Suzanne de Bruijn

219 Structural variants cause ectopic enhancer-gene contact in retinitis pigmentosa TTCTTAATTTTGATAAAGTTCAATTTACCAATTTTTTTCCTTTTATAAAT -----ATCATATCTTTTTAAAGGAGCTCCCACCTTACCTTGGCAAACTGG AF-AG AF-[AH] [AG-AH] -----ATCATATCTTTTTAAAGGAGCTCCCACCTTACCTTGGCAAACTGG AGTCTATGTCTTGTCTTTTAATTTTCTTAATTGTGTCTTTCAAAAA---G ** * * *** ** ** * * ** *** * H ATGTCTCATTTCAAAGAGGTAATATTTTTT--GTTTGTGGCTTAAACATT ATGTCTCATTTCAAAGAGGTAATATTTTTT--GTTTGTGGCTTAAACATT * * *** * * ** * * ** *** * ** * * * TGTGTTGAGAAGCATATGTGTGTTTTCTTGTCA--TAGTAAGTTCTTACT TGTGTTGAGAAGCATATGTGTGTTTTCTTGTCA--TAGTAAGTTCTTACT TGT-------GCTTTTGGTGTGGTATCTTAGAAATCTTTGCCTAATCCAA *** * ***** * **** * * * * AAAAGTAACTGACCTCTAAGTTTGTTCCCTCAGGCCTACAAATCTGAATA AAAAGTAACTATGTTTTCATATATTTTCTTATTT-ATTCCTTTATT--TA TGTCACAAAGATGTTTTCATATATTTTCTTATTT-ATTCCTTTATT--TA ** * * * * ** * * * * * * ** CTTGAAAATTATCTGACGTGAAATTATCAGGTCCAAAGAGTTAAGTGATT TTTTTAATTTTTCTTTTTT----------TGAGACAAGATCTCTCTCTGT TTTTTAATTTTTCTTTTTT----------TGAGACAAGATCTCTCTCTGT ** ** ** *** * * **** * * * CATTCTGCTTAAATTCATGTA-------------CAGTTAACTTAAACCT CTTCCAGGCTGGAATGCAGTGGCACGATCACACAATGAAGCCTCGAACTT CTTCCAGGCTGGAATGCAGTGGCACGATCACACAATGAAGCCTCGAACTT PRR11 SMG8 GDPD1 YPEL2 LINC01476 WT AE AF AG AH AI PRR11 SMG8 GDPD1 UK-SV8 AE AF * * * * * * * ** * ** *** * GAACACTGATTGCAAGAAACATT- CTGGGCTCAGTGAACCTCCCACTT CTGGGCTCAGTGAACCTCCCACTT ** * ** * ** * GCGCACCCCA------------CCACGCCCGGCTAATTTTTGCATTTTTA -----CAGCACAACATATGCCA------TAGGTCTTATCTGTGATTTTTG [AE-AF] [AF]-AH AG-AH -----CAGCACAACATATGCCA------TAGGTCTTATCTGTGATTTTTG TGATTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAG ** * * * * ** *** **** * TTGTTGTTCAATATGTGGCTTTACAATTTATTATCGTTTATCCATTTCCA TTGTTGTTCAATATGTGGCTTTACAATTTATTATCGTTTATCCATTTCCA * ** ** * *** * ***** * --------GAGTTCTCAACTCACTGTACCTGCTATGAAGTAGGGGCAGTG --------GAGTTCTCAACTCACTGTACCTGCTATGAAGTAGGGGCAGTG GTGGAGACGGGGTTTCACCATATTGTCCAGGC--------TGGTCTTGAA * * * *** * * *** * ** ** * ACAACAAAGATCTTAGAG CT AAACAGAAAAAGCAAGGGGCTAAGACC--- ACAACAAAGATCTTAGAG CT GCCTGCCTCAGCCTCTGACAAGTCTTGGGA CTCCTGACCTCAGGTGAT CT GCCTGCCTCAGCCTCTGACAAGTCTTGGGA * ** ** * * * -------CGTGAGGCCTCGTCCCTTTGCTCCTGCCCTTCACAATTTTGGG TTACAGGCATAAGCCACCGTGCCT-GGCTCTTT--CTCCAAATTTTTGCG TTACAGGCATAAGCCACCGTGCCT-GGCTCTTT--CTCCAAATTTTTGCG * * ** * *** *** **** ** ** * ***** * TATCACCAAGGAACTTGATTAGGGGTAG--CATGCTCTAAGAGGAGGAAA TGGCTGACTCTCACTTGGTTCTCAGAGCTACTTCCTGACGGACCAGTTAT * * ***** ** * * * ** ** ** * TGGCTGACTCTCACTTGGTTCTCAGAGCTACTTCCTGACGGACCAGTTAT GAAGAACCTGGTCACATCTCCACTACGCAGAA CTAGAA------CAGCTCCTCCCTTCTCTG-- **** ** ** * ** * * * CTAGAA------CAGCTCCTCCCTTCTCTG-- SMG8 GDPD1 YPEL2 LINC01476 AH AG AF PRR11 YPEL2 LINC01476 AH AI AF-AG AF-[AH] [AG-AH] AF-AG AF-[AH] [AG-AH] AF-AG AF-[AH] [AG-AH] AF-AG AF-[AH] [AG-AH] AF-AG AF-[AH] [AG-AH] AF-AG AF-[AH] [AG-AH] [AE-AF] [AF]-AH AG-AH [AE-AF] [AF]-AH AG-AH [AE-AF] [AF]-AH AG-AH [AE-AF] [AF]-AH AG-AH [AE-AF] [AF]-AH AG-AH [AE-AF] [AF]-AH AG-AH MIR4729 MIR4729 MIR4729 Figure S5. Assessment of microhomology at breakpoint sequences. (A-H) Breakpoint regions of structural variants (SVs) were assessed for presence of microhomology using multiple sequence alignment between the junction fragment and the 5’ and 3’ breakpoint regions using Clustal Omega. 150 bp reference sequences flanking each side of the breakpoint were used as input. Regions of microhomology are indicated in red. Breakpoint annotation of genomic regions as illustrated in Figure 2 .