Supplemental Figure S8: Multiple sequence alignment and schematic overview of breakpoint - PowerPoint Presentation

1. Supplemental Figure S8: Multiple sequence alignment and schematic overview of breakpoint analysisSequences of 150 bp surrounding each breakpoint were aligned to the normal wild-type proximal and distal sequences using Clustal Omega. The normal proximal and distal wild-type sequences are shown in orange and black respectively. The junction sequence was obtained from Sanger sequencing. The orange and black color of this junction sequence indicate the proximal and distal origins. Microhomology between the proximal and the distal sequences are indicated by shaded yellow box. Inserted sequences are in bold blue and are highlighted in yellow. Known genomic elements (Repetitive elements, non-B conformation motifs, Oligo(G)n tracts) are indicated above and below the sequences. Orientation of these elements are given by arrows. Electropherograms are shown below. However, for deletions 7 and 11, it was not possible to obtain the exact boundaries by Sanger sequencing.

2. Copia-30 FV-ICopia-30 FV-IProximal GAGAATTTGGAGAGGAAGAGGATGGGATGCCGTGGAATTGGGACCAGGAAJunction GAGAATTTGGAGAGGAAGAGGATGGGATGCCGTGGAATTGGGACCAGGAADistal GACTGCTCTCTCAAGTCCCAGGAAACTCACTTTCAGCTTGTCTTAAAAAG  Proximal AGAATGGGGACATGTGATGGTTAAAGCTAGTTAGAGAAGAACTGGGAGATJunction AGAATGGGGACATGTGATGGTTAAAGCAACATGAAATAAGACACCGCAGTDistal CAAGCTGAAGGCTTTTAAAAATGAAGCAACATGAAATAAGACACCGCAGT  Proximal AAACAGTCACCCATGCCCCTGAAGCACTCGGGGTGAAGAGATTGGCATTTJunction TTCTGGCACGGTCCACGCTTAATCCCCTTCAATGTGTGACTTTCCGTGGADistal TTCTGGCACGGTCCACGCTTAATCCCCTTCAATGTGTGACTTTCCGTGGA Deletion 1: c.443-1219_768+1439del Oligo(G)n tractOligo(G)n tract Deletion 2: c.571-801_768+3062del Proximal CACTATCCTTGAGCTACCTAGGAGCTGCAGAATGTGCACTCTGCAGGGCTJunction CACTATCCTTGAGCTACCTAGGAGCTGCAGAATGTGCACTCTGCAGGGCTDistal CTTTTCCATTTGACAAATGGATTACACTAAAAACAAAAATTTACAAAAAA Proximal TAGGGCCTGCAGACAAGATAGATGCAGGGTGTCTAGTTAAATTCGAACTTJunction TAGGGCCTGCAGACAAGATAGATGCAGGCATTAAAATGGGACTTTGCCTTDistal AAAAAAAAAACCTGAAAGAAATTGCAGGCATTAAAATGGGACTTTGCCTT Proximal CAGATAAACAACAAATAATTTTTTCAAATAATTGTGTTCTATTCGGTCCCJunction TATTGCTCCTGGGCCCATCCTATTTGGGTTTTTAGAAAAACAAGCCTGAGDistal TATTGCTCCTGGGCCCATCCTATTTGGGTTTTTAGAAAAACAAGCCTGAGMER53MER53Short tandem repeatInverted repeatInverted repeat Intron 6Intron 4GTTAAAGCAACATGAAIntron 6Intron 5GATGCAGGCATTAAAA

3. Deletion 3: c.699_768+341del  Proximal CCTCCTGGAGCGCTTCATCATCTTCAGCCAGAGACGCGGGGCAAAGACGGJunction CCTCCTGGAGCGCTTCATCATCTTCAGCCAGAGACGCGGGGCAAAGACGGDistal GAGGAGGCCTGGTTTGACTCCCTGACCTGCTATTTCCTAGCCAGGTGATC Proximal TGCGCTATGCCCTGTGCTCCCTCTCCCAGGGCACCCTACAGTGGATAGAAJunction TGCGCTATGCCCTGTGCTCCCTCTCATGGTAAGATATTGAACCTTTTCTGDistal CCTGCTATTTCCTAGCCAGGTGATCATGGTAAGATATTGAACCTTTTCTG Proximal GACACTCTGTATGCCAACGTGGACTTCTTCAAGCTCTTCCGTGTGGTAAGJunction GTCCCAGTACTCATCTATAAAACAAATATAATACTTTACAGAGTGGTAGGDistal GTCCCAGTACTCATCTATAAAACAAATATAATACTTTACAGAGTGGTAGGL1-72 DRL1-72 DROligo(G)n tractMIRbMIRbMIRbDeletion 4: c.1555-1033_1937+615delinsAGC Proximal GAGGCTCTTCCTCCAGGCAGCCTTCCCTGATCCCTCCAGGAAGACTTAGCJunction GAGGCTCTTCCTCCAGGCAGCCTTCCCTGATCCCTCCAGGAAGACTTAGCDistal TGACCAGGAATAAGCCAAGCAAGCAGCCTACTGTTTGACTGAATATGGAT Proximal TGCGTCCCTCCGCTGGGCTTCC----CCAATACACTGGGCTTGCTTTCAT Junction TGCGTCCCTCCGCTGGGCTTCCCAGCCCGGGGTGGAGGGTTGGGAGGCTCDistal TTGGGGGGTGGTAGAGAAAGGG----CCGGGGTGGAGGGTTGGGAGGCTC Proximal TAGAACCTGATCCTTCCACATTATGGTTGTTGGTTTGCTCCAATCCTCTCJunction ATTTGTCATTATAGATGGGGTCAGACACACTACCAAAACAGCAGCAGAGADistal ATTTGTCATTATAGATGGGGTCAGACACACTACCAAAACAGCAGCAGAGAL2cL2cL2cOligo(G)n tractOligo(G)n tractOligo(G)n tractExon 6Intron 6TCCCTCTCATGGTAAG Intron 13Intron 11GGCTTCCCAGCCCGGGGTG

