Extended Data Fig. 5: ESC sequences are identical regardless of subsequent relapse.
From: Excised DNA circles from V(D)J recombination promote relapsed leukaemia
a, Alignment of LAM-ESC reads for the SJs examined in Fig. 3c. The schematic above each plot shows the position of the 12- and 23-RSS; the reference (expected) SJ sequence is shown at the top of each alignment. LAM-ESC sequences from the patients indicated to the left, are aligned and confirm that the RSSs are from identical recombination events. Differences in linear amplification during LAM-ESC results in variability in sequence length. Processing of the SJ junction is observed for some SJs, potentially due to SJ reopening by RAGs. These small changes are negligible within 20 kb to 1 Mb of the whole ESC. b, Differential gene expression of PCNA, RBX1, POLE3 and POLE4 determined by DESeq2 for patients who later relapse with high SJ levels (n = 4) and with low SJ levels (n = 3) where the SJ levels were determined in Fig. 2a. Significance of the difference determined by a (two-sided) Wald test with the Benjamini-Hochberg correction for multiple testing (padj).
