Prognostic, Oncogenic evidence:

Oncogenic: The abstract states that "LncRNA SNHG4 has been reported to be an oncogenic lncRNA in osteosarcoma" and confirms its upregulation in glioblastoma (GBM), indicating that SNHG4 contributes to tumor development or progression in this context. Additionally, the mention of SNHG4's role in promoting the proliferation of GBM cells further supports its oncogenic nature.

Prognostic: The abstract notes that "lower survival rate of GBM patients was observed in patients with high SNHG4 expression level," suggesting that the expression level of SNHG4 correlates with disease outcome, specifically survival, independent of therapy.

Predictive, Prognostic evidence:

Predictive: The study indicates that Nek1 knockdown sensitized cancer cells to ionizing radiation, suggesting a correlation with treatment response, particularly in the context of radiation therapy.

Prognostic: The results show that elevated levels of Nek1 were associated with impaired cancer-specific and overall survival, indicating its potential role as a prognostic marker for disease outcome in cervical cancer patients.

Predictive, Diagnostic evidence:

Predictive: The study identifies PTEN gene copy number loss as a promising mechanistic biomarker predictive of cetuximab resistance in head and neck squamous cell carcinoma (HNSCC), indicating that this variant correlates with resistance to the therapy. The mention of "predictive of cetuximab resistance" directly supports this classification.

Diagnostic: The abstract discusses the prevalence of PTEN gene copy number loss in HNSCC, suggesting its potential use as a biomarker for identifying patients who may not respond to cetuximab treatment. This aligns with the diagnostic evidence type as it relates to classifying a disease subtype based on the presence of the variant.

Predictive, Diagnostic evidence:

Predictive: The study indicates that CXCR7 is a critical regulator of prostate cancer sensitivity to enzalutamide, suggesting a correlation between the variant and resistance to this specific therapy. The mention of "therapeutic potential of MAPK/ERK inhibitors" further supports the predictive nature of the findings regarding treatment response.

Diagnostic: The findings suggest that CXCR7 may serve as a biomarker of resistant disease in patients with prostate cancer, indicating its role in classifying or defining a subtype of the disease, particularly in the context of enzalutamide resistance.

Predictive, Functional evidence:

Predictive: The study discusses the correlation between miR-200c-3p expression and progression-free survival (PFS) in patients undergoing EGFR-TKI treatment, indicating that higher expression is associated with longer PFS, which suggests a predictive role in therapy response.

Functional: The research demonstrates that miR-200c-3p overexpression inhibits the epithelial-to-mesenchymal transition (EMT) process and promotes cell death in EGFR TKI-resistant cell lines, indicating that this variant alters molecular function related to drug sensitivity.

Predictive, Diagnostic evidence:

Predictive: The study identifies that cell lines with activating PIK3CA mutations or loss of PTEN expression are more resistant to cetuximab, indicating that these mutations correlate with treatment response. This suggests that the mutation status of these genes could serve as a predictive biomarker for cetuximab sensitivity in colorectal cancer.

Diagnostic: The examination of mutation status of signaling components downstream of EGFR, such as PIK3CA and PTEN, is used to classify the sensitivity or resistance of colon cancer cell lines to cetuximab. This classification based on mutation status supports the use of these variants as biomarkers for determining patient eligibility for cetuximab therapy.

Predictive, Oncogenic evidence:

Predictive: The abstract mentions that the progression-free survival (PFS) benefit of everolimus was maintained irrespective of PIK3CA genotypes, indicating that the variant E542K may not affect the response to this therapy, which is a predictive aspect of the variant's role in treatment outcomes.

Oncogenic: The results section discusses how PIK3CA mutations, including E542K, contribute to aberrant signaling in the PI3K/AKT/mTOR pathway, which is implicated in tumorigenesis and progression, thus supporting the oncogenic nature of this variant.

Predictive, Oncogenic evidence:

Oncogenic: The abstract discusses TRK fusions as oncogenic drivers in various tumor types, indicating that these genetic alterations contribute to tumor development. The results section confirms the presence of a brain tumor with specific cellular characteristics, and the mention of BRAF V600E being negative suggests that the study is focused on the oncogenic role of other variants rather than V600E itself.

Predictive: The abstract highlights the successful treatment of a TRK fusion-driven HGG with larotrectinib, a selective pan-TRK inhibitor, indicating a correlation between the presence of the TRK fusion and the response to this specific therapy. This suggests that the variant plays a predictive role in treatment outcomes.

Predictive, Oncogenic evidence:

Predictive: The Gly101Val mutation in BCL2 is associated with resistance to venetoclax in patients, indicating that this variant correlates with treatment response and highlights its role in therapeutic resistance.

Oncogenic: The acquisition of the Gly101Val mutation is linked to the development of resistance in chronic lymphocytic leukemia, suggesting that this somatic variant contributes to tumor progression and treatment failure.

Predictive evidence:

Predictive: The study assesses the efficacy of ivosidenib, a targeted inhibitor of mutated IDH1, in patients with IDH1-mutant cholangiocarcinoma, indicating that the presence of the IDH1 mutation correlates with improved progression-free survival when treated with this therapy. The results show a significant improvement in progression-free survival with ivosidenib compared to placebo, highlighting the predictive nature of the IDH1 mutation in response to treatment.

Predictive, Diagnostic evidence:

Predictive: The study discusses the sensitivity of ASS1-deficient ovarian cancer cells to the arginine-depriving therapeutic ADI-PEG20, indicating a correlation with treatment response. This suggests that the variant's status may predict the effectiveness of this specific therapy in treating SCCOHT and other ovarian cancer subtypes.

