Additional file 1: Figure S1. of CATCHing putative causative variants in consanguineous families

Flow chart diagram explaining the process of identification and ranking of putative candidate variants. After assignment of the pathogenicity scores according to SIFT, PolyPhen (PP) and MutationTaster (MT), CATCH classifies the variants according to ROHs (see Fig. 1 and main text). Only Class I and Class III are further labeled as: pathogenic - being a known pathogenic or a predicted pathogenic variant inside a know pathogenic gene related to the phenotype; strong candidate - predicted pathogenic variant in a gene likely involved in the pathology according to supporting literature data; Variant of Unknown significance (VUS) - predicted pathogenic variant in a gene not known to be related to the phenotype; − Benign - predicted non pathogenic variants not reported as causative in the literature. (DOCX 56 kb

Additional file 2: Table S1. of CATCHing putative causative variants in consanguineous families

Class I pathogenic variants in known disease-causing genes identified in 17 consanguinous families. (DOCX 15 kb

The overall DNA methylation level at single CpG resolution, and over genomic features.

<p>The probability density distribution and the box-plot of DNA methylation shows differences between the T21 twin and the normal twin at the level of A) single CpG sites, B) promoters, C) CpG islands, D) Exons, E) Introns, F) LADs, and G) iLADs. The red line in the probability plot shows the probability distribution of T21 twin methylome subtracted from the normal twin methylome (T21—N). While, the blue line shows the probability distribution of the normal twin methylome subtracted from T21 twin methylome (N—T21). DNA hyper-methylation in T21 twin (T21 > Normal) is observed at the level of CpGs, and all the genomic features, but the effect is more pronounced in promoters and CpG islands.</p

DMRs in MZ twin discordant for T21.

<p><b>*</b>Meth (T21 –N) represents the percent methylation difference between T21 twin and normal twin. The positive sign means T21 twin is more methylated than the Normal twin, and the negative sign means Normal twin is more methylated than T21 twin.</p><p>DMRs in MZ twin discordant for T21.</p

GO terms associated with DMRs identified in MZ twins discordant for T21.

<p><i>P</i>, nominal p-value.</p><p><i>FDR</i>, False Discovery Rate- Benjamini–Hochberg.</p><p>GO terms associated with DMRs identified in MZ twins discordant for T21.</p

GO terms associated with DMRs identified in T21 MZ twins discordant for CHD.

<p><i>P</i>, nominal <i>p</i>-value.</p><p><i>FDR-BH</i>, False Discovery Rate- Benjamini–Hochberg.</p><p>GO terms associated with DMRs identified in T21 MZ twins discordant for CHD.</p

Common DMRs observed in the two sets of T21 MZ twins discordant for AVSD and VSD.

<p>Methylation differences show the DNA methylation percent difference between normal twin and twin with cardiac defect. Log₂FC shows log₂ fold change of RPKM value of gene expression in T21 normal twin over T21 twin with VSD. Gene expression data for T21 twins discordant for AVSD is not available. NA, Not available.</p><p>Common DMRs observed in the two sets of T21 MZ twins discordant for AVSD and VSD.</p

DNA methylation profile over a “Gene Model”.

<p>DNA methylation fold change in A) Monozygotic twins discordant for T21, B) Unrelated T21 and normal cases, C) Normal MZ twins, D) T21 MZ twins. TSS and TTS represent transcription start site and transcription termination sites, respectively. The plot shows an increase in the level of DNA methylation around TSS in T21 twin compared to the normal twin.</p

CpGs Coverage of MZ-twins discordant for T21.

<p>A) Distributions of covered CpGs (≥20X read coverage) by RRBS in promoters, exons, introns, and intergenic regions are shown in the pie chart. The blue bar in the histogram panel shows how many percentages of the genomic features are covered by RRBS. B) Distributions of covered CpGs (≥20X read coverage) by RRBS in CpG islands.</p

Histone modification and TFBS enrichment analyses of DMRs associated with AVSD.

<p><i>P</i>, nominal p-value.</p><p><i>FDR</i>, False Discovery Rate- Benjamini–Hochberg.</p><p>Histone modification and TFBS enrichment analyses of DMRs associated with AVSD.</p