Fig. 3: Copy-number evolution in 56 near diploid and 12 aneuploid BE cells from a high-grade dysplastic Barrett’s esophagus determined by single-cell sequencing. | Nature Communications

Fig. 3: Copy-number evolution in 56 near diploid and 12 aneuploid BE cells from a high-grade dysplastic Barrett’s esophagus determined by single-cell sequencing.

From: Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma

Fig. 3

A Phylogenetic tree with annotated haplotype-specific copy number alterations (blue for losses, red for gains). Each open circle represents a single cell; large filled circles represent subclones (with annotated cell counts) with identical copy number; small filled circles represent inferred intermediate states (gray for pre-WGD, black for post-WGD). Aneuploid cells are separated into two branches each inferred to have undergone an independent whole-genome duplication (WGD) event (black solid line). B–H Examples of copy-number alterations before (B–E) and after (F–H) p53 inactivation. Gray and black dots represent haplotype-specific DNA copy number of parental chromosomes. B Ancestral 3p uniparental disomy (UPD) shared by all but four cells. C Sporadic 3p terminal gain after 3p UPD in one cell. D Large paracentric deletion on 1p and uniparental disomy (UPD) at the 1q-terminus shared by five cells. E Progressive 9p UPD in a subclone of 14 cells. Only four cells are shown, see ”Online Data” for the others. F Terminal duplication adjacent to terminal deletion on 9p shared by cell G1 and D11 that is consistent with two rounds of breakage-fusion-bridge cycles. G Chromothripsis of chr22q shared by cell C5, F2, and F7. H Focal amplification spanning the ERBB2 gene on chr17q (~40 Mb) in cell C5 and F7 (red circles) that displays the signature copy-number pattern of breakage-fusion-bridge cycles. For a detailed list of alterations in each cell, see Supplementary Data 3.

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