Diagnostic: The abstract mentions that low ASS1 expression was validated through immunohistochemistry (IHC) in large patient cohorts, indicating that ASS1 deficiency can be used to classify or define certain ovarian cancer subtypes, including SCCOHT. This establishes a diagnostic role for the variant in identifying patients with these rare cancer types.

Predictive, Oncogenic evidence:

Oncogenic: The ETV6-NTRK3 gene fusion is described as a "potent oncogenic driver" in infantile fibrosarcoma (IFS), indicating its role in tumor development and progression.

Predictive: The study reports a "very rapid, complete, and sustained response" of chemotherapy-refractory IFS to the TRK inhibitor larotrectinib, demonstrating that the presence of the ETV6-NTRK3 fusion correlates with a positive therapeutic response to this specific treatment.

Predictive, Oncogenic evidence:

Oncogenic: The abstract discusses the link between the Fli-1 signaling network and oncogenesis in glioblastoma multiforme (GBM), indicating that Fli-1 is associated with tumor development and progression, particularly in the context of radio/TMZ-resistant GBM.

Predictive: The study highlights that lumefantrine, identified as a Fli-1 inhibitor, promotes growth suppression and apoptosis in both parental and radio/TMZ-resistant GBM, suggesting its potential as a therapeutic agent that correlates with response to treatment.

Oncogenic, Functional evidence:

Oncogenic: The MPL Y252H mutation is described as a "disease-driving mutation" that contributes to the development of essential thrombocythemia (ET), indicating its role in tumor progression. The evidence of increased TPO/MPL-mediated cell growth and survival upon cytokine withdrawal further supports its oncogenic potential.

Functional: The study demonstrates that the Y252H mutation results in increased sensitivity to thrombopoietin (TPO) and enhanced cell growth and survival, indicating that it alters the molecular function of the MPL receptor. This functional alteration is evidenced by the in vitro assays conducted with BaF3 cells.

Prognostic evidence:

Prognostic: The abstract indicates that low expression of OTUD3 in glioma may contribute to patient survival, suggesting a correlation between the variant and disease outcome independent of therapy.

Predictive, Diagnostic evidence:

Diagnostic: The abstract states that "MACF1 represents a diagnostic marker with target specificity in glioblastomas," indicating that the variant is used to define or classify a specific disease subtype.

Predictive: The abstract mentions that MACF1 "can enhance the efficacy of radiation while minimizing normal tissue toxicity," suggesting that the variant correlates with response to a specific therapy (radiation treatment) in glioblastoma patients.

Predictive evidence:

Predictive: The study identifies ccRCC molecular subtypes that are associated with different responses to sunitinib treatment, indicating that these subtypes can predict treatment outcomes in patients with metastatic clear-cell renal cell carcinoma. The results show significant differences in response rates and survival outcomes based on the identified subtypes, supporting their use in personalized treatment strategies.

Diagnostic, Oncogenic evidence:

Oncogenic: The study discusses somatic mutations in the VHL gene as the most common cause of renal cell carcinoma (RCC), indicating that these mutations contribute to tumor development. The identification of somatic mutations in 29% of patients supports the role of VHL mutations in oncogenesis.

Diagnostic: The paper presents data on the frequencies of molecular alterations in the VHL gene among RCC patients, which can be used to classify or define the disease. The mention of specific mutation frequencies and their association with RCC indicates a diagnostic relevance of the VHL gene alterations.

Prognostic, Oncogenic evidence:

Oncogenic: The study indicates that SMAD4 loss is required for collective invasion in pancreatic ductal adenocarcinoma (PDAC) organoids, suggesting that the somatic mutation in SMAD4 contributes to tumor progression through altered invasion mechanisms. This aligns with the definition of oncogenic variants that drive tumor development or progression.

Prognostic: The abstract mentions that PDAC organoids with predominantly mesenchymal invasion showed a worse prognosis, indicating a correlation between the variant status (specifically SMAD4 mutations) and disease outcome, independent of therapy.

Predictive, Oncogenic evidence:

Oncogenic: The study functionally characterized the somatic variant V871I in the EPHB4 gene, demonstrating that it contributes to increased proliferation, migration, and invasion properties in neuroblastoma cell lines, indicating its role in tumor development and progression.

Predictive: The use of EPHB4 inhibitors JI-101 and NVP-BHG712 to rescue the phenotype driven by the V871I variant suggests that this variant correlates with response to specific therapies, highlighting its potential as a therapeutic target in high-risk neuroblastoma.

Predictive, Oncogenic evidence:

Predictive: The study discusses the potential of combined inhibition of MYC and mTOR pathways as a therapeutic strategy for MYC-driven medulloblastoma, indicating that this approach may correlate with improved treatment response, as evidenced by the significant suppression of cell growth and prolonged survival in xenografted mice.

Oncogenic: The abstract highlights that the MYC oncogene is frequently amplified in medulloblastoma, particularly in group 3 patients, suggesting that this somatic variant contributes to tumor development and progression, as it is associated with the worst prognosis and is a target for therapeutic intervention.

Prognostic evidence:

Prognostic: The study indicates that high expression of miR-143 is associated with improved overall survival (OS) in ER-positive breast cancer patients, suggesting a correlation between the variant and disease outcome independent of therapy.

Prognostic, Oncogenic evidence:

Oncogenic: The study provides evidence that TESC contributes to tumor development and progression in cholangiocarcinoma, as indicated by the knockdown of TESC suppressing tumor growth and its upregulation through the EGFR-STAT3 pathway, which mediates tumor cell proliferation.

