Fig. 6

NODAL heterozygous copy number variant (CNV) deletion alleles in laterality defect cases. A Proband LAT1415 pedigree (Family 30) (delCNV/+ heterozygous, +/+ WT homozygous). B HMZDelFinder analyses detected a CNV deletion at the 5′ start of NODAL using ES read count data (RPKM); red vertical dashed lines align to each gene exon, horizontal jagged lines (black: controls; red: deletion CNV subject) show distribution of individual read depth values for that given exon. C The Alu-Alu mediated rearrangement (AAMR) risk score for NODAL and EIF4EBP2 using AluAluCNVpredictor tool. D Family 30 aCGH showed a 46-kb deletion in proband and father. E The 1% agarose gel electrophoresis of PCR products showing the recombinant junction. The junction primer pair was designed to produce an amplicon size of 465 base pairs for deleted alleles resulting from AAMR with the formation of a chimeric Alu. F Family 31 pedigree of proband (CVG007). G Confirmation by aCGH showed a ~4 kb deletion CNV spanning NODAL exon 3. H The gel electrophoresis of PCR products showing the recombinant junction with lighter 700 base pair bands representing heterozygous deleted alleles and more intense bands (~4 kb) representing WT allele. I A schematic representation of NODAL and EIF4EBP2. Note convergent transcripts for NODAL and EIF4EBP2 (black arrow heads representing gene’s orientation). Breakpoint sequences for NODAL deletions are also shown. The proximal reference sequence and its matching proband breakpoint sequences are shown in green for LAT1415 and orange for CVG007, the distal reference sequence and its matching proband breakpoint sequences are in blue for LAT1415 and purple for CVG007, and microhomology at the junction is shown in red. The 46 kb deletion in LAT1415 presumably results from AAMR between AluSx1/AluSq2, whereas the 4 kb deletion in CVG007 proposed to result from AAMR between AluSg/AluSq2