Fig. 3: Somatic copy number alterations (SCNAs) and structural variants (SVs) in skull-base chordoma patients. | Nature Communications

Fig. 3: Somatic copy number alterations (SCNAs) and structural variants (SVs) in skull-base chordoma patients.

From: Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival

Fig. 3

a Genome-wide SCNAs. Patients were clustered into five groups. Group 1: extensive SCNAs, lacking deletions of 4, 9, and 14; Group 2: extensive SCNAs, lacking amplifications; Group 3: scattered SCNAs, most of which are deletions; Group 4: no or few SCNAs; and Group 5: extensive amplifications demonstrating characteristic consistent with whole-genome doubling. b Representative examples showing complex rearrangements at chromosome 9p. Plots show copy ratios (tumor vs. matched normal) of the chromosome 9p21 region. All three samples show an arm-level deletion coupled with complex rearrangements (top) and focal deletions of the 9p21.3 region (middle) or the CDKN2A/2B locus (bottom), resulting in the homozygous loss of CDKN2A/2B. c An example of complex rearrangements at chromosome 3p. D deletion, TD tandem duplication, HH head-to-head inverted, TT tail-to-tail inverted. d A chordoma sample showing chromothripsis of the 6q region, where the TBXT gene is located. See also Supplementary Tables 4 and 5.

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