Prognostic: The abstract mentions that elevated cellular levels of TESC are correlated with larger tumor size and predict a poor survival outcome for patients, indicating its potential role in assessing disease outcome independent of therapy.

Prognostic, Oncogenic evidence:

Prognostic: The abstract states that YTHDF2 expression is negatively correlated with HCC patient survival, indicating that this variant may have implications for disease outcome independent of therapy.

Oncogenic: The study demonstrates that YTHDF2 contributes to tumor development and progression, as evidenced by the reduction of tumor burden and inhibition of lung metastasis in vivo following YTHDF2 depletion.

Predictive, Diagnostic evidence:

Diagnostic: The EBF1-PDGFRB gene fusion is associated with the Philadelphia-like ALL subtype, indicating its role in classifying and defining a specific disease context within B-cell precursor acute lymphoblastic leukemia (ALL).

Predictive: The study reports that EBF1-PDGFRB-positive patients who are refractory to conventional chemotherapy can achieve a complete response when treated with the tyrosine kinase inhibitor imatinib, suggesting a correlation between the variant and treatment response.

Predictive evidence:

Predictive: The abstract discusses the use of a tyrosine kinase inhibitor, imatinib, to treat the patient with BCP-ALL harboring the EBF1-PDGFRB fusion, indicating a correlation between the variant and response to therapy. This suggests that the presence of the fusion transcript may influence treatment decisions and outcomes.

Predictive evidence:

Predictive: The abstract discusses the C481S mutation in BTK as a factor that disables ibrutinib's capacity to irreversibly bind to its target, indicating that this variant is associated with resistance to ibrutinib therapy in patients with chronic lymphocytic leukemia (CLL). This suggests a correlation between the C481S variant and treatment response, classifying it as predictive evidence.

Prognostic evidence:

Prognostic: The study reports that cancer patients have a significantly increased case fatality rate (CFR) from COVID-19, indicating that the presence of cancer correlates with worse disease outcomes, such as mortality, independent of therapy. The mention of increased mortality associated with various factors, including age and comorbidities, further supports this classification.

Oncogenic evidence:

Oncogenic: The study discusses the KRAS G12D variant as a key tumor maintenance gene in pancreatic ductal adenocarcinoma (PDAC), indicating its role in tumor development and progression. The use of a Kras G12D;Trp53 -/- PDAC mouse model further supports the notion that this somatic variant contributes to tumor growth and resistance mechanisms.

Predictive evidence:

Predictive: The study demonstrates that the G598V mutation in EGFR influences the sensitivity of brain tumor stem cells (BTSCs) to the EGFR inhibitor afatinib, indicating a correlation between the variant and response to therapy. The results show that BTSC cultures harboring the G598V mutation were more sensitive to afatinib treatment compared to EGFR-wildtype cultures.

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Diagnostic, Oncogenic evidence:

Diagnostic: The abstract states that mutations in FGFR1 have been associated with Hartsfield syndrome, indicating that these mutations are used to define or classify this specific disease. This association highlights the role of FGFR1 mutations in the context of a clinically distinct syndrome, fulfilling the criteria for diagnostic evidence.

Oncogenic: The abstract mentions that five distinct mutations in the FGFR1 kinase domain behave as dominant-negative mutations in zebrafish over-expression assays, suggesting that these mutations contribute to tumor development or progression. This evidence supports the classification of these variants as oncogenic due to their functional impact in a model organism.

Diagnostic, Prognostic evidence:

Prognostic: The study indicates that high VAP-1 expression levels are associated with poor prognosis in glioma patients, as evidenced by the significant correlation with overall survival (p < 0.0001) and the multivariate analysis identifying VAP-1 as an independent prognostic indicator.

Diagnostic: The research highlights that VAP-1/CD163 coexpression exhibited excellent diagnostic accuracy in gliomas (AUC = 0.8008), suggesting its potential use as a biomarker for classifying glioma malignancy.

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Missing abstract

Oncogenic evidence:

Oncogenic: The study discusses a novel case of acute promyelocytic leukemia characterized by the rearrangement of the RARA gene and its fusion with the OBFC2A gene, indicating that this somatic variant contributes to tumor development. The presence of the OBFC2A/RARA fusion transcript suggests a role in the leukemogenesis of the patient's acute promyelocytic leukemia.

Predictive evidence:

Predictive: The study demonstrates that a T > C variation at position 21 of the BCL2 sequence predicts a patient's response to paclitaxel, indicating that this variant correlates with treatment resistance. This is supported by the findings that tumors with this specific variant are more resistant to the chemotherapy drug.

Predictive, Functional evidence:

Predictive: The study discusses how DGKA activity is necessary for cisplatin resistance in ovarian cancer, indicating that targeting DGKA could sensitize cells to cisplatin treatment. This suggests a correlation between the DGKA variant and resistance to platinum-based therapy, which aligns with the predictive evidence type.

Functional: The research highlights that DGKA facilitates the recruitment of c-JUN N-terminal kinase to c-JUN, leading to its activation, which alters the molecular function of the signaling pathway involved in cisplatin resistance. This demonstrates a direct alteration in biochemical function due to the DGKA variant, supporting the functional evidence type.

Prognostic evidence:

Prognostic: The abstract states that "the expression of LRG1 was negatively related to patient survival," indicating that the variant correlates with disease outcome independent of therapy. This suggests that LRG1 expression levels may serve as a prognostic marker for patient survival in ccRCC.

Oncogenic evidence:

Oncogenic: The abstract states that CENPA is "overexpressed in tumors" and suggests it "might be an oncogenic factor in the development of HCC patients," indicating that this variant contributes to tumor development or progression.

