105P RADseq for tumour mutation burden estimation and mutation signature analysis
نویسندگان
چکیده
Tumour mutation burden (TMB) is a biomarker for cancer immune checkpoint blockade (ICB) response, and signatures provide “life history” of tumour evolution. Researchers have repurposed gene panels (CGPs) to cheaply estimate these parameters. The low coverage CGPs, however, may be problematic in the exploration TMB as ICB. Restriction enzyme associated DNA sequencing (RADseq) uses restriction enzymes achieve at random loci throughout genome. It was hypothesised that RADseq could recapitulate breast samples. In silico libraries were generated by scanning human genome cut sites filtering regions with adjacent sites. resulting fragments overlapped mutations from whole (WGS) genomes. evaluated terms accuracy estimation profile recapitulation, compared CGP used A mouse cell line transfected APOBEC enzymes, which are known cause cancer, profiled using RADseq. Using cosine similarity (CS) WGS measure recapitulation quality, able signatures, while performed relatively poorly this regard (e.g. enzyme_1 CS=0.90±0.06 vs CS=0.28±0.19). had higher error than an library comparable (CGP range 0.0034-8.83 mutations/mb enzyme_2 0.0029-7.50, Wilcox p<0.001). RADseq, increased signature detected APOBEC3A, both absent control lines. methods do not accurately capture “genome-wide” parameters such signatures. This warrants investigation into whether can ICB trials. By comparison, offer cheap, effective solution estimation. also use researchers seeking study evolution model systems, we demonstrated.
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ژورنال
عنوان ژورنال: Annals of Oncology
سال: 2022
ISSN: ['0923-7534', '1569-8041']
DOI: https://doi.org/10.1016/j.annonc.2022.09.106