17 Matching Annotations
  1. Last 7 days
  2. pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov
    Untitled document
    17
    1. karim2001khoury 19 Feb 2026
      Genetic Variants Were Associated With the Prognosis of Head and Neck Squamous Carcinoma

      [Paper-level Aggregated] PMCID: PMC7099049

      Evidence Type(s): Prognostic, Functional

      Justification: Prognostic: The SNPs rs16879870, rs2641256, rs2761591, and rs854936 were significantly associated with HNSCC survival, indicating their potential role in predicting patient outcomes. Functional: The genotypes of rs16879870 and rs854936 were significantly associated with the expression of genes GJB7 and RTN4R, respectively, suggesting a functional impact on gene expression related to HNSCC.

      Gene→Variant (gene-first): FGFR4(2264):AUC from 0 NA:rs16879870 SCIMP(388325):rs2641256 DCDC1(341019):rs2761591 NA:rs854936

      Genes: FGFR4(2264) NA SCIMP(388325) DCDC1(341019)

      Variants: AUC from 0 rs16879870 rs2641256 rs2761591 rs854936

      CIViC paper-level aggregated PMC7099049
    2. karim2001khoury 19 Feb 2026
      To further explore potential functions of these SNPs, we performed the eQTL analysis for selected SNPs and mRNA expression of their corresponding genes in cancer tissues by using TCGA dataset. As shown in Figure 3, the a

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 13

      Evidence Type(s): Functional, Prognostic

      Justification: Functional: The passage discusses how the alleles of rs16879870 and rs854936 are associated with increased mRNA expression levels of their corresponding genes, indicating an alteration in molecular function. Prognostic: The passage reports that higher expression levels of the genes GJB7 and RTN4R correlate with worse prognosis in HNSCC patients, indicating a relationship with disease outcome independent of therapy.

      Gene→Variant (gene-first): NA:rs16879870 NA:rs854936

      Genes: NA

      Variants: rs16879870 rs854936

      CIViC paragraph-level PMC7099049 Functional Prognostic
    3. karim2001khoury 19 Feb 2026
      Furthermore, stratification analyses were conducted to examine whether the effects of risk genotypes on death with HNSCC was modified by sex, age, smoking, drinking status, and clinical stage. However, the heterogeneity

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 11

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage discusses the effects of risk genotypes, including rs2761591, on death with HNSCC, indicating a correlation with disease outcome.

      Gene→Variant (gene-first): 341019:rs2761591

      Genes: 341019

      Variants: rs2761591

      CIViC paragraph-level PMC7099049 Prognostic
    4. karim2001khoury 19 Feb 2026
      ROC model was built to assess the ability of NRG in prediction of HNSCC survival by using the area under the curve (AUC). We constructed two models to compare their ability, one for clinical variables and the other for b

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 9

      Evidence Type(s): Prognostic, Predictive

      Justification: Prognostic: The passage discusses the ability of a model to predict survival in HNSCC, indicating a correlation between the variant and disease outcome. Predictive: The mention of using NRG in a prediction model for HNSCC survival suggests a relationship with treatment response or sensitivity, aligning with predictive evidence.

      Gene→Variant (gene-first): 2264:AUC from 0

      Genes: 2264

      Variants: AUC from 0

      CIViC paragraph-level PMC7099049 Prognostic Predictive
    5. karim2001khoury 19 Feb 2026
      To provide a better estimation of the hazards of survival, the risk genotypes (i.e., rs16879870 CA+AA, rs2641256 AA, rs2761591 GA, and rs854936 AC) were combined into one variable as the number of risk genotypes (NRG), w

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 7

      Evidence Type(s): Prognostic, Diagnostic

      Justification: Prognostic: The passage discusses how the number of risk genotypes (NRG) correlates with the hazard of death in patients with HNSCC, indicating a relationship between the variants and disease outcome. Diagnostic: The variants are used to define and classify patients into groups based on the number of risk genotypes, which is associated with survival outcomes in HNSCC.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic Diagnostic
    6. karim2001khoury 19 Feb 2026
      In the discovery stage, univariate and multivariable Cox regression analysis were further performed to evaluate the effects on risk of death for each of selected SNPs (Table 2), with adjusting of age, gender, smoking, dr