Prognostic, Functional evidence:

Prognostic: The abstract states that CEP55 is a determinant of prognosis in liver cancer patients, indicating that the variant correlates with disease outcome independent of therapy.

Functional: The mention of DNA hypomethylation contributing to the overexpression of CEP55 suggests that the variant alters molecular function, specifically in relation to gene expression in liver cancer.

Oncogenic evidence:

Oncogenic: The study hypothesizes that miR-484 acts as an oncogene in prostate cancer by increasing cancer cell mobility, indicating its role in tumor development or progression. This suggests that the variant contributes to the oncogenic process, aligning with the definition of oncogenic evidence.

Predictive, Diagnostic, Oncogenic evidence:

Predictive: The study indicates that clinical response to anti-PD-1 immunotherapy in glioblastomas is associated with specific molecular alterations, suggesting a correlation between the presence of certain mutations (like PTEN) and the response to therapy. This aligns with the definition of predictive evidence, as it discusses how these variants relate to treatment outcomes.

Diagnostic: The abstract mentions that PTEN mutations are significantly enriched in non-responders, which implies that these mutations can be used to classify or define the response to immunotherapy in glioblastomas. This supports the classification of the variant as diagnostic, as it relates to the identification of a specific disease response subtype.

Oncogenic: The presence of PTEN mutations and their association with immunosuppressive expression signatures suggests that these somatic variants contribute to tumor behavior and progression in glioblastomas. This aligns with the oncogenic evidence type, as it indicates a role in tumor development.

Prognostic evidence:

Prognostic: The abstract states that age-related genes have significant prognostic effects in LGG patients, indicating that the variant correlates with disease outcome, such as survival or progression, independent of therapy.

Diagnostic, Prognostic, Functional evidence:

Diagnostic: The study indicates that LINC00691 is "highly expressed in GC" and is "a potential biomarker for GC diagnosis," suggesting its role in defining or classifying gastric cancer.

Prognostic: The abstract mentions that the expression of LINC00691 is "associated with clinicopathological features and survival time," indicating that it correlates with disease outcome independent of therapy.

Functional: The study describes how the knockdown of LINC00691 "suppressed proliferation, colony formation, migration, and invasion," demonstrating that the variant alters molecular functions related to cancer cell behavior.

Predictive, Diagnostic, Oncogenic evidence:

Diagnostic: The BCL2L14-ETV6 fusion is described as being "exclusively detected in TNBC" and is associated with "more aggressive histopathological features," indicating its role in classifying and defining a specific subtype of breast cancer.

Predictive: The study mentions that BCL2L14-ETV6 fusions "endow resistance to paclitaxel treatment," suggesting that this variant correlates with treatment response and resistance, which is a key aspect of predictive evidence.

Oncogenic: The ectopic expression of BCL2L14-ETV6 fusions is reported to "enhance cell motility and invasiveness" in TNBC, indicating that this somatic variant contributes to tumor development and progression.

Prognostic evidence:

Prognostic: The abstract states that RGS16 serves as an independent prognostic factor in glioma progression, indicating a correlation with disease outcome, specifically in GBM patients. This suggests that the variant is associated with survival or progression independent of therapy.

Predictive evidence:

Predictive: The abstract indicates that inhibiting the Wnt/beta-catenin pathway may enhance the effectiveness of paclitaxel in treating ovarian cancer, suggesting a correlation between the variant and response to therapy.

Predictive, Prognostic evidence:

Predictive: The abstract mentions that FUCA1 can be used as a valuable target for glioma treatment, indicating a potential correlation with response to therapy.

Prognostic: The abstract describes FUCA1 as a prognostic biomarker, suggesting that it correlates with disease outcome, which is independent of therapy.

Predictive, Prognostic evidence:

Predictive: The study discusses the use of a CSF-1R inhibitor targeting tumor-associated macrophages (TAMs) in a mouse proneural GBM model, which "dramatically increased survival" and "regressed established tumors," indicating a correlation between the variant's therapeutic targeting and response to treatment.

Prognostic: The abstract mentions that "gene signatures were associated with enhanced survival in proneural GBM patients," suggesting that the variant's presence correlates with improved disease outcomes independent of therapy.

Diagnostic, Prognostic evidence:

Prognostic: The study indicates that TNFSF14 is a significant adverse prognostic factor, correlating with overall survival (OS) in glioblastoma (GBM) patients. This suggests that the variant's expression levels can predict disease outcomes independent of therapy.

Diagnostic: The abstract mentions that TNFSF14 serves as a biomarker to identify immunologic subtypes in GBM, which aligns with the definition of a diagnostic role in classifying or confirming disease characteristics.

Predictive, Prognostic evidence:

Prognostic: The abstract discusses the poor patient prognosis associated with glioblastomas, indicating that the variant's presence correlates with disease outcome, specifically mentioning the median survival of 14 months.

Predictive: The study highlights the effectiveness of PLX3397 in blocking glioma progression and restoring sensitivity to tyrosine kinase inhibitors, suggesting that the variant may correlate with response to specific therapies.

Predictive, Oncogenic evidence:

Predictive: The study discusses the potential of FS118 to overcome resistance mechanisms to PD-L1 blockade, indicating that the variant's interaction with therapies may correlate with treatment response. The mention of "reinvigorate exhausted immune cells" and "antitumor activity" suggests a relationship between the variant and therapeutic efficacy.

Oncogenic: The results indicate that the bispecific antibody significantly suppressed tumor growth in syngeneic tumor mouse models, suggesting that the variant contributes to tumor development or progression. The study's focus on the antitumor activity of FS118 supports this classification.

