Homozygous and rare SNP variant selection criteria identify the KEGG Fanconi anemia pathway to be strongly associated with MMC response.

Volcano plot showing the significance of the associations between MMC response and ‘pathway-mutation’ classification in the individual KEGG pathways as determined by the presence of homozygous and rare SNP variants in these pathway genes. The x-axis shows the difference in mean MMC IC50 between ‘pathway mutated’ and ‘pathway non-mutated’ cell lines. Pathway mutated cell lines are those with one or more variants in any gene of the individual KEGG pathway. The y-axis shows the significance values (Wilcoxon rank-sum test p-value) of the difference that were found in the MMC IC50 between ‘pathway-mutated’ and ‘non-mutated’ cell lines. Dot size is proportional to the number of ‘pathway-mutated’ cell lines, dot color intensity proportional to significance value. (A) Results after applying the variant selection strategy that selects homozygous variants (VAF ≥ 0.8) and includes rare SNPs (MAF ≤ 1%). (B) Results of analyses that select variants regardless of zygosity status, including rare SNPs (MAF ≤ 1%).</p

Bland-Altman plot of the final model with observed and predicted EQ-5D-3L values.

Bland-Altman plot of the final model with observed and predicted EQ-5D-3L values.</p

Characteristics of the final model (Model 1d) without shrinkage.

Characteristics of the final model (Model 1d) without shrinkage.</p

Mirrored histogram of observed and predicted EQ-5D-3L values.

Mirrored histogram of observed and predicted EQ-5D-3L values.</p

Summary results of the regression models.

Summary results of the regression models.</p

Loss of heterozygosity events are more common in tumor suppressor genes.

(A) The percentage of HNSCC samples with LOH per TSG (dark red) and OG (dark blue). HNSCC TSG and oncogenes (OG) are as reported by Leemans et al. Light colors represent the percentage of samples without LOH (wt). Fraction of samples with LOH are indicated by numbers and dark colors. (B) Boxplot representation of the percentage of HNSCC tumor samples with LOH in any TSGs or OGs as shown in Fig 3A. TSGs are enriched for LOH events (p<0.005).</p

High VAF and low MAF selection criteria improve functional association.

The positive predictive value (PPV) for MMC sensitivity was used to quantify the ability of variants to mark repair defected cell lines, i.e. ten most MMC sensitive, by the different variant selection criteria. Statistical analyses were omitted at sample sizes of a group of less than two and these data points and lines have been excluded in the figures. Asterisks mark a significant association with MMC response. (A) PPV values at each VAF threshold that was applied for variant selection are shown. Lines show the results for the canonical FA/HR genes and of the two controls: the “nearest genes” and the 10.000 similar sized randomly grouped gene sets. Error bars delineate the first and third quartile from the median in the latter. (B) PPV with progressively decreasing maximum MAF thresholds. Line coloring is identical to Fig 1A. (C) Impact of canonical FA/HR gene variant selection filters on PPV when combining multiple maximum MAF thresholds (as indicated in in-figure legend) with increasing minimum VAF thresholds (x-axis). (D) Influence of filters on PPVs after applying decreasing maximum MAF thresholds for multiple minimum VAF thresholds for canonical FA/HR gene variant selection as indicated.</p

Summary results of HRQoL data derived from 361 observations.

Summary results of HRQoL data derived from 361 observations.</p

Flowchart of model development.

The grey rectangles display the three predictor sets with their criteria; the white rectangles the different models. The squares indicate the assessment of the models during model comparison; the rhombuses indicate the decision-making in the process. Assessment of the model performance is displayed with a dotted line. The EORTC QLQ-C30 and QLQ-H&N35 scales included in the predictor sets are highlighted in grey circles. The scales that were excluded are colored white. Abbreviations: AL, appetite loss; Cough, coughing; CF, cognitive functioning; CP, constipation; DH, diarrhea; DP, dyspnea; DM, dry mouth; EF, emotional functioning; EORTC, European Organization for Research and Treatment of Cancer; EQ-5D-3L, three-level EuroQol five-dimensional questionnaire; FD, financial difficulties; FG, fatigue; FI, felt ill; FT, feeding tube; GHS/QoL, global health status/quality of life; HRQoL, health-related quality of life; IS, insomnia; LS, less sexuality; NT, nutritional supplements; NV, nausea and vomiting; OLS, ordinary least-squares, OM, opening mouth; PF, physical functioning; PK, pain killers; Quality of Life Questionnaire-Core 30; QLQ-H&N35, Quality of Life Questionnaire-Head and Neck35; RF, role functioning; SC, trouble with social contact; SE, trouble with social eating; SpP, speech problems; SeP, senses problems; SL, swallowing; SF, social functioning; SS, sticky saliva; WG, weight gain; WL, weight loss.</p

Patient, tumor and treatment characteristics.

Tumors were staged according to cTNM clinical classification of the Union for International Cancer Control (UICC) (2009, 7th edition) [24].</p