4. Deletion 5: c.1555-3491_1938-83delins1734_1761-107inv    BP1-BP2: (Distal is complementary strand) Proximal GATATTTGTGGCTCCTGCCTGCCATATTGGACAGGGCAGATATAGAACAAJunction GATATTTGTGGCTCCTGCCTGCCATATTGGACAGGGCAGATATAGAACAADistal ACGGGCTTGGATAGCTCACTCACACCTCCCGACCACAGGGTGACTCGGAA Proximal TTCCATCACTGCAGAAAGTTCTACTGAACAATGCTGCTCTGGAGCAGAAGJunction TTCCATCACTGCAGAAAGTTCTACTAAACGCTTCAAAAGGATCCAATTCT Distal CTCATTCTCTTAAAATCTTTCTCCTAAACGCTTCAAAAGGATCCAATTCT Proximal ATCTTCTTGTTCAGGGATGTTACACCCCCGCTTGTGGCTAGAGTGTGGCTJunction ATTTCCTAGTCCTCAGTTTAAATCTCAGTTTTGAATATTAGCCACAATGTDistal ATTTCCTAGTCCTCAGTTTAAATCTCAGTTTTGAATATTAGCCACAATGT MER3MER3Inverted repeatInverted repeatBP3-BP4: (proximal is complementary strand) Proximal TTCCCACTGACTTTGGAGAAATGCAGCGAGCCCTTCCTGAAACATCACCTJunction TTCCCACTGACTTTGGAGAAATGCAGCGAGCCCTTCCTGAAACATCACCTDistal AAAAGATTCCAGCCCATTAAATGTCCAGGGGAGGTTTTCCTGTTTTCCTT Proximal GTCTTTAATCTTATTGGTTTTCTCCACCACGTCTATGTCCATTCGGATCTJunction GTCTTTAATCTTATTGGTTTTCTCCACACATTCATTCAACAAACATTTATDistal TCCCTCCATCTGGGCTTTGTTCTCAACACATTCATTCAACAAACATTTAT Proximal TATACTTCACGTGGGGTGGTAGAGAGCTGGTCCAGGGATACATGTCAGGGJunction TCTGCCTCTACCAGGTACAGAGCACTCTACTATTCTGCTTCTCTCCTTTTDistal TCTGCCTCTACCAGGTACAGAGCACTCTACTATTCTGCTTCTCTCCTTTT Oligo(G)n tractL2aL2aGTTCTACTAAACGCTT Intron 12Intron 11TTTTCTCCACACATTC Intron 13Intron 12

5. Deletion 6: c.1555-2428_2161-101delins2160+7_2160+230invATGAATGinsBP1-BP2 (Distal is complementary strand) Proximal GGCCCAAAGAAATACCAATTCCATATCATTTTAAGATCATTATTAATATCJunction GGCCCAAAGAAATACCAATTCCATATCATTTTAAGATCATTATTAATATCDistal CACCCTGTGCAGGGCTCTGCTAATAGCAGCTTCTCCAGATGGTCACGGAA Proximal TCATCAGCGTGGTGTCACTTAAGCCTGGGCCCTTTAGAATTTTTCATGTAJunction TCATCAGCGTGGTGTCACTTAAGCCATGGACCCCTGGGCAGGAAGTGGGADistal TGGGACTGGGAAGTCTGTGTGGACCATGGACCCCTGGGCAGGAAGTGGGA Proximal CCTGTGTTCCTCTGCCCATATCAGCTGGAACACTAATAGTTTTCTTCCTTJunction GATGGGAGGATGCTGTGATACAGTGGCTCCTTCAGGAGATTTCGTCTCTTDistal GATGGGAGGATGCTGTGATACAGTGGCTCCTTCAGGAGATTTCGTCTCTT Inverted repeatOligo(G)n tractOligo(G)n tractBP3-BP4 (proximal is complementary strand) Proximal TCCAGGCACATGAACAGGAGGAAAGGGGAAAGGAACCAAAGTATTCAAGAJunction TCCAGGCACATGAACAGGAGGAAAGGGGAAAGGAACCAAAGTATTCAAGADistal CTACTCCTCCCAGGGAAAATGGCATTCCTAGGATTAAAGGAACTCAGCAC Proximal TTTTCTGGGCCTTCTCCATTTG-------GCTTACCATGATGAATATCGTJunction TTTTCTGGGCCTTCTCCATTTGATGAATGGACACTAACTGCAGGCTGGTGDistal ATGGAGTGTGCGTAGAAATTTA-------GACACTAACTGCAGGCTGGTG Proximal CAGGAGGAAGATGCTCATCGACATGATGGAGAAGCTGTCCAGGAACCAGGJunction GGAGAGAGCCCTTTAGGGCAGAATGAGAAGGCGTCCGGCCAAGGGCAGGADistal GGAGAGAGCCCTTTAGGGCAGAATGAGAAGGCGTCCGGCCAAGGGCAGGA  Copia-14_Mac-I Copia-14_Mac-I Oligo(G)n tractMamTip2bMamTip2bOligo(G)n tractOligo(G)n tractOligo(G)n tractOligo(G)n tractIntron 14Intron 11CTTAAGCCATGGACCCIntron 14Intron 14TCCATTTGATGAATGGACACTAA