Predictive, Oncogenic evidence:

Predictive: The abstract mentions that repotrectinib is effective against ROS1G2032R, indicating that this variant correlates with response to a specific therapy, which is the novel ROS1-TKI. This suggests that the presence of the G2032R variant may influence treatment outcomes.

Oncogenic: The results section discusses the ROS1 G2032R mutation as a common and resistant mutation found in crizotinib-resistant patients, indicating that this somatic variant contributes to tumor progression and resistance mechanisms in non-small-cell lung cancer (NSCLC). This supports the classification of G2032R as an oncogenic variant.

Predictive evidence:

Predictive: The study identifies that miR-185 levels anticipate the response to ABL tyrosine kinase inhibitors (TKIs), indicating its role as a predictive biomarker for therapy response. The restoration of miR-185 expression impaired survival of drug-resistant cells and sensitized them to TKIs, further supporting its predictive nature in overcoming drug resistance.

Predictive, Diagnostic evidence:

Diagnostic: The study discusses the correlation of PD-L1 expression with poor prognosis in pancreatic ductal adenocarcinomas (PDAC), indicating that high PD-L1 expression can be used to classify or define a disease subtype, particularly in the context of PDAC samples from patients.

Predictive: The findings suggest that the combination of PD-L1 and CCL-5 blockade may provide an effective therapy for patients with PDAC that have high C-FOXP3 levels, indicating a potential predictive relationship between PD-L1 expression and response to therapy.

Predictive, Prognostic evidence:

Prognostic: The study reports that high expression levels of TNFA and SPATA2 are associated with poor recurrence-free survival and disease-specific survival in endometrial cancer patients, indicating that these markers can predict clinical outcomes independent of therapy.

Predictive: The findings suggest that TNF signaling may modulate the course of endometrial cancer, which implies a potential therapeutic utilization of targeting this pathway, thus indicating a correlation with treatment response.

Diagnostic evidence:

Diagnostic: The study identifies the variant rs259919 as associated with the risk of squamous cell carcinoma of the head and neck (SCCHN), indicating its role in defining or classifying disease susceptibility. The mention of "cancer susceptibility loci" further supports its diagnostic relevance in the context of SCCHN.

Predictive, Oncogenic evidence:

Predictive: The study discusses how the upregulation of p63 contributes to acquired resistance to MAPK inhibitors in melanoma, indicating that this variant correlates with resistance to specific therapies. The mention of "treatment of MAPK inhibitor-resistant melanoma cells" and the potential for Nutlin-3A to restore sensitivity to apoptosis further supports this classification.

Oncogenic: The abstract describes the role of p63 in the context of melanoma and its association with therapy resistance, suggesting that alterations in p63 contribute to tumor progression and development. The findings regarding FBXW7-inactivating mutations and MDM2 upregulation in clinical samples indicate a somatic variant behavior that is relevant to oncogenesis.

Prognostic evidence:

Prognostic: The study indicates that the combination of INHBA expression with a clinical nomogram enhances prognostic power in colon adenocarcinoma, particularly in predicting recurrence, which correlates with disease outcome independent of therapy.

Prognostic, Functional evidence:

Prognostic: The abstract indicates that patients with high B4GALNT2 expression in cancer tissues display longer survival than non-expressers, suggesting a correlation between the expression level of this gene and disease outcome.

Functional: The results describe how B4GALNT2 expression affects the growth of cancer cells in different conditions, indicating that it alters molecular or biochemical functions related to cancer cell behavior.

Functional evidence:

Functional: The study discusses the formation of a covalent bond between the novel FLT3 inhibitor, FF-10101, and the cysteine residue at 695 of FLT3, indicating that this variant alters the molecular interaction and function of the FLT3 protein, which is crucial for the inhibitor's selectivity and activity.

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Diagnostic, Prognostic, Oncogenic evidence:

Diagnostic: The study discusses the classification of glioma patients into different types based on RNA sequencing data from TCGA and CGGA, indicating that the variant (CGGA 94) is used to define or classify a subtype of glioma.

Prognostic: The abstract mentions that survival analysis was performed and identified RBPs significantly associated with the overall survival of glioblastoma patients, suggesting that the variant's presence may correlate with disease outcome.

Oncogenic: The results section indicates that various molecular alterations, including TERT mutations, are closely linked to the clinical phenotype of glioma, implying that the variant may contribute to tumor development or progression.

Diagnostic, Predisposing evidence:

Predisposing: The study identifies rs78062588 as a new lung cancer susceptibility locus, indicating that this variant is associated with an inherited risk for developing lung cancer. The odds ratio (OR = 0.86) and statistical significance (P = 1.65 x 10^-6) support its role in predisposition to the disease.

Diagnostic: The mention of rs78062588 being associated with lung cancer risk suggests that it can be used to classify or define susceptibility to lung cancer, fulfilling the criteria for a diagnostic evidence type. The results indicate a clear association with lung cancer, which aligns with the diagnostic category.

Oncogenic evidence:

Oncogenic: The study discusses that mutations in GNAQ and GNA11, including the hotspot mutations Q209P/L, are associated with the development of uveal melanoma (UM) through the activation of oncogenic pathways. This indicates that these variants contribute to tumor development and progression.

Diagnostic, Prognostic evidence:

Prognostic: The study reports that patients with PTEN mutation showed a significantly prolonged overall survival (OS) time and disease-free survival (DFS) time compared to those without the mutation, indicating that PTEN mutation serves as an independent prognostic factor in DFS.

Diagnostic: The abstract mentions that PTEN mutation was significantly associated with various clinical characteristics such as age, histological type, clinical stage, and grade, suggesting its role in classifying or defining disease subtypes in endometrial carcinoma.

