Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR

• Published in: British journal of cancer Vol. 123; no. 12; pp. 1790 - 1795
• Main Authors: Arroyo Mühr, Laila Sara, Lagheden, Camilla, Lei, Jiayao, Eklund, Carina, Nordqvist Kleppe, Sara, Sparén, Pär, Sundström, Karin, Dillner, Joakim
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 08.12.2020; Nature Publishing Group UK
• Subjects: Adult; Aged; Aged, 80 and over; Alphapapillomavirus - isolation & purification; Cervical cancer; Cervix; Confidence Intervals; DNA, Viral - isolation & purification; Female; High-Throughput Nucleotide Sequencing - methods; High-Throughput Nucleotide Sequencing - statistics & numerical data; Human papillomavirus; Humans; Invasiveness; Medical screening; Medicin och hälsovetenskap; Middle Aged; Negative Results - statistics & numerical data; Nucleotide sequence; Paraffin; Pilot projects; Polymerase chain reaction; Quality assurance; Reverse Transcriptase Polymerase Chain Reaction; Sweden; Tumors; Uterine Cervical Neoplasms - pathology; Uterine Cervical Neoplasms - virology; Sweden
• DOI: 10.1038/s41416-020-01111-0
• ISSN: 0007-0920; 1532-1827

Human papillomavirus (HPV) is a necessary cause of cervical cancer, although some invasive cervical cancers may test negative by HPV PCR. We previously requested all invasive cervical cancers in Sweden during 10 years and subjected them to PCR. We also optimised methods for deep sequencing of formalin-fixed paraffin-embedded samples. Using Novaseq 6000, we simultaneously sequenced total DNA and cDNA from 392 HPV PCR-negative cervical cancers. Non-human reads were queried against all known HPVs. The complete database now contains PCR and/or deep sequencing data on 2850 invasive cervical cancers. HPV sequences were detected in 169/392 of HPV PCR-negative cervical cancers. Overall, 30 different HPV types were detected, but only 5 types were present in proportions above 3% of cancers. More than 92% of tumours were HPV-positive in PCR and/or sequencing (95% confidence interval: 91.1-93.1%). Exploring possible reasons for failure to previously detect HPV suggest that more sensitive type-specific PCRs for HPV 31, 33, 45 and 73 targeting retained regions of HPV would have detected most of these (117/392). Unbiased deep sequencing provides comprehensive data on HPV types in cervical cancers and appears to be an important tool for quality assurance of HPV screening.