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.

Predictive, Oncogenic evidence:

Oncogenic: The study establishes a causal link between USP10 and hyperactivated YAP/TAZ in hepatocellular carcinoma, indicating that the aberrant activation of YAP/TAZ contributes to tumor progression. This suggests that the variant's role is related to tumor development or progression in the context of hepatocellular carcinoma.

Predictive: The findings provide a rationale for potential therapeutic interventions in patients with hepatocellular carcinoma harboring a high level of YAP/TAZ, indicating that the variant may correlate with treatment response or sensitivity to specific therapies targeting YAP/TAZ.

Prognostic, Oncogenic evidence:

Prognostic: The study found that high GAL1 expression was significantly associated with poor recurrence-free survival (RFS) and low cancer-specific survival (CSS), indicating that GAL1 expression correlates with disease outcome independent of therapy. The multivariate analysis further supports that GAL1-high is an independent predictive factor for RFS and CSS, reinforcing its prognostic significance in upper tract urothelial carcinoma (UTUC).

Oncogenic: The research indicates that GAL1 promotes invasion and metastasis in urothelial carcinoma by activating specific signaling pathways, suggesting that GAL1 contributes to tumor development and progression. The in vitro studies demonstrated that GAL1 knockdown significantly reduced migration and invasiveness, highlighting its role in oncogenic processes.

Prognostic evidence:

Prognostic: The abstract indicates that NUSAP1 may serve as a valuable indicator of poor survival in CESC, suggesting a correlation between the variant and disease outcome independent of therapy.

Prognostic evidence:

Prognostic: The study reports that overexpression of SQLE is significantly associated with worse overall survival (OS) and disease-free survival (DFS) in patients with HCC, indicating that this variant correlates with disease outcome independent of therapy. The hazard ratio and statistical significance further support its role as a prognostic biomarker for HCC.

Prognostic, Oncogenic evidence:

Oncogenic: The study indicates that FAM83A is an over-expressed oncogene in non-small cell lung cancer (NSCLC) and plays a role in tumorigenesis, as evidenced by the inhibition of cell proliferation and tumor growth upon silencing FAM83A. This suggests that FAM83A contributes to tumor development and progression in NSCLC.

Prognostic: The abstract mentions that high expression levels of FAM83A in NSCLC are associated with poor prognosis, indicating that this variant correlates with disease outcome independent of therapy.

Diagnostic, Prognostic, Oncogenic evidence:

Prognostic: The study indicates that high miR-31 expression is significantly associated with poorer mortality and shorter median survival time in patients with advanced CRC, suggesting that it serves as a prognostic biomarker.

Diagnostic: The abstract mentions that the study evaluates the potential of miRNAs as prognostic biomarkers for patients with advanced CRC, and specifically highlights the association of miR-31 with the BRAF V600E mutation, indicating its role in classifying disease subtypes.

Oncogenic: The results section discusses the role of miR-31 in regulating BRAF protein expression and its association with the BRAF V600E mutation, suggesting that this variant contributes to tumor progression in CRC.

Diagnostic, Prognostic evidence:

Prognostic: The study indicates that the upregulation of MYBL2 expression is significantly associated with poor overall survival (OS) in patients with clear cell renal cell carcinoma (ccRCC), suggesting that it can independently predict prognosis. This is supported by the use of Cox regression analysis to assess the relationship between MYBL2 expression and patient outcomes.

Diagnostic: The abstract mentions that MYBL2 expression is significantly associated with various clinicopathological factors, which implies its potential use in classifying or defining disease characteristics in ccRCC. The analysis of MYBL2 expression in relation to tumor stage and histological grade further supports its role in disease classification.

Prognostic, Functional evidence:

Prognostic: The study indicates that elevated BCL11A levels are correlated with unfavorable overall survival (OS) in patients with triple-negative breast cancer (TNBC), suggesting that this variant may serve as a prognostic marker for disease outcome.

Functional: The results demonstrate that BCL11A-knockdown significantly inhibited proliferation, migration, and invasion in TNBC cell lines, indicating that the variant alters molecular functions related to tumor growth and metastasis.

Oncogenic, Functional evidence:

Oncogenic: The study demonstrates that SLC6A14 is essential for colon cancer, indicating that its up-regulation contributes to tumor development and progression. The evidence includes the reduction of tumor growth upon silencing SLC6A14 and the protective effect of its deletion in mouse models of colon cancer.

