HPV	Human papillomavirus
HR-HPV	High-risk human papillomavirus
Alpha9	Alphapapillomavirus species 9 (HPV16-related)
Alpha7	Alphapapillomavirus species 7 (HPV18-related)
CIN3	Cervical intraepithelial neoplasia grade 3
CpG site	CG dinucleotide
AIS	Adenocarcinoma in situ
SCC	Squamous cell cancer
URR	Upstream regulatory region
OR	Odds ratio
CI	Confidence interval
AUC	Area under the curve
SNP	Single nucleotide polymorphism
NGS	Next-generation sequencing
NCR1	Noncoding region 1
VWAS	Viral genome wide association study
PaP cohort	HPV Persistence and Progression
KPNC	Kaiser Permanente Northern California
NCI	National Cancer Institute
HC2	Hybrid capture 2
NILM	Negative for intraepithelial lesions or malignancy
bp	Base pair
ML	Maximum likelihood
MCMC	Markov chain Monte Carlo