Genomic footprints of activated telomere maintenance mechanisms in cancer
Sandra D. Koser,
Delia M. Braun,
Peter J Park,
David TW Jones,
on behalf of the PCAWG Structural Variation Working Group, PCAWG SNV Calling Working Group, PCAWG Drivers and Functional Interpretation Group, PCAWG Evolution and Heterogeneity Working Group, PCAWG Technical Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network
Posted 30 Jun 2017
bioRxiv DOI: 10.1101/157560 (published DOI: 10.1038/s41467-019-13824-9)
Posted 30 Jun 2017
Cancers require telomere maintenance mechanisms for unlimited replicative potential. We dissected whole-genome sequencing data of over 2,500 matched tumor-control samples from 36 different tumor types to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) was increased, tumors with TERT modifications showed a moderate decrease of telomere content. One quarter of all tumor samples contained somatic integrations of telomeric sequences into non-telomeric DNA. With 80% prevalence, ATRX/DAXXtrunc tumors display a 3-fold enrichment of telomere insertions. A systematic analysis of telomere composition identified aberrant telomere variant repeat (TVR) distribution as a genomic marker of ATRX/DAXXtrunc tumors. In this clinically relevant subgroup, singleton TTCGGG and TTTGGG TVRs (previously undescribed) were significantly enriched or depleted, respectively. Overall, our findings provide new insight into the recurrent genomic alterations that are associated with the establishment of different telomere maintenance mechanisms in cancer.
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