Functional: The research shows that blocking SLC6A14 with alpha-methyltryptophan induces amino acid deprivation, decreases mTOR activity, increases autophagy, promotes apoptosis, and suppresses cell proliferation and invasion. This indicates that the variant alters molecular functions related to cancer cell survival and growth.

Predictive, Oncogenic evidence:

Predictive: The study discusses how low CHD1 levels correlate with shorter clinical responses to enzalutamide, indicating that the F877L variant may influence treatment response, which is a key aspect of predictive evidence.

Oncogenic: The F877L variant is described as a positive control in an in vivo screen, where it is shown to contribute to tumor development in the context of enzalutamide treatment, demonstrating its role in tumor progression.

Predictive, Oncogenic evidence:

Predictive: The study identifies loss of AKT1 p.E17K as a mechanism of acquired resistance to AZD5363, suggesting that this variant may correlate with treatment response, thereby serving as a predictive biomarker for sensitivity to the therapy.

Oncogenic: The mention of loss of AKT1 p.E17K in the context of acquired resistance implies that this somatic variant may contribute to tumor progression or development, indicating its oncogenic potential.

Predictive, Prognostic, Oncogenic evidence:

Predictive: The study indicates that MALAT1 expression is high in sorafenib-resistant HCC cells and that knockdown of MALAT1 increases sorafenib sensitivity, suggesting a correlation between MALAT1 levels and response to sorafenib treatment.

Prognostic: The findings show that upregulated MALAT1 is closely correlated with poor survival outcomes in patients with HCC, indicating its potential role as a prognostic biomarker.

Oncogenic: The study describes MALAT1 as an oncogene that promotes cell proliferation, migration, and epithelial-mesenchymal transition in HCC cells, demonstrating its contribution to tumor development and progression.

Predictive evidence:

Predictive: The study discusses the use of the DNA-PK inhibitor M3814 (peposertib) in combination with ionizing radiation (IR) and DSB-inducing agents, indicating that the variant correlates with enhanced sensitivity to these therapies, which is a key aspect of predictive evidence. The results show that M3814 sensitizes multiple cancer cell lines to IR, supporting its potential as a therapeutic strategy.

Predictive evidence:

Predictive: The abstract indicates that high expression of NKCC1 regulates epithelial-mesenchymal transition (EMT) in gliomas, suggesting a potential therapeutic strategy that could influence treatment response by targeting this pathway.

Predictive, Diagnostic, Prognostic evidence:

Diagnostic: The study identifies associations between LOXL2 expression status and various molecular characterizations of cervical carcinoma, indicating its potential use in classifying or defining the disease.

Prognostic: High LOXL2 expression was associated with poor overall survival (OS) and poor disease-free survival (DFS) in cervical carcinoma, suggesting that it may serve as a prognostic marker for disease outcomes.

Predictive: The study suggests that LOXL2 may serve as a potential therapeutic target for cervical carcinoma, indicating a correlation with treatment response or sensitivity to therapies targeting this pathway.

Predictive, Diagnostic, Oncogenic evidence:

Oncogenic: The study demonstrates that GPX2 acts as an oncogene in lung adenocarcinoma (LUAD) and promotes cisplatin (DDP) resistance, indicating its role in tumor development and progression. This is supported by the finding that GPX2 was significantly upregulated in DDP-resistant cell lines and its expression correlated with adverse disease-free survival in LUAD cases.

Predictive: The evidence suggests that GPX2 is involved in mediating DDP resistance, as knockdown of GPX2 expression decreased the IC50 values of DDP, indicating a correlation with sensitivity to this specific therapy. The study highlights the role of GPX2 in influencing treatment response in the context of lung adenocarcinoma.

Diagnostic: The study reports that elevated GPX2 expression was found in 58.6% of LUAD cases, indicating its potential use as a biomarker for disease classification and association with adverse outcomes. This suggests that GPX2 could be utilized to define or confirm the presence of a specific disease subtype in lung adenocarcinoma.

Predictive, Oncogenic, Functional evidence:

Predictive: The study indicates that "chemical inhibition of CDK5 blocks the metastatic spread of patient-derived melanomas," suggesting that the variant's activity correlates with resistance to metastatic progression, which is relevant for therapeutic strategies.

