Table S1 from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers

List of the human and HPV genomic locations for the 320 identified integration events.</p

Table S2 from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers

HPV gene expression levels in the 84 HNSCC tumors.</p

Table S3 from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers

Network statistics for network constructed from 89 genes with/near integration events.</p

Data_Sheet_1_Adherence to a priori-Defined Diet Quality Indices Throughout the Early Disease Course Is Associated With Survival in Head and Neck Cancer Survivors: An Application Involving Marginal Structural Models.docx

No studies, to date, have scrutinized the role of a priori dietary patterns on prognosis following a head and neck squamous cell carcinoma (HNSCC) diagnosis. The purpose of this analysis was to evaluate the associations between adherence to six a priori defined diet quality indices (including AHEI-2010, aMED, DASH, and three low-carbohydrate indices) throughout the first 3 years of observation and all-cause and cancer-specific mortalities in 468 newly diagnosed HNSCC patients from the University of Michigan Head and Neck Specialized Program of Research Excellence (UM-SPORE). The dietary intake data were measured using a food frequency questionnaire administered at three annual time points commencing at study entry. Deaths and their causes were documented throughout the study using various data sources. Marginal structural Cox proportional hazards models were used to evaluate the role of diet quality, as a time-varying covariate, on mortality. There were 93 deaths from all causes and 74 cancer-related deaths adjudicated throughout the observation period. There was a strong inverse association between adherence to the AHEI-2010, all-cause mortality (HRQ5–Q1:0.07, 95% CI:0.01–0.43, ptrend:0.04), and cancer-specific mortality (HRQ5–Q1:0.15, 95% CI:0.02–1.07, ptrend:0.04). Other more modest associations were noted for the low-carbohydrate indices. In sum, higher adherence to the AHEI-2010 and a plant-based low-carbohydrate index throughout the first 3 years since diagnosis may bolster survival and prognosis in newly diagnosed patients with HNSCC.</p

Supplemental Materials and Methods; Supplementary Tables 5-14; Supplementary Figures 1-3. from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers

Supplemental Methods, Tables S5-S14, and Figures S1-S3</p

Table S4 from HPV Integration in HNSCC Correlates with Survival Outcomes, Immune Response Signatures, and Candidate Drivers

GO terms and KEGG pathways enriched for genes differentially expressed between integration-positive and integration-negative HNC tumors.</p

Supplemental Figure 2 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

Differential mRNA expression of genes with copy number alterations. The relative mRNA expression of amplified genes was assessed across the all publically available next generation sequencing data where matched genome or exome-sequencing and transcriptome sequencing were available using the Oncomine database. Three plots were generated for each gene with copy number alterations, the respective gene is indicated on top of the plot. RNA expression was not evaluable for TCGA-CN-A49A, which harbored a SMOC1 amplification. DNA copy number calculated from exome or whole genome sequencing data is shown along the x-axis and absolute fragments per kilobase million are shown along the y-axis (Values are presented as Log base 2). Samples within the plots have either do not have genomic alterations or have mutations, gene fusions or copy number alterations as indicated in the inset legend. Blue dashed line indicates the limit for calling genomic deletions and the pink line for genomic amplifications. The black line indicates best fit for correlation between DNA copy number and gene expression.</p

Supplementary methods and figures. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures

Supplementary methods and figures. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signature

Supplemental Table 4 from Genomic Integration of High-Risk HPV Alters Gene Expression in Oropharyngeal Squamous Cell Carcinoma

Number of viral-cellular amplicons generated and sequenced from responsive and recurrent tumors.</p

Table S5. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures

The list of genes displayed in Figure 1D. </p