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Supplementary Table S2 Identification of cryptic recombination signal sequences spanning breakpoint sequences

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Supplementary Table S2 Identification of cryptic recombination signal sequences spanning breakpoint sequences

Patient BKPa Strand RIC

scoreb 5’ breakpoint sequence Filler DNA/MH 3’ breakpoint sequence

RIC

scoreb Strand BKPa

P002 +14 - -38.71 TATCTTCTAAGTATATATGTAATAT ACCCT ACTCCGGTGAGAAGCTCATAGCATA -38.93 - -5

P003 +21 + -30.62 TCTGAATTGACGGCATCCAGGGATC CTCCAT CGGAAGGGAGCCTGCATCATCAGTA -65.26 - -10

P034 -11 + -58.15 TACATTTTAAAGCACTCGGGTTAGT CAG GGTCACCCATGAAGTTCACCTTCAA -63.94 + -48

P056 -9 + -62.80 TTTTTCCTTGCATCCTCAGAGAGAG GCAACGTGTTTACATCTCCAA CAGGCGGATCACTTAAGGTCAGGAG -58.76 - -11

P068 -1 + -30.62 ATCTCAGAAATTATTAGTACATCCC GGCCC ATCCAAGTCAGTAAACCTAAACAGA -60.04 + -9

P069 +7 + -28.01 AACGTAGAGTTTCAGAGGATCAGCA CTCGGACCC TATCCAAGTCAGTAAACCTAAACAG -60.04 + -8

P074 +6 + -64.50 TGAATCCCTTTTCCTTCCATTGTTC None TTGCAAATTAACTCAGGTACCTTGT -61,82 - +24

P086 -35 + -65.63 TGTTTACCAAGTCTTGGTTCACTCC CAG CTCTGCCAATACACCACTGTGGGTG -61,58 + -2

P120 -4 + -51.90 AGAAGTCTGCCAGTCAAGAATATCA TG TCTTTCATCTTATTAATGTCTTTTC -47,01 + -27

P121 +5 + -50.07 TATAATACCATTATCCTATACCAAA T CCGGTGAGAAGCTCATAGCATAAAA -38,93 - -7

P147 -14 - -42.07 TTATTTTGGTGTGAAGTAAGTCATA Not avaliable GACAGTCCACTTAGGATATATCACT -47,67 + -44

aCalculation of the distance between motif start and breakpoint.

bRSSsite (https://www.itb.cnr.it/rss/analyze.html) search was performed using the left (-5) and right (-3) strand surrounding ±50 bp of each breakpoint. The RIC scores similar to RAG consensus sequences are highlighted in bold (12 cRSS: RIC score > -38.81; 23 cRSS: RIC score > -58.45).

BKP, breakpoint; MH, microhomology between 5’ and 3’ sequences.

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