Oncogenic, Functional evidence:

Oncogenic: The study demonstrates that upregulated miR-3174 promotes cell proliferation and inhibits cell apoptosis in hepatocellular carcinoma (HCC), indicating its role in tumor development and progression. This is supported by the findings that miR-3174 is associated with tumor size and Edmondson grade, which are indicative of oncogenic behavior.

Functional: The research confirms that miR-3174 regulates the expression of key proteins such as Bim, P21, cyclin D1, and c-MYC by directly targeting FOXO1, indicating that it alters molecular function. The use of dual-luciferase reporter gene assays further supports the functional impact of miR-3174 on gene expression.

Prognostic evidence:

Prognostic: The study reports that patients with higher FOS expression displayed significantly shorter time to recurrence (TTR) and overall survival (OS) compared with patients with lower expression, indicating that FOS correlates with disease outcome independent of therapy.

Prognostic, Oncogenic evidence:

Prognostic: The study indicates that dysregulated expression of CASC5 is closely associated with patient overall survival (OS) in multiple cancer types, including lung adenocarcinoma (LUAD), suggesting its role in predicting disease outcomes independent of therapy.

Oncogenic: The findings reveal that CASC5 is identified as a novel oncogenic gene in LUAD, indicating its contribution to tumor development and progression, supported by functional experiments demonstrating its role in promoting cell proliferation.

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Prognostic evidence:

Prognostic: The abstract states that "STEAP1 is a potential prognostic biomarker for LUAD," indicating that the variant correlates with disease outcome, specifically in the context of lung adenocarcinoma (LUAD). This suggests that the variant may provide information about the prognosis of patients with this disease.

Predictive, Diagnostic, Prognostic evidence:

Diagnostic: The study suggests that the 38 common differentially expressed peroxisome pathway genes (C-DEPGs) could discriminate NSCLC tumors from non-tumor controls, indicating their potential use as markers for diagnosis.

Prognostic: The Kaplan-Meier survival and Cox regression analyses demonstrated that 11 of the C-DEPGs have prognostic effects on overall survival in NSCLC, highlighting their relevance in predicting disease outcomes.

Predictive: The study mentions associations of the identified genes with anti-cancer drug sensitivity, suggesting that these genes may correlate with treatment response in NSCLC.

Prognostic evidence:

Prognostic: The study indicates that the SNP rs2641256 is significantly correlated with HNSCC patients' survival, as evidenced by the reported hazard ratio (HRadjusted = 0.67) and the statistical significance (Padjusted = 7.51 x 10-6), suggesting its role in disease outcome independent of therapy.

Prognostic evidence:

Prognostic: The study indicates that high GOT1 expression is associated with shorter event-free survival (EFS) and overall survival (OS) in acute myeloid leukemia (AML) patients, suggesting that GOT1 expression may serve as a prognostic indicator for disease outcomes independent of therapy.

Predictive, Oncogenic evidence:

Predictive: The study discusses the role of the ABCG2 transporter in the development of resistance to oxaliplatin, indicating that the variant correlates with resistance to this specific therapy in colorectal cancer. The mention of "multi drug resistance" and the effects of ABCG2 on drug efficacy supports this classification.

Oncogenic: The development of oxaliplatin-resistant (OXA-R) colon cancer cells suggests that the variant contributes to tumor progression, as it is associated with the ability of cancer cells to evade the effects of chemotherapy. The study's focus on the molecular mechanisms involved in resistance further supports this classification.

Predictive, Oncogenic, Functional evidence:

Oncogenic: The study indicates that CUL7 plays a significant role in promoting tumorigenesis, suggesting that it contributes to tumor development or progression in human gliomas.

Functional: The mention of CUL7 being negatively regulated by miR-3940-5p implies that this variant alters molecular function, specifically in the context of its regulation and activity in gliomas.

Predictive: The statement that CUL7 might be a candidate molecular target for the treatment of glioma suggests a potential correlation with response to therapy, indicating its predictive value in treatment contexts.

Prognostic evidence:

Prognostic: The study reports that low expression of SULT1B1, MOGAT2, and C1orf115 is closely correlated with poorer survival of colorectal cancer (CRC) patients, indicating that these genes may serve as prognostic markers for disease outcome.

Predictive, Prognostic evidence:

Prognostic: The abstract states that "low expression of RGL4 is accompanied by worse outcomes and prognosis in LUAD patients," indicating a correlation between the variant and disease outcome independent of therapy. This suggests that RGL4 expression levels can serve as a prognostic indicator for lung adenocarcinoma.

Predictive: The abstract mentions that "RGL4 may also be used in combination with immune checkpoints to identify the benefits of immunotherapy," which implies that RGL4 expression could correlate with response to immunotherapy, thus serving as a predictive biomarker for treatment outcomes.

Predictive, Prognostic, Oncogenic evidence:

Predictive: The study discusses the combination of FLT3 TKIs with arsenic trioxide (ATO) and its synergistic effects in reducing proliferation and viability in FLT3/ITD+ leukemia cells, indicating a potential improvement in treatment response for patients with this variant. The mention of "synergistic effects" and "increased apoptosis" suggests a correlation with therapeutic sensitivity, which aligns with predictive evidence.

Prognostic: The abstract states that AML patients with FLT3/ITD mutations have a "poor prognosis," indicating that this variant correlates with disease outcome independent of therapy. This suggests that the presence of the FLT3/ITD mutation is associated with a negative impact on survival or disease progression.

