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Genome complexity in CLL: karyotype versus microarrays
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Figure 1. Distribution of the number of copy number abnormalities detected by genomic microarrays among the groups identified by chromosome banding analysis. Patients were divided according to the risk groups defined by chromosome banding analysis (CBA) in non- complex karyotype (non-CK) (0-2 abnormalities [abn.]), low/intermediate-CK (3-4 abn.) or high- CK (≥5 abn.). Each plot represents copy number abnormality (CNA) counts found when non-clas- sical chronic lymphocytic leukemia (CLL) abnor- malities were filtered by different strategies: (A) Current recommended criteria for genomic microarrays (GM) analysis (cut-off size: ≥5 Mb); (B) considering all the CNA irrespectively of their size; (C) considering only those CNA ≥1 Mb; (D) filtering by 1 Mb cut-off and grouping small contiguous abnormalities or considering those CNA included in a chromothripsis event as a unique CNA. Spearman correlation coeffi- cient between CBA and GM counts is shown for each GM analysis.
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correlation in the number of abnormalities counted by CBA and GM was achieved. Similar results were observed when including all the abnormalities irrespective of their size, using 1 Mb as a cut-off for non-classical CLL CNA, or if CNA separated by <1 Mb or chromothripsis patterns were counted as one event to evaluate the effect of joining con- secutive aberrations (Figure 1).
Parallel analyses of the abnormalities detected by CBA and GM were also performed to identify other potential causes of discrepancy. Among those abnormalities recorded only by CBA, differences were mainly due to the presence of balanced translocations (n=28 patients) or abnormalities
represented in a minor proportion of tumor cells probably expanded during the cytogenetics culture which were missed by GM (n=40 patients). Moreover, FISH with chro- mosome painting probes performed in two high-CK cases by CBA, who showed low-GC, revealed that some appar- ently unbalanced abnormalities were complex balanced rearrangements that ultimately did not lead to loss of mate- rial (Online Supplementary Figure S2). On the other hand, when assessed by GM, most of the more complex cases showed aberrations <10 Mb, which is the resolution threshold of CBA, or multiple CNA that corresponded to complex rearrangements recorded as single abnormalities in
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