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 6

      Evidence Type(s): Prognostic, Diagnostic

      Justification: Prognostic: The passage discusses the association of specific SNP genotypes with survival outcomes in HNSCC, indicating that these variants correlate with risk of death independent of therapy. Diagnostic: The passage mentions the classification performance of risk genotypes of selected SNPs, suggesting their use in defining or classifying disease risk.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic Diagnostic
    7. karim2001khoury 19 Feb 2026
      As shown in Supplementary Figure 1, after QC, we performed Cox proportional hazards regression models to assess associations of 31,075 qualified genetic variants with HNSCC survival, with adjustment for age, gender, smok

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 5

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage discusses the correlation of specific SNPs with HNSCC patients' survival, indicating that these variants are associated with disease outcome independent of therapy.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic
    8. karim2001khoury 19 Feb 2026
      Conclusion: Our findings suggested that the SNPs (rs16879870, rs2641256, rs2761591, rs854936) might play a crucial role in prognosis of HNSCC.

      [Paragraph-level] PMCID: PMC7099049 Section: ABSTRACT PassageIndex: 4

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage indicates that the SNPs are suggested to play a crucial role in the prognosis of HNSCC, which correlates with disease outcome.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic
    9. karim2001khoury 19 Feb 2026
      Results: After combining the result of the two stages, 4 SNPs were significantly associated with HNSCC survival (rs16879870 at 6q14.3: adjusted HR = 2.02, 95%CI = 1.50-2.73, P = 3.88 x 10-6; rs2641256 at 17p13.2: adjuste

      [Paragraph-level] PMCID: PMC7099049 Section: ABSTRACT PassageIndex: 3

      Evidence Type(s): Prognostic, Functional

      Justification: Prognostic: The passage discusses the association of SNPs with HNSCC survival, indicating that these variants correlate with disease outcome, specifically overall survival, independent of therapy. Functional: The passage mentions that the genotype of rs16879870 and rs854936 is significantly associated with the expression of specific genes in cancer tissues, suggesting that these variants alter molecular function.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic Functional
    10. karim2001khoury 19 Feb 2026
      To further explore potential functions of these SNPs, we performed the eQTL analysis for selected SNPs and mRNA expression of their corresponding genes in cancer tissues by using TCGA dataset. As shown in Figure 3, the a

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 13

      Evidence Type(s): Functional, Prognostic

      Justification: Functional: The passage discusses how the alleles of rs16879870 and rs854936 are associated with increased mRNA expression levels of their corresponding genes, indicating an alteration in molecular function. Prognostic: The passage reports that higher expression levels of the genes GJB7 and RTN4R correlate with worse prognosis in HNSCC patients, indicating a relationship with disease outcome independent of therapy.

      Gene→Variant (gene-first): NA:rs16879870 NA:rs854936

      Genes: NA

      Variants: rs16879870 rs854936

      CIViC paragraph-level PMC7099049 Functional Prognostic
    11. karim2001khoury 19 Feb 2026
      Furthermore, stratification analyses were conducted to examine whether the effects of risk genotypes on death with HNSCC was modified by sex, age, smoking, drinking status, and clinical stage. However, the heterogeneity

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 11

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage discusses the effects of risk genotypes, including rs2761591, on death with HNSCC, indicating a correlation with disease outcome.

      Gene→Variant (gene-first): 341019:rs2761591

      Genes: 341019

      Variants: rs2761591

      CIViC paragraph-level PMC7099049 Prognostic
    12. karim2001khoury 19 Feb 2026
      ROC model was built to assess the ability of NRG in prediction of HNSCC survival by using the area under the curve (AUC). We constructed two models to compare their ability, one for clinical variables and the other for b

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 9

      Evidence Type(s): Prognostic, Predictive

      Justification: Prognostic: The passage discusses the ability of a model to predict survival in HNSCC, indicating a correlation between the variant and disease outcome. Predictive: The mention of using NRG in a prediction model for HNSCC survival suggests a relationship with treatment response or sensitivity, aligning with predictive evidence.