Oncogenic: The FLT3/ITD mutation is implicated in the development of leukemia, as the study explores its role in the context of treatment and tumor behavior. The evidence of ATO's effects on FLT3 protein degradation and signaling pathways further supports the notion that this somatic variant contributes to tumor progression.

Functional evidence:

Functional: The study discusses the somatic DNMT3A-V716F mutation and predicts that it affects methyltransferase activity, indicating that this variant alters molecular function. This is supported by the context in which the mutation is mentioned, specifically in relation to its predicted impact on enzyme activity.

Diagnostic, Oncogenic evidence:

Diagnostic: The study identifies the variant p.Arg183Gln in GNAQ as being present in 88% of participants with Sturge-Weber syndrome and 92% with nonsyndromic port-wine stains, indicating its association with these conditions and supporting its use as a biomarker for diagnosis.

Oncogenic: The findings suggest that the p.Arg183Gln variant is a somatic activating mutation that contributes to the development of Sturge-Weber syndrome and port-wine stains, confirming its role in tumor development or progression as hypothesized in the background of the study.

Predictive evidence:

Predictive: The abstract discusses treatment resistance in the context of IGF1R-directed targeted therapy, indicating that the variant may correlate with resistance to this specific therapy, which is a key aspect of predictive evidence. The mention of "treatment resistance mechanisms" suggests that understanding the variant's role could help in selecting effective therapies.

Diagnostic, Prognostic, Oncogenic evidence:

Oncogenic: The study discusses how overexpression of ANXA2 in GBM cells enhances cell invasion, angiogenesis, and proliferation, indicating that ANXA2 contributes to tumor development and progression in glioblastoma.

Prognostic: The results indicate that mice bearing ANXA2-overexpressing GBM exhibited shorter survival times compared to control tumor-bearing mice, suggesting that ANXA2 expression correlates with disease outcome in terms of survival.

Diagnostic: The study uncovers a significant relationship between ANXA2 and OSMR expression in clinical GBM specimens, demonstrating their correlation with tumor histopathology and patient prognosis, which supports their potential use as biomarkers in diagnosing or classifying the disease.

Predictive, Oncogenic evidence:

Predictive: The study discusses the use of an FLT3 tyrosine kinase inhibitor, PKC412, in patients with acute myeloid leukemia (AML) harboring an activating mutation in the FLT3 gene, indicating that the presence of this mutation correlates with response to the therapy. The results show a significant reduction in peripheral blast counts in patients treated with PKC412, demonstrating the variant's predictive value for treatment response.

Oncogenic: The abstract mentions that 30% of patients with AML have an activating mutation in the FLT3 gene, which is implicated in tumor development, suggesting that this somatic variant contributes to the progression of the disease. The activation of FLT3 is a known driver in AML, supporting its classification as oncogenic.

Predictive, Diagnostic evidence:

Predictive: The study discusses the use of an FLT3 tyrosine kinase inhibitor, PKC412, in patients with acute myeloid leukemia (AML) harboring an activating mutation in the FLT3 gene, indicating that the presence of this mutation correlates with response to the therapy. The results show a significant reduction in peripheral blast counts in a majority of patients, demonstrating the variant's predictive value for treatment response.

Diagnostic: The abstract mentions that 30% of patients with acute myeloid leukemia have an activating mutation in the FLT3 gene, which is used to identify patients who may benefit from targeted drug therapy. This association highlights the role of the FLT3 mutation in classifying and confirming the disease subtype in these patients.

Predictive, Prognostic, Oncogenic evidence:

Predictive: The study discusses the correlation between the FLT3-ITD variant and treatment response, indicating that patients with FLT3-ITD-positive acute myeloid leukaemia have poorer responses to salvage therapy compared to those with FLT3 wild-type disease. This suggests that the presence of the FLT3-ITD variant is predictive of treatment outcomes with quizartinib versus chemotherapy.

Prognostic: The abstract mentions that patients with FLT3-ITD-positive acute myeloid leukaemia have a poor prognosis, including high frequency of relapse and shorter overall survival, which indicates that the variant is associated with adverse disease outcomes independent of therapy.

Oncogenic: The study highlights the FLT3-ITD variant as a driver mutation in acute myeloid leukaemia, suggesting its role in tumor development and progression, which aligns with the definition of oncogenic variants.

Predictive, Oncogenic evidence:

Oncogenic: The abstract states that activating mutations in the receptor tyrosine kinase FLT3 are present in approximately 30% of acute myeloid leukemia (AML) patients, implicating FLT3 as a driver of the disease. This indicates that the variant contributes to tumor development or progression in AML.

Predictive: The abstract discusses AC220 as a second-generation FLT3 inhibitor and highlights its efficacy in animal models, suggesting that the presence of FLT3 mutations correlates with response to this specific therapy. This indicates a predictive relationship between the variant and treatment response.

Functional evidence:

Functional: The study discusses how the substitution of phenylalanine with leucine (F691L) in the FLT3 tyrosine kinase domain alters the resistance profile to ponatinib, indicating that this variant affects the molecular function of the protein in the context of drug resistance.

Predictive, Oncogenic evidence:

Predictive: The study discusses how FLT3-ITD mutations are associated with resistance to FLT3 inhibitors, indicating that these variants correlate with treatment response and suggesting the need for targeted combination drug strategies to enhance therapy efficacy.

Oncogenic: The identification of acquired point mutations in the FLT3 gene that contribute to sorafenib resistance in AML cells suggests that these somatic variants play a role in tumor progression and development, as they were shown to affect the response to targeted therapies.

Predictive evidence:

Predictive: The abstract indicates that FOXC2 induces epithelial-mesenchymal transition (EMT) to promote oxaliplatin resistance, suggesting a correlation between the variant and resistance to a specific therapy (oxaliplatin) in colorectal cancer (CRC). This aligns with the predictive evidence type as it discusses treatment response.

