HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study.

Autor: Warden CD; Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, 91010, USA., Cholli P; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37212, USA., Qin H; Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, 91010, USA., Guo C; Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, 91010, USA., Wang Y; Molecular Pathology Core, City of Hope National Medical Center, Duarte, CA, 91010, USA., Kancharla C; Research Informatics, City of Hope National Medical Center, Duarte, CA, 91010, USA., Russell AM; Clinical Informatics, City of Hope National Medical Center, Duarte, CA, 91010, USA., Salvatierra S; Biorepository, City of Hope National Medical Center, Duarte, CA, 91010, USA., Mutsvunguma LZ; Department of Immuno-Oncology, City of Hope National Medical Center, Duarte, CA, 91010, USA., Higa KK; Office of Faculty and Institutional Support, City of Hope National Medical Center, Duarte, CA, 91010, USA., Wu X; Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, 91010, USA., Wilczynski S; Department of Pathology, City of Hope National Medical Center, Duarte, CA, 91010, USA., Pillai R; Molecular Pathology Core, City of Hope National Medical Center, Duarte, CA, 91010, USA.; Department of Pathology, City of Hope National Medical Center, Duarte, CA, 91010, USA., Ogembo JG; Department of Immuno-Oncology, City of Hope National Medical Center, Duarte, CA, 91010, USA. jogembo@coh.org.
Jazyk: angličtina
Zdroj: Infectious agents and cancer [Infect Agent Cancer] 2022 Aug 09; Vol. 17 (1), pp. 44. Date of Electronic Publication: 2022 Aug 09.
DOI: 10.1186/s13027-022-00456-w
Abstrakt: Background: Human papillomavirus (HPV) is the primary cause of invasive cervical cancer (ICC). The prevalence of various HPV genotypes, ranging from oncogenically low- to high-risk, may be influenced by geographic and demographic factors, which could have critical implications for the screening and prevention of HPV infection and ICC incidence. However, many technical factors may influence the identification of high-risk genotypes associated with ICC in different populations.
Methods: We used high-throughput sequencing of a single amplicon within the HPV L1 gene to assess the influence of patient age, race/ethnicity, histological subtype, sample type, collection date, experimental factors, and computational parameters on the prevalence of HPV genotypes detected in archived DNA (n = 34), frozen tissue (n = 44), and formalin-fixed paraffin-embedded (FFPE) tissue (n = 57) samples collected in the Los Angeles metropolitan area.
Results: We found that the percentage of off-target human reads and the concentration of DNA amplified from each sample varied by HPV genotype and by archive type. After accounting for the percentage of human reads and excluding samples with especially low levels of amplified DNA, the HPV prevalence was 95% across all ICC samples: HPV16 was the most common genotype (in 56% of all ICC samples), followed by HPV18 (in 21%). Depending upon the genotyping parameters, the prevalence of HPV58 varied up to twofold in our cohort. In archived DNA and frozen tissue samples, we detected previously established differences in HPV16 and HPV18 frequencies based on histological subtype, but we could not reproduce those findings using our FFPE samples.
Conclusions: In this pilot study, we demonstrate that sample collection, preparation, and analysis methods can influence the detection of certain HPV genotypes and must be carefully considered when drawing any biological conclusions based on HPV genotyping data from ICC samples.
(© 2022. The Author(s).)
Databáze: MEDLINE
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