Warden Charles D, Cholli Preetam, Qin Hanjun, Guo Chao, Wang Yafan, Kancharla Chetan, Russell Angelique M, Salvatierra Sylvana, Mutsvunguma Lorraine Z, Higa Kerin K, Wu Xiwei, Wilczynski Sharon, Pillai Raju, Ogembo Javier Gordon
Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, 91010, USA.
Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37212, USA.
Infect Agent Cancer. 2022 Aug 9;17(1):44. doi: 10.1186/s13027-022-00456-w.
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.
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.
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.
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.
人乳头瘤病毒（HPV）是浸润性宫颈癌（ICC）的主要病因。从致癌低风险到高风险的各种HPV基因型的流行率可能受地理和人口因素影响，这可能对HPV感染的筛查和预防以及ICC发病率具有关键意义。然而，许多技术因素可能影响不同人群中与ICC相关的高危基因型的鉴定。
我们使用HPV L1基因内单个扩增子的高通量测序来评估患者年龄、种族/民族、组织学亚型、样本类型、采集日期、实验因素和计算参数对在洛杉矶大都市区收集的存档DNA（n = 34）、冷冻组织（n = 44）和福尔马林固定石蜡包埋（FFPE）组织（n = 57）样本中检测到的HPV基因型流行率的影响。
我们发现脱靶人类读数的百分比以及从每个样本中扩增的DNA浓度因HPV基因型和存档类型而异。在考虑人类读数的百分比并排除扩增DNA水平特别低的样本后，所有ICC样本中的HPV流行率为95%：HPV16是最常见的基因型（在所有ICC样本中的占比为56%），其次是HPV18（占比为21%）。根据基因分型参数，在我们的队列中，HPV58的流行率变化高达两倍。在存档DNA和冷冻组织样本中，我们检测到基于组织学亚型在HPV16和HPV18频率上先前已确定的差异，但使用我们的FFPE样本无法重现这些发现。
在这项初步研究中，我们证明样本采集、制备和分析方法可影响某些HPV基因型的检测，并且在基于ICC样本的HPV基因分型数据得出任何生物学结论时必须仔细考虑这些因素。