Predictive, Diagnostic evidence:

Predictive: The study indicates that combined MEK and BET inhibitors are effective in approximately 50% of KRAS-mutant NSCLC, suggesting a correlation between the KRAS G12C variant and response to this specific therapy. The mention of HOXC10 as a biomarker of response further supports the predictive nature of the findings regarding treatment efficacy.

Diagnostic: The abstract and results highlight that HOXC10 is overexpressed in KRAS-mutant tumors, which implies that the presence of the KRAS G12C variant can be associated with specific tumor characteristics, thus serving as a potential biomarker for diagnosis or classification of the disease.

Predictive, Diagnostic evidence:

Diagnostic: The abstract states that hypermethylation of the SST gene is common in tumor entities and represents a promising pan-cancer biomarker, indicating its use in defining or classifying disease.

Predictive: The mention of somatostatin agonist octreotide reducing proliferation and migration of pancreatic cancer cells suggests that variations in SST methylation may correlate with response to therapy, indicating predictive potential.

Diagnostic, Prognostic evidence:

Diagnostic: The abstract mentions that certain genes may help to outline the prognosis of patients with breast cancer and that some previously overlooked genes have the potential to become additional biomarkers for breast cancer, indicating a role in defining or classifying the disease.

Prognostic: The abstract discusses the potential relationship between tumor microenvironment and breast cancer prognosis, suggesting that the identified genes may correlate with disease outcomes such as survival or progression.

Prognostic, Oncogenic evidence:

Oncogenic: The study characterizes TP73-AS1 as an oncogenic lncRNA in gastric cancer (GC), indicating its role in tumor development or progression. The findings suggest that altered expression of TP73-AS1 is associated with cancer cell invasion and migration, which are key aspects of oncogenic behavior.

Prognostic: The expression levels of miR-223-5p and TP73-AS1 were found to be inversely correlated and predicted poor disease-specific survival in gastric cancer patients. This suggests that these variants may serve as prognostic indicators for disease outcomes.

Predictive, Prognostic evidence:

Prognostic: The study indicates that LTF downregulation and LRP1 upregulation combined predict a poor overall survival rate in ccRCC patients, suggesting a correlation between these factors and disease outcome independent of therapy.

Predictive: The administration of recombinant LTF protein significantly suppresses cell migration ability and lung metastatic potential, indicating that LTF may influence response to therapeutic interventions in metastatic ccRCC.

Prognostic, Oncogenic evidence:

Oncogenic: The study identifies MAFB as a key transcriptional regulator in osteosarcoma progression, indicating that its expression is required for the proliferation and tumorigenicity of osteosarcoma cells, which supports the notion that MAFB contributes to tumor development.

Prognostic: The expression levels of MAFB and Sox9 were found to be highly correlated with disease progression and combined detection of both was suggested as a promising prognostic biomarker that stratifies patients with the shortest overall survival, indicating their relevance in predicting disease outcomes.

Diagnostic, Prognostic evidence:

Prognostic: The study indicates that upregulation of the VEGFR-1 ligands VEGF-A and PlGF is associated with a significant reduction in overall survival for patients with glioblastoma (GB), suggesting that these factors may correlate with disease outcome independent of therapy.

Diagnostic: The investigation of VEGFR-1 expression in GB-associated microglia/macrophages (GAMs) and the analysis of surgical specimens from patients with GB suggest that VEGFR-1 may be used to classify or define aspects of the disease, particularly in relation to its expression in tumor microenvironments.

Prognostic, Oncogenic, Functional evidence:

Prognostic: The abstract states that "USP19 downregulation was associated with ccRCC progression and poor prognostic outcomes in TCGA cohort," indicating that the variant correlates with disease outcome independent of therapy.

Oncogenic: The findings suggest that "USP19 overexpression inhibited ccRCC proliferation and migration," while "USP19 knockdown promoted ccRCC proliferation and migration," demonstrating that USP19 contributes to tumor development or progression in clear cell renal cell carcinoma.

Functional: The study describes that "USP19 exerted its inhibitory effect on ccRCC proliferation and migration by suppressing the activation of ERK," indicating that the variant alters molecular function related to cancer cell behavior.

Predictive, Prognostic evidence:

Prognostic: The study indicates that TP53 mutations were a negative prognostic factor for disease-free survival (DFS) in untreated patients, suggesting that these mutations correlate with worse outcomes independent of therapy.

Predictive: The results show that TP53 mutations were a positive predictive factor for the efficacy of gemcitabine treatment, indicating that the presence of these mutations correlates with a better response to this specific therapy.

Functional evidence:

Functional: The study indicates that Actinomycin D downregulated Sox2, suggesting that the variant alters the molecular function of Sox2, which is relevant to the stem cell population in GBM tumors. This alteration in expression demonstrates a biochemical effect of the treatment on the variant's activity.

Prognostic, Functional evidence:

Prognostic: The study indicates that higher expression of ELFN1-AS1 is associated with shorter patient survival in esophageal cancer (ESCA), suggesting a correlation with disease outcome independent of therapy.

Functional: The research demonstrates that down-regulation of ELFN1-AS1 restrains cell proliferation, migration, and invasion in ESCA, indicating that this lncRNA alters molecular functions related to cancer progression.

Predictive evidence:

Predictive: The study investigates the association between ABCC11 expression and resistance to alectinib, indicating that increased ABCC11 expression correlates with decreased sensitivity to the drug, which is a clear example of predictive evidence regarding treatment response.