6. Deletion 8: c.4254-197_4672delinsGCTTTTT Proximal ACTGCTTGGGAAGGCCGAATGGGGAAAGGAATGCAAAGCTTAGGTGAATGJunction TTGGGAAGGCCGAATGGGGAAAGGAATGCAAAGCTTAGGTGAATGGGTTGDistal GAGAGAGCTACTAGTAGGCGTGAAGTTCGTGGCCCTGGTCTGAGGATTTC Proximal GGTTGAAGCGCCATCTTTTT-------GAGGCATAGGTGACATGCCATCA Junction AAGCGCCATCTTTTTGAGGCGCTTTTTGAGGAATTTCCATTGGAGGAAAGDistal CTGTTTCCTTGTCAGGTATG-------GAGGAATTTCCATTGGAGGAAAG Proximal GACCACTGCGAGTGTTCAGGCAGCCTACCGCACTCCCAGGAGAGCTAGCGJunction CTCCCAGTCGTCCCCATCACGGGGGAAGCACTTGTTGGGTTTTTAAGCGADistal CTCCCAGTCGTCCCCATCACGGGGGAAGCACTTGTTGGGTTTTTAAGCGAOligo(G)n tractOligo(G)n tractOligo(G)n tractDeletion 9: c.6005+658_6147+757delinsTTTAACAGTGTT Proximal AAACTGGCGTGTGCCCTTGGATTCTGGAGGGTGACTGCTGCTCTCTGTAAJunction AAACTGGCGTGTGCCCTTGGATTCTGGAGGGTGACTGCTGCTCTCTGTAADistal ACAGTACTTCTGGGGATATATTTTTGTATAGTTTTAATTTTTGGAAGCAT Proximal TAAAATGTGTTTAAACAG-------------ACTGGTCCCCTATGGGCAGJunction TAAAATGTGTTTAAACAGTTTTAACAGTGTTAAATCAGTAAGAATGGGAADistal GTTCCACATATTCAAAAA-------------AAATCAGTAAGAATGGGAA Proximal GACAGAGAGGATGAGCTCTCACTCATCTGCCTCTTTCCTGGCTGCAGGAAJunction GTAGGCAAAAATGAAAACAAAAAGAAAACCTAACACTGACAGCAAACTAADistal GTAGGCAAAAATGAAAACAAAAAGAAAACCTAACACTGACAGCAAACTAAInverted repeatOligo(G)n tractOligo(G)n tractLIMC4aLIMC4aLIMC4aExon 33Intron 28TTTGAGGCGCTTTTTGAGGAATTIntron 44Intron 43TTAAACAGTTTTAACAGTGTTAAATCAGT

7. Deletion 10: c.6282+63_6546delProximal GCTGGTGCTGCTGGTAACTGCGGGCTTGGGCCGCACCAAGGGCTTAAACCJunction GCTGGTGCTGCTGGTAACTGCGGGCTTGGGCCGCACCAAGGGCTTAAACCDistal TCCCCTAGATTTGGAGATGGCTATATCGTCACAATGAAGATCAAATCCCC Proximal AAGTGCTGGGTCTCTTGGGTTGGGGAAATAGGTTCTGGGTCGGCAGATTTJunction AAGTGCTGGGTCTCTTGGGTTGGGGAACCCTGTGGAGCAGTTCTTCCAGG Distal GAAGGACGACCTGCTTCCTGACCTGAACCCTGTGGAGCAGTTCTTCCAGG Proximal AGAAACTGCAGCAGTTTGGCTTTAGTCTGGACTGTTTCCTGTGTTGCTCAJunction GGAACTTCCCAGGCAGTGTGCAGAGGGAGAGGCACTACAACATGCTCCAGDistal GGAACTTCCCAGGCAGTGTGCAGAGGGAGAGGCACTACAACATGCTCCAG Inverted repeatOligo(G)n tractOligo(G)n tractOligo(G)n tractGGTTGGGGAACCCTGTExon 48Intron 45