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. Author manuscript; available in PMC: 2020 Nov 1.
Published in final edited form as: Oral Oncol. 2019 Sep 18;98:53–61. doi: 10.1016/j.oraloncology.2019.09.004

Figure 1. Low-coverage sequencing results of a representative panel of HNSCC cell lines.

Figure 1

Copy number profiles of a panel of HNSCC cell lines were obtained using low coverage whole-genome sequencing. Using the ACE package [19], the absolute copy numbers of all chromosomes per cell line was determined. Red represents a gain of the chromosomal region, blue a loss, white is neutral (no genomic aberration). All HNSCC lines, except for VU-SCC-040, showed large copy number aberrations with a high frequency of gains and losses.

a

ACE analysis revealed that 5 cell lines were near diploid, of which one HPV-positive cell line (UM-SCC-47) and one FA-HNSCC cell line (CCH-FAHNSCC-2). Interestingly, VU-SCC-040, a HPV-negative HNSCC line showed a copy number silent profile with just 3 single gains.

b

The majority of HNSCC lines (n=19) exhibited many copy number gains and losses, and became aneuploid to near 3N.