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. 2015 Jun 30;10(6):e0130666. doi: 10.1371/journal.pone.0130666

Fig 4. Classification of tumours by mechanism of retention/loss of heterozygosity at markers proximal and distal to Bcl11b on chromosome 12.

Fig 4

C-TL (n = 93) and G-TL (n = 16) were classified according to the LOH results at D12Mit132 (Proximal to Bcl11b) and D12nds2 (Distal to Bcl11b) on chromosome 12 combined with DNA copy number results from array CGH and/or DNA copy number RQ-PCRs at D12Mit132, D12nds2 and within Bcl11b (the remaining 8 C-TL samples had insufficient DNA for copy number screening). The frequencies of Telomeric Deletion LOH (deletion at both sites), Telomeric Recombination LOH (recombination at both sites) and Paired Deletion & Recombination (both mechanisms in either order) were similar for both carbon and gamma groups, yet the overall distribution of the classes was significantly different between carbon and gamma groups (P<0.0001, Pearson’s Chi-Squared) since although 5/16 gamma tumours (31%) retained both alleles either side of Bcl11b (Retained Heterozygosity), 0/93 carbons tumours retained both alleles (P = 0.0001, Fisher’s Exact). In contrast, 32/93 carbon tumours (34%) lost one allele at D12Mit132 (upstream of Bcl11b) and yet retained both alleles towards the telomere at D12nds2 (Interstitial Deletion or Recombination LOH) while this was not observed (0/16) in gamma tumours (P = 0.003, Fisher’s Exact).