Genomic and transcriptomic characterization of tumor cell lines displaying ring or giant marker chromosomes with neocentromeres

Genomic amplification in the form of rings or giant chromosomes is reported as a common genetic alteration in soft tissue tumours. The mitotic stability of these structures is often rescued by the emergence of perfectly functioning analphoid neocentromeres, which, thus, significantly contribute to cancer progression. Here, we analyzed three well-differentiated liposarcoma (WDLPS) cell lines (93T449, 94T778, 95T1000) and one lung sarcomatoid carcinoma (LSC) cell line (04T036) by ChIP-seq using a polyclonal antibody directed against the CENP-A centromeric protein, to specifically investigate their neocentromere structures and reconstruct their genomic organization at nucleotide-resolution level. In parallel, we performed whole-genome sequencing (WGS) to confirm complex amplicon architecture identified from ChIP-seq data, and transcriptome sequencing (Total RNA-seq) to profile gene expression pattern and chimeric transcripts originating from rings/giant chromosomes. The same samples were characterized also by SNP array technology for genomic profiling (Affymetrix SNP 6.0, raw data available in Array Express repository under Accession Number E-MTAB-5625).