower bound ≥1; dashed line indicating the null hypothesis, OR = 1, and untransformed ORs to the right.).

Article Snippet: hPSC-Derived Cardiomyocyte Isolation Kit , Miltenyi Biotec , cat# 130-110-188.

Techniques: Sequencing, Hi-C, Variant Assay, Binding Assay, Derivative Assay