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Figure S2. D3 specific structure variations (SVs) analysis. Alignments of reads in both D3 (top panel) and D4 (bottom panel) at each break points detected by CREST. The header lines in blue given the detail information of each structure variation (columns meanings: left_chr, left_pos, left_strand, number of left soft-clipped reads, right_chr, right_pos, right_strand, number right soft-clipped reads, SV type, coverage at left_pos, coverage at right_pos, assembled length at left_pos, assembled length at right_pos, average percent identity at left_pos, percent of non-unique mapping reads at left_pos, average percent identity at right_pos, percent of non-unique mapping reads at right_pos, start position of consensus mapping to genome, starting chromosome of consensus mapping, position of the genomic mapping of consensus starting position, end position of consensus mapping to genome, ending chromosome of consensus mapping, position of genomic mapping of consensus ending position, and consensus sequences). (PDF 626 kb)

Figure S12. DNA methylation detection of ZIC3 from clinical samples. Bisulfite sequencing tested DNA methylation status of DMRs in ZIC3 in 20 clinical samples, five normal providers (1â 5) and fifteen DORV patients (6â 20). Methylated and unmethylated CpG sites are indicated as respective black and white circles. (PDF 5226 kb)

Figure S4. Comparison of systemic changes of methylome between two samples. (A) Cumulative depth distribution of RRBS data. The x-axis represents the depth of cytosine, and the y-axis represents the fraction of cytosine â ¤ depth. (B) Methylation levels distribution in two samples of three different kinds of cytosine (CG, CHG, CHH). The x-axis is the methylation level; y-axis shows the log2 counts of the cytosine under a methylated level. (C) CHH methylation profile in the gene body, upstream and downstream. (D) CHG methylation profile in the gene body, upstream and downstream. (PDF 891 kb)

Figure S4. Comparison of systemic changes of methylome between two samples. (A) Cumulative depth distribution of RRBS data. The x-axis represents the depth of cytosine, and the y-axis represents the fraction of cytosine â ¤ depth. (B) Methylation levels distribution in two samples of three different kinds of cytosine (CG, CHG, CHH). The x-axis is the methylation level; y-axis shows the log2 counts of the cytosine under a methylated level. (C) CHH methylation profile in the gene body, upstream and downstream. (D) CHG methylation profile in the gene body, upstream and downstream. (PDF 891 kb)

Figure S9. Aberrant methylation in the upstream regions of MTA2. Visualizing the methylation levels of DMRs near MTA2 with UCSC genome browser. Methylated levels in the twins are showed in blue (D3) and red (D4). Transcription factor binding sites are also showed in zooming-in panels, which indicated by black bars with names marked in front. An arrow gives TSS and transcriptional orientation. Transcription factor binding sites, Pol II ChIP-seq and TBP ChIP-seq data from ENCODE. (PDF 633 kb)

Figure S11. Aberrant methylation in the upstream regions of SUV39H1. Visualizing the methylation levels of DMRs near SUV39H1 with UCSC genome browser. Methylated levels in the twins are showed in blue (D3) and red (D4). Transcription factor binding sites are also showed in zooming-in panels, which indicated by black bars with names marked in front. An arrow gives TSS and transcriptional orientation. Transcription factor binding sites, Pol II ChIP-seq and TBP ChIP-seq data from ENCODE. (PDF 748 kb)

Figure S8. Aberrant methylation in the upstream regions of NSD1. Visualizing the methylation levels of DMRs near NSD1 with UCSC genome browser. Methylated levels in the twins are showed in blue (D3) and red (D4). Transcription factor binding sites are also showed in zooming-in panels, which indicated by black bars with names marked in front. An arrow gives TSS and transcriptional orientation. Transcription factor binding sites, Pol II ChIP-seq and TBP ChIP-seq data from ENCODE. (PDF 781 kb)

Figure S13. DNA methylation detection of NR2F2 from clinical samples. Bisulfite sequencing detected DNA methylation status of DMRs in NR2F2 in 20 clinical samples, five normal providers (1â 5) and fifteen DORV patients (6â 20). Methylated and unmethylated CpG sites are indicated as black and white circles, respectively. (PDF 5463 kb)

Figure S10. Aberrant methylation in the upstream regions of MECP2. Visualizing the methylation levels of DMRs near MECP2 with UCSC genome browser. Methylated levels in the twins are showed in blue (D3) and red (D4). Transcription factor binding sites are also showed in zooming-in panels, which indicated by black bars with names marked in front. Arrows give TSSs and transcriptional orientation. Transcription factor binding sites, Pol II ChIP-seq and TBP ChIP-seq data from ENCODE. (PDF 969 kb)

Figure S7. Aberrant methylation in the upstream regions of SOX3. Visualizing the methylation levels of DMRs near SOX3 with UCSC genome browser. Methylated levels in the twins are showed in blue (D3) and red (D4). Transcription factor binding sites are also showed in zooming-in panels, which indicated by black bars with names marked in front. An arrow gives TSS and transcriptional orientation. Transcription factor binding sites, Pol II ChIP-seq and TBP ChIP-seq data from ENCODE. (PDF 590 kb)

Figure S5. Aberrant methylation in the upstream regions of CITED1. Visualizing the methylation levels of DMRs near CITED1 with UCSC genome browser. Methylated levels in the twins are showed in blue (D3) and red (D4). Transcription factor binding sites are also showed in zooming-in panels, which indicated by black bars with names marked in front. Arrows give TSSs and transcriptional orientation. Transcription factor binding sites, Pol II ChIP-seq and TBP ChIP-seq data from ENCODE. (PDF 910 kb)

Figure S6. Aberrant methylation in the upstream regions of GATA2. Visualizing the methylation levels of DMRs near GATA2 with UCSC genome browser. Methylated levels in the twins are showed in blue (D3) and red (D4). An arrow gives TSS and transcriptional orientation. Transcription factor binding sites, Pol II ChIP-seq and TBP ChIP-seq data from ENCODE. (PDF 767 kb)