      Gene→Variant (gene-first): 2264:AUC from 0

      Genes: 2264

      Variants: AUC from 0

      CIViC paragraph-level PMC7099049 Prognostic Predictive
    13. karim2001khoury 19 Feb 2026
      To provide a better estimation of the hazards of survival, the risk genotypes (i.e., rs16879870 CA+AA, rs2641256 AA, rs2761591 GA, and rs854936 AC) were combined into one variable as the number of risk genotypes (NRG), w

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 7

      Evidence Type(s): Prognostic, Diagnostic

      Justification: Prognostic: The passage discusses how the number of risk genotypes (NRG) correlates with the hazard of death in patients with HNSCC, indicating a relationship between the variants and disease outcome. Diagnostic: The variants are used to define and classify patients into groups based on the number of risk genotypes, which is associated with survival outcomes in HNSCC.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic Diagnostic
    14. karim2001khoury 19 Feb 2026
      In the discovery stage, univariate and multivariable Cox regression analysis were further performed to evaluate the effects on risk of death for each of selected SNPs (Table 2), with adjusting of age, gender, smoking, dr

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 6

      Evidence Type(s): Prognostic, Diagnostic

      Justification: Prognostic: The passage discusses the association of specific SNP genotypes with survival outcomes in HNSCC, indicating that these variants correlate with risk of death independent of therapy. Diagnostic: The passage mentions the classification performance of risk genotypes of selected SNPs, suggesting their use in defining or classifying disease risk.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic Diagnostic
    15. karim2001khoury 19 Feb 2026
      As shown in Supplementary Figure 1, after QC, we performed Cox proportional hazards regression models to assess associations of 31,075 qualified genetic variants with HNSCC survival, with adjustment for age, gender, smok

      [Paragraph-level] PMCID: PMC7099049 Section: RESULTS PassageIndex: 5

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage discusses the correlation of specific SNPs with HNSCC patients' survival, indicating that these variants are associated with disease outcome independent of therapy.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic
    16. karim2001khoury 19 Feb 2026
      Conclusion: Our findings suggested that the SNPs (rs16879870, rs2641256, rs2761591, rs854936) might play a crucial role in prognosis of HNSCC.

      [Paragraph-level] PMCID: PMC7099049 Section: ABSTRACT PassageIndex: 4

      Evidence Type(s): Prognostic

      Justification: Prognostic: The passage indicates that the SNPs are suggested to play a crucial role in the prognosis of HNSCC, which correlates with disease outcome.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic
    17. karim2001khoury 19 Feb 2026
      Results: After combining the result of the two stages, 4 SNPs were significantly associated with HNSCC survival (rs16879870 at 6q14.3: adjusted HR = 2.02, 95%CI = 1.50-2.73, P = 3.88 x 10-6; rs2641256 at 17p13.2: adjuste

      [Paragraph-level] PMCID: PMC7099049 Section: ABSTRACT PassageIndex: 3

      Evidence Type(s): Prognostic, Functional

      Justification: Prognostic: The passage discusses the association of SNPs with HNSCC survival, indicating that these variants correlate with disease outcome, specifically overall survival, independent of therapy. Functional: The passage mentions that the genotype of rs16879870 and rs854936 is significantly associated with the expression of specific genes in cancer tissues, suggesting that these variants alter molecular function.

      Gene→Variant (gene-first): NA:rs16879870 388325:rs2641256 341019:rs2761591 NA:rs854936

      Genes: NA 388325 341019

      Variants: rs16879870 rs2641256 rs2761591 rs854936

      CIViC paragraph-level PMC7099049 Prognostic Functional
    Visit annotations in context

    Tags

    Annotators

    URL

    pmc.ncbi.nlm.nih.gov/articles/PMC7099049/pdf/fonc-10-00372.pdf