Oncogenic: The findings demonstrate that CDK5 is essential for the metastatic spread of melanoma, indicating that it contributes to tumor progression, which aligns with the definition of an oncogenic variant.

Functional: The research shows that CDK5 alters the molecular function by "directly phosphorylating an intermediate filament protein, vimentin," which affects the assembly of vimentin filaments, highlighting its role in cellular invasiveness.

Predictive, Oncogenic evidence:

Predictive: The study discusses how the inhibition of Pin1 sensitizes BRCA1-proficient tumors to PARP inhibitors, indicating a correlation with treatment response. The mention of "sensitized breast tumors to olaparib" suggests that the variant's effect is related to the response to a specific therapy.

Oncogenic: The research highlights that loss of Pin1 or introduction of a BRCA1-mutant affects the ability of BRCA1 to localize to repair foci and augments DNA damage, indicating that these variants contribute to tumor development or progression. The context of BRCA1's role in homologous recombination and DNA repair supports the oncogenic classification.

Predictive, Oncogenic evidence:

Predictive: The study discusses how the EGFRL858R variant is associated with resistance to osimertinib and highlights the importance of understanding resistance mutations for determining subsequent treatment approaches, indicating a correlation with therapy response.

Oncogenic: The variant EGFRL858R is described as a driver mutation in the context of lung adenocarcinoma, suggesting its role in tumor development and progression, particularly in the transgenic mouse models used in the study.

Prognostic, Oncogenic evidence:

Prognostic: The abstract indicates that the downregulation of hsa-miR-143 positively correlates with adverse prognosis in renal cell carcinoma (RCC), suggesting that this variant may be associated with disease outcome independent of therapy.

Oncogenic: The study suggests that hsa-miR-143 acts as a potential tumor suppressor, and its involvement in inhibiting cell adhesion, migration, and epithelial-mesenchymal transition (EMT) implies a role in tumor development or progression, which aligns with oncogenic behavior.

Prognostic evidence:

Prognostic: The abstract states that CTGF is an "unfavorable and independent prognostic marker for glioma patients," indicating that the variant correlates with disease outcome, specifically in terms of prognosis for glioma.

Predictive, Diagnostic, Prognostic evidence:

Predictive: The study suggests that OTUD4 may serve as a predictive factor for several human cancers, indicating its potential role in response to treatment or therapy.

Prognostic: The results indicate that OTUD4 could be a useful biomarker for the prognosis of human cancers, correlating with disease outcomes such as survival or progression.

Diagnostic: The mention of OTUD4 as a potential molecular target for diagnosis implies its role in classifying or defining certain cancers, supporting its use as a diagnostic biomarker.

Predictive evidence:

Predictive: The abstract mentions that ponatinib demonstrates activity against T315I mutant clones, indicating that this variant correlates with response to the therapy, specifically the third-generation TKI ponatinib. This suggests that the presence of the T315I variant is predictive of treatment efficacy with ponatinib in patients with CML and Ph+ ALL.

Diagnostic, Prognostic evidence:

Prognostic: The abstract states that hsa-mir-124 expressions were associated with overall survival in BRCA patients, indicating a correlation with disease outcome independent of therapy.

Diagnostic: The abstract mentions that hsa-mir-124 expressions are associated with tumor molecular phenotype and pathologic characteristics in BRCA, suggesting its potential use as a biomarker for classification or diagnosis of the disease.

Predictive, Oncogenic evidence:

Predictive: The abstract mentions that lifirafenib is an inhibitor with antitumor activity in patients with B-RAFV600-mutated solid tumors, indicating a correlation between the B-RAFV600E variant and response to this specific therapy.

Oncogenic: The results section discusses the role of B-RAF mutations in tumorigenesis, specifically noting that B-RAF mutations occur in a significant percentage of various cancers, which supports the notion that the B-RAFV600E variant contributes to tumor development or progression.

Predictive evidence:

Predictive: The study indicates that low mRNA expression of glycerol-3-phosphate dehydrogenase 1 (GPD1) may predict a poor response to metformin treatment, suggesting a correlation between GPD1 expression levels and therapeutic response to metformin in cancer cell lines. This aligns with the predictive evidence type as it discusses the relationship between a variant and treatment response.

