Table 2.

Summary of GWAS on HPV+ head and neck cancer.

1st Author, Year, Reference	No. of Cases	No. of Controls	Ethnicity	No. of SNPs Tested	Gene Variants	Main Findings
Mckay JD, Plos Genet. 2011 [95]	2091 (oral cavity, pharynx, larynx and esophagus)	3513	European	nd	rs1494961, rs4767364	-two novel variants were associated with susceptibility to UADT cancers (q421 and FAM175A) -these variants encode proteins involved in DNA repair machinery -no statistical significance in those who never used alcohol, tobacco or were younger than 50 -no definitive conclusions on the role of 4q21 in HNSCC susceptibility
Liang C. Head Neck, 2012 [96]	545 (HNSCC)	676	none specified, conducted in Greater Boston, Massachusetts	nd	rs4767364, rs1494961	-the variant rs4767464 in the FLJ13089 gene was significantly associated with HNSCC -the genetic variation in the HEL308 gene is more relevant to high risk populations
Levovitz C. Cancer Res. 2014 [97]	2091 UADT cancer patients (HNSCC)	8334	European	296,728	variants in 14 immune-related genes, TGFβR1	-variants in genes related to transforming growth factor beta signaling were found to be associated with susceptibility to HPV-related HNSCC -TGFβR1 was overexpressed in oropharyngeal, cervical and HPV+ Head and neck cancer tumors
Lesseur C. Nat Genet. 2016 [98]	6034 (oral cavity, pharyngeal cancer)	6585	Europe, North America and South America	nd	rs3828805, rs201982221, rs1453414, rs6547741, rs928674, rs8181047, rs10462706	-A GWAS of oral cavity and pharyngeal cancer detected 8 loci, with 7 being novel for these cancer sites -oral cancer associated with two new region -oropharyngeal cancer associations were limited to the HLA region -HLA allele imputation revealed a protective association with the class II haplotype -associations of oropharyngeal cancer was considerably stronger in HPV+ cancers compared to HPV- cancers
Shete S. Cancer Res. 2020 [99]	2171 GWAS, 5205 cohort	4493 GWAS, 3232 cohort	European	nd	rs1265081, rs3135001, rs13211972, rs259919, rs142021700,	-four previously reported loci, and two novel loci were associated with SCCHN risk (highlighting the importance of HLA loci for oropharyngeal cancer risk) -the variant rs259919 in the 6p22.1 region correlated with significantly lower levels of ZFP57 transcripts in various tissues and an increased risk of SCCHN

Abbreviations: SNP: single nucleotide polymorphism; HPV: human papillomavirus; nd: no data; SCCHN: Squamous cell carcinoma of head and neck; UADT: upper aero-digestive tract; FAM175: FAMILY WITH SEQUENCE SIMILARITY 175. This gene also known as abraxas 1 or BRCA1 A complex subunit; GWAS: Genome-wide association study.