Fig. 5: HATCHet identifies WGDs in three of four pancreas cancer patients. | Nature Communications

Fig. 5: HATCHet identifies WGDs in three of four pancreas cancer patients.

From: Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data

Fig. 5: HATCHet identifies WGDs in three of four pancreas cancer patients.The alternative text for this image may have been generated using AI.

a HATCHet predicts a WGD in all 31 samples from three patients (Pam02, Pam03, and Pam04). In contrast, published analysis used Control-FREEC and excluded WGDs. b In four samples of patient Pam02, HATCHet predicts a WGD and infers two tumor clones (ellipses in upper right of plot with corresponding proportions) with seven large tumor-clonal clusters (arrows with corresponding copy-number states). These clusters preserve their relative positions in the scaled BAF-RDR plot (each point corresponds to 50kb genomic bin) across samples and their fractional copy numbers correspond to sample-clonal clusters in each sample (dashed black lines), supporting the inference of a tumor-clonal CNA (i.e,. unique copy-number state across samples) for each of these clusters. Note that without a WGD three clusters (red dashed squares) would correspond to subclonal CNAs in all samples. Two additional clusters (peach and olive, starred) are tumor-subclonal as they change their relative position across samples (Pam02_PT18 and Pam02_LiM4 vs. Pam02_LiM3 and Pam02_LiM5), supporting the inference of two distinct tumor clones in this patient. The total copy numbers inferred by Control-FREEC in published analysis are shown on the right y-axis labels in the first scaled BAF-RDR plot.

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