Predictive evidence:

Predictive: The abstract discusses that the HER2 L755S mutation in a patient with metastatic breast cancer led to a partial response to the HER2/EGFR tyrosine kinase inhibitor neratinib, indicating that this variant correlates with sensitivity to a specific therapy. The mention of treatment response and improvement in the patient's condition supports the classification as predictive evidence.

Prognostic, Oncogenic evidence:

Prognostic: The study indicates that high expression levels of WDR12 are dramatically related to shorter overall survival and reduced disease-free survival in glioblastoma, suggesting that it correlates with disease outcome independent of therapy.

Oncogenic: The report suggests that WDR12 drives malignant behavior in glioblastoma, indicating its contribution to tumor development or progression, particularly through the findings from cell biology experiments that demonstrate its role in promoting apoptosis and inhibiting proliferation.

Diagnostic, Prognostic evidence:

Prognostic: The survival analysis revealed that the higher expressions of WNT5A and WNT16 were associated with poor overall survival (OS) in patients with glioma, indicating a correlation between these variants and disease outcome.

Diagnostic: The conclusion states that WNT5A can serve as a candidate to diagnose glioma, suggesting its role in defining or classifying the disease.

Oncogenic evidence:

Oncogenic: The study demonstrates that TFB2M significantly promotes HCC cell proliferation, migration, and invasion, indicating its role in tumor development and progression. Additionally, the findings suggest that TFB2M contributes to xenograft tumorigenesis and lung metastasis, further supporting its oncogenic function in hepatocellular carcinoma.

Prognostic evidence:

Prognostic: The abstract indicates that high WTAP expression is associated with poor prognosis, suggesting that this variant correlates with disease outcome independent of therapy.

Prognostic evidence:

Prognostic: The abstract states that CARD9 is an "independent prognostic factor in NSCLC patients," indicating that the variant correlates with disease outcome independent of therapy. This suggests that the presence of CARD9 has implications for the prognosis of patients with non-small cell lung cancer (NSCLC).

Prognostic, Functional evidence:

Prognostic: The study indicates that high expression of PIK3CD-AS2 is associated with shorter patient survival and poor disease-free survival in p53 wild-type patients, suggesting a correlation with disease outcome independent of therapy.

Functional: The research demonstrates that PIK3CD-AS2 alters the stability of YBX1 by impeding its ubiquitination and degradation, indicating a change in molecular function that affects p53 signaling.

Prognostic, Functional evidence:

Prognostic: The study indicates that patients with higher MAGI-2 expression had longer biochemical recurrence-free survival, suggesting that MAGI-2 serves as a predictor of tumor recurrence in Han Chinese patients with prostate cancer.

Functional: The presence of tryptophan-tryptophan (WW) domains in MAGI-2 is mentioned, which are involved in various protein interactions, indicating that these domains alter the molecular function of MAGI-2 in supporting cell junctions and maintaining cell integrity.

Predictive, Oncogenic evidence:

Predictive: The study discusses the therapeutic potential of combined AXL and HDAC inhibition in H3K27M DIPG cells, indicating that this treatment can reverse the therapy-resistant phenotype and has a synergistic antitumor effect, which correlates with sensitivity to the therapy.

Oncogenic: The abstract mentions that mutations in genes encoding histone 3 (H3K27M) drive the development of DIPG, suggesting that this somatic variant contributes to tumor progression in this specific type of brain cancer.

Predictive evidence:

Predictive: The study discusses the potential of EB1 expression as a response-predictive biomarker of BAL101553 in GBM, indicating that the variant's expression level correlates with treatment response. This suggests that the variant may influence the effectiveness of the therapy being tested.

Predictive, Diagnostic evidence:

Predictive: The study discusses how low levels of POLA1, POLE, and POLE2 protein expression in NSCLC and colorectal cancer cells correlate with sensitivity to CHK1 inhibitors, indicating that these variants may serve as biomarkers for predicting response to therapy.

Diagnostic: The identification of POLA1, POLE, and POLE2 as potential biomarkers for CHK1 inhibitor sensitivity suggests that these variants can be used to classify or define a specific phenotype in cancer patients, particularly in relation to their response to treatment.