biostudies-literatureAldersley JNIDA NIH HHSNIAID NIH HHSNCI NIH HHS1308-1321https://www.ebi.ac.uk/biostudies/studies/S-EPMC8349846biostudies-literatureUnknown19(8)The incidence of anal squamous cell carcinoma (ASCC) has been increasing, particularly in populations with HIV. Human papillomavirus (HPV) is the causal factor in 85% to 90% of ASCCs, but few studies evaluated HPV genotypes and integrations in relation to genomic alterations in ASCC. Using whole-exome sequence data for primary (<i>n</i> = 56) and recurrent (<i>n</i> = 31) ASCC from 72 patients, we detected HPV DNA in 87.5% of ASCC, of which HPV-16, HPV-18, and HPV-6 were detected in 56%, 22%, and 33% of HIV-positive (<i>n</i> = 9) compared with 83%, 3.2%, and 1.6% of HIV-negative cases (<i>n</i> = 63), respectively. Recurrent copy-number variations (CNV) involving genes with documented roles in cancer included amplification of PI3KCA and deletion of APC in primary and recurrent tumors; ampMolecular cancer research : MCRGenomic Landscape of Primary and Recurrent Anal Squamous Cell Carcinomas in Relation to HPV Integration, Copy-Number Variation, and DNA Damage Response Genes.PMC8349846T32 AI007386P50 CA127003R01 DA040391Gabuzda DLorenz DRAldersley JMouw KWD'Andrea ADfalseGenomic Landscape of Primary and Recurrent Anal Squamous Cell Carcinomas in Relation to HPV Integration, Copy-Number Variation, and DNA Damage Response Genes.The incidence of anal squamous cell carcinoma (ASCC) has been increasing, particularly in populations with HIV. Human papillomavirus (HPV) is the causal factor in 85% to 90% of ASCCs, but few studies evaluated HPV genotypes and integrations in relation to genomic alterations in ASCC. Using whole-exome sequence data for primary (<i>n</i> = 56) and recurrent (<i>n</i> = 31) ASCC from 72 patients, we detected HPV DNA in 87.5% of ASCC, of which HPV-16, HPV-18, and HPV-6 were detected in 56%, 22%, and 33% of HIV-positive (<i>n</i> = 9) compared with 83%, 3.2%, and 1.6% of HIV-negative cases (<i>n</i> = 63), respectively. Recurrent copy-number variations (CNV) involving genes with documented roles in cancer included amplification of PI3KCA and deletion of APC in primary and recurrent tumors; amp2021-01-01T00:00:00Z2021 Aug2026-05-08T18:00:17.358Z2022-02-11T15:44:28.252ZS-EPMC83498463388318510.1158/1541-7786.MCR-20-088410.1158/1541-7786.mcr-20-0884