Salivary HPV DNA informs locoregional disease status in advanced HPV-associated oropharyngeal cancer

Hanna, Glenn J.; Lau, Christie J.; Mahmood, Umair; Supplee, Julianna; Mogili, Abhishek; Haddad, Robert I.; Jänne, Pasi A.; Paweletz, Cloud P.

doi:10.1016/j.oraloncology.2019.06.019

Cited by 38 publications

(50 citation statements)

References 27 publications

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“…123 Additional papers on saliva-based liquid biopsies have also shown promising results, especially in oropharyngeal cancer. 19,124,125 The role of circulating EBV in NPC has also been assessed in many studies. 126 The presence of plasma EBV-DNA has been shown to be of clinical value in prognostication, 127,128 monitoring of recurrence 129,130 and even in screening for NPC.…”

Section: Virus-specific Dna Elementsmentioning

confidence: 99%

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

et al. 2020

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Cell-free DNA (cfDNA) derived from tumours is present in the plasma of cancer patients. The majority of currently available studies on the use of this circulating tumour DNA (ctDNA) deal with the detection of mutations. The analysis of cfDNA is often discussed in the context of the noninvasive detection of mutations that lead to resistance mechanisms and therapeutic and disease monitoring in cancer patients. Indeed, substantial advances have been made in this area, with the development of methods that reach high sensitivity and can interrogate a large number of genes. Interestingly, however, cfDNA can also be used to analyse different features of DNA, such as methylation status, size fragment patterns, transcriptomics and viral load, which open new avenues for the analysis of liquid biopsy samples from cancer patients. This review will focus on the new perspectives and challenges of cfDNA analysis from mutation detection in patients with solid malignancies.

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Section: Virus-specific Dna Elementsmentioning

confidence: 99%

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

et al. 2020

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“…Over the past decade, several studies have demonstrated the potential applications of ctDNA analysis for early detection of relapse, treatment selection and response monitoring, as well as tracking of tumour heterogeneity in a variety of cancer types including non-small cell lung cancer [9,10], colon cancer [11,12], breast cancer [6,[13][14][15] and others [7,[16][17][18]. For the subset of HPV-associated oropharyngeal SCC, circulating tumour HPV DNA (ctHPVDNA) has emerged as a promising biomarker for monitoring treatment response and recurrence [19][20][21][22][23][24][25][26]. In contrast, except for a few published studies, ctDNA in HPV-negative HNSCC has not yet been sufficiently studied [27][28][29][30][31][32][33][34].…”

Section: Introductionmentioning

confidence: 99%

Liquid BIOpsy for MiNimal RESidual DiSease Detection in Head and Neck Squamous Cell Carcinoma (LIONESS)—a personalised circulating tumour DNA analysis in head and neck squamous cell carcinoma

Flach

Howarth²,

Hackinger³

et al. 2022

Br J Cancer

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Background Head and neck squamous cell carcinoma (HNSCC) remain a substantial burden to global health. Cell-free circulating tumour DNA (ctDNA) is an emerging biomarker but has not been studied sufficiently in HNSCC. Methods We conducted a single-centre prospective cohort study to investigate ctDNA in patients with p16-negative HNSCC who received curative-intent primary surgical treatment. Whole-exome sequencing was performed on formalin-fixed paraffin-embedded (FFPE) tumour tissue. We utilised RaDaRTM, a highly sensitive personalised assay using deep sequencing for tumour-specific variants, to analyse serial pre- and post-operative plasma samples for evidence of minimal residual disease and recurrence. Results In 17 patients analysed, personalised panels were designed to detect 34 to 52 somatic variants. Data show ctDNA detection in baseline samples taken prior to surgery in 17 of 17 patients. In post-surgery samples, ctDNA could be detected at levels as low as 0.0006% variant allele frequency. In all cases with clinical recurrence to date, ctDNA was detected prior to progression, with lead times ranging from 108 to 253 days. Conclusions This study illustrates the potential of ctDNA as a biomarker for detecting minimal residual disease and recurrence in HNSCC and demonstrates the feasibility of personalised ctDNA assays for the detection of disease prior to clinical recurrence.

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“…We used oral rinse samples from each patient and extracted DNA from cell pellets prior to sequencing. DNA extracted from oral rinse samples has been reported to be a sensitive and specific method for www.nature.com/scientificreports/ the identification of patients with oropharyngeal cancer [18][19][20][21][22] as well as the detection of persistent or recurrent cancer in patients who have completed treatment [23][24][25] . Our sequencing methodology using MSS was also sound with comparable reads in both tumor and control samples.…”

Section: Discussionmentioning

confidence: 99%

“…The detection of HPV in oral rinse samples and saliva samples using PCR has been reported as being a sensitive and specific method for the detection of HPV related oropharyngeal cancer [18][19][20][21][22][23][24][25] . This technique has been reported as a potential screening method for HPV oropharynx cancer [18][19][20][21][22] and also for the detection of persistent disease or recurrent disease following treatment in patients with HPV related oropharyngeal cancer [23][24][25] . We therefore used oral rinse specimens from patients with oral cavity cancer and patients with no head and neck cancer for the detection of HPV genotypes.…”

Section: Detection Of All 200 Genotypes Of Hpv In Mouthwash Samples Omentioning

confidence: 99%

Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing

Ganly

Pei

Hao

et al. 2021

Sci Rep

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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.

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Salivary HPV DNA informs locoregional disease status in advanced HPV-associated oropharyngeal cancer

Cited by 38 publications

References 27 publications

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

Liquid BIOpsy for MiNimal RESidual DiSease Detection in Head and Neck Squamous Cell Carcinoma (LIONESS)—a personalised circulating tumour DNA analysis in head and neck squamous cell carcinoma

Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing

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