Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing
Abstract The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gen...
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Nature Portfolio
2021
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oai:doaj.org-article:28c3bdf55796428aa654af7e652236f02021-12-02T14:21:58ZCase control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing10.1038/s41598-021-83197-x2045-2322https://doaj.org/article/28c3bdf55796428aa654af7e652236f02021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-83197-xhttps://doaj.org/toc/2045-2322Abstract The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gender, race, smoking status and alcohol status. DNA was extracted from oral wash samples from all patients and whole genome shotgun sequencing performed. The raw sequence data was cleaned, reads aligned with the human genome (GRCH38), nonhuman reads identified and then HPV genotypes identified using HPViewer. In the 50 patients with OC-SCC, the most common subsite was tongue in 26 (52%). All patients were treated with primary resection and neck dissection. All but 2 tumors were negative on p16 immunohistochemistry. There were no statistically significant differences between the cases and controls in terms of gender, age, race/ethnicity, alcohol drinking, and cigarette smoking. There was no statistically significant difference between the cancer samples and control samples in the nonhuman DNA reads (medians 4,228,072 vs. 5,719,715, P value = 0.324). HPV was detected in 5 cases (10%) of OC-SCC (genotypes 10, 16, 98) but only 1 tumor sample (genotype 16) yielded a high number of reads to suggest a role in the etiology of OC-SCC. HPV was detected in 4 control patients (genotypes 16, 22, 76, 200) but all had only 1–2 HPV reads per human genome. Genotypes of HPV are rarely found in patients with oral cancer.Ian GanlyZhiheng PeiYuhan HaoYingfei MaMatthew RosenthalZhenglin WuJocelyn MigliacciBin HuangNora KatabiWenzhi TsengStuart BrownYi-Wei TangLiying YangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021) |
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Medicine R Science Q Ian Ganly Zhiheng Pei Yuhan Hao Yingfei Ma Matthew Rosenthal Zhenglin Wu Jocelyn Migliacci Bin Huang Nora Katabi Wenzhi Tseng Stuart Brown Yi-Wei Tang Liying Yang Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing |
| description |
Abstract The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gender, race, smoking status and alcohol status. DNA was extracted from oral wash samples from all patients and whole genome shotgun sequencing performed. The raw sequence data was cleaned, reads aligned with the human genome (GRCH38), nonhuman reads identified and then HPV genotypes identified using HPViewer. In the 50 patients with OC-SCC, the most common subsite was tongue in 26 (52%). All patients were treated with primary resection and neck dissection. All but 2 tumors were negative on p16 immunohistochemistry. There were no statistically significant differences between the cases and controls in terms of gender, age, race/ethnicity, alcohol drinking, and cigarette smoking. There was no statistically significant difference between the cancer samples and control samples in the nonhuman DNA reads (medians 4,228,072 vs. 5,719,715, P value = 0.324). HPV was detected in 5 cases (10%) of OC-SCC (genotypes 10, 16, 98) but only 1 tumor sample (genotype 16) yielded a high number of reads to suggest a role in the etiology of OC-SCC. HPV was detected in 4 control patients (genotypes 16, 22, 76, 200) but all had only 1–2 HPV reads per human genome. Genotypes of HPV are rarely found in patients with oral cancer. |
| format |
article |
| author |
Ian Ganly Zhiheng Pei Yuhan Hao Yingfei Ma Matthew Rosenthal Zhenglin Wu Jocelyn Migliacci Bin Huang Nora Katabi Wenzhi Tseng Stuart Brown Yi-Wei Tang Liying Yang |
| author_facet |
Ian Ganly Zhiheng Pei Yuhan Hao Yingfei Ma Matthew Rosenthal Zhenglin Wu Jocelyn Migliacci Bin Huang Nora Katabi Wenzhi Tseng Stuart Brown Yi-Wei Tang Liying Yang |
| author_sort |
Ian Ganly |
| title |
Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing |
| title_short |
Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing |
| title_full |
Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing |
| title_fullStr |
Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing |
| title_full_unstemmed |
Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing |
| title_sort |
case control study comparing the hpv genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/28c3bdf55796428aa654af7e652236f0 |
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