Deletion´s molecular characterization
SNP-array analysis on III4 detected that the deletion spans about 450kb.
Also, it allowed us to delimit the 5’ deletion breakpoint within an
interval defined by SNPs rs1950112 (NC_00023.11:g.32095444) and
rs1795577 (NC_00023.11:g.32092321), while the 3’ breakpoint by SNPs
rs2030002 (NC_00023.11:g.31646698) and rs5972426
(NC_00023.11:g.31646233). Given that distances between these SNPs were
short, we could design a LR-PCR to sequence the breakpoint junction
(Figure 2A). Combination of primers AF1 and AR1 did not amplified,
suggesting that AR1 mapped inside the deletion. Whilst AF1 and AR2
amplified a product of approximately 2,435bp, delimiting the deletion to
446,477bp (NM_004006.3:c.6438+123812_8027+11362del). This deletion
breakpoint junction was confirmed by the several aligned chimeric reads
(i.e., reads that did not map entirely on the reference sequence, such
as ID6762, ID9251, ID26052) obtained by WGS (Figure 2B, Supplementary
Figure 1A). Lastly, characterization of the deletion breakpoint junction
showed a single base “T” of microhomology between introns 44 and 54
(Figure 2C, Table 1).