Predictive, Prognostic evidence:

Predictive: The study discusses the addition of trastuzumab (T) to carboplatin/paclitaxel (C/P) and its impact on progression-free survival (PFS) and overall survival (OS) in patients with HER2/Neu-positive uterine-serous-carcinoma (USC). The results indicate that the combination therapy significantly improves PFS and OS, demonstrating a predictive relationship between the HER2/Neu-positive variant and treatment response.

Prognostic: The results show that the median overall survival (OS) was higher in the trastuzumab arm compared to the control arm, indicating that the HER2/Neu-positive status correlates with better survival outcomes independent of therapy. This suggests a prognostic role of the variant in determining disease outcome.

Predictive, Prognostic evidence:

Prognostic: The abstract states that "PDCD1 upregulation was found in more malignant phenotypes of glioma and indicated a worse prognosis," indicating a correlation between the variant and disease outcome independent of therapy.

Predictive: The mention of "Immunotherapy of targeting PD-1 or combined with other checkpoint molecules... may represent a promising treatment strategy for glioma" suggests that the variant is associated with response to specific therapies, indicating its predictive nature.

Functional evidence:

Functional: The study demonstrates that BRCA1 variants of uncertain significance (VUS) were tested for their ability to complement Brca1-deficient mouse embryonic stem cells in homologous recombination DNA repair (HRR), indicating that these variants alter molecular function related to DNA repair mechanisms. The results showed that 45 out of 238 VUS exhibited functional defects, confirming the impact of these variants on HRR.

Predictive, Prognostic evidence:

Predictive: The study demonstrates that the presence of ESR1 mutations correlates with progression-free survival (PFS) and overall survival (OS) in patients treated with exemestane and fulvestrant, indicating that these mutations can predict treatment response. The interaction between ESR1 mutation status and treatment outcomes further supports this predictive relationship.

Prognostic: The results indicate that patients with detected ESR1 mutations have inferior PFS and OS, suggesting that these mutations are associated with worse disease outcomes independent of the specific therapy used. This correlation highlights the prognostic significance of ESR1 mutations in hormone receptor-positive metastatic breast cancer.

Predictive, Oncogenic evidence:

Predictive: The study indicates that neuroblastoma cell lines harboring the NRAS Q61K mutation were resistant to SHP2 inhibitors, suggesting a correlation between the presence of this variant and resistance to specific therapies. This highlights the predictive nature of the variant in terms of treatment response.

Oncogenic: The mention of the NRAS Q61K mutation being commonly detected at relapse implies its role in tumor development or progression, supporting the classification of this variant as oncogenic. The context of resistance to therapies further emphasizes its contribution to cancer behavior.

Oncogenic evidence:

Oncogenic: The abstract indicates that HSP47 supports the growth of colorectal cancer (CRC) tumors, suggesting that this variant contributes to tumor development or progression. The mention of its role in modulating AKT signaling further supports its oncogenic potential.

Predictive, Oncogenic evidence:

Predictive: The abstract mentions that taletrectinib has potent preclinical activity against the ROS1 G2032R solvent-front mutation, indicating that this variant correlates with response to the therapy. The context of discussing treatment efficacy suggests a predictive relationship between the variant and therapeutic response.

Oncogenic: The mention of the ROS1 G2032R mutation in the context of being a target for a tyrosine kinase inhibitor implies that this somatic variant contributes to tumor development or progression, which aligns with the oncogenic evidence type.

Prognostic evidence:

Prognostic: The abstract states that "High expression level of UPP1 predicts poor prognosis in glioma," indicating that the variant correlates with disease outcome independent of therapy.

Oncogenic evidence:

Oncogenic: The study indicates that the BRAF mutation p.K601E is shown to be oncogenic and can be targeted by MEK inhibitors, suggesting its role in tumor development or progression in chronic lymphocytic leukemia (CLL).

Predictive, Functional evidence:

Predictive: The presence of the BCL-2 G101V mutation in patient samples was predictive of clinical progression, indicating that this variant correlates with resistance to venetoclax therapy in chronic lymphocytic leukaemia patients.

Functional: The BCL-2 G101V mutation reduces the affinity for venetoclax by approximately 180-fold while maintaining affinity for pro-apoptotic proteins, demonstrating that this variant alters the molecular function of the BCL-2 protein in the context of drug interaction.

Predictive, Oncogenic evidence:

Predictive: The study discusses the resistance to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) in the context of the T790M mutation, indicating that this variant is associated with resistance to therapy, which is a key aspect of predictive evidence.

Oncogenic: The mention of T790M in relation to EGFR-TKI resistance suggests that this somatic variant contributes to tumor progression and development, aligning with the definition of oncogenic evidence.

Oncogenic evidence:

Oncogenic: The variant EGFR G724S is described as an acquired mutation in patients who developed resistance to osimertinib, indicating its role in tumor progression and resistance mechanisms. This suggests that G724S contributes to the oncogenic process in the context of EGFR-mutant lung cancers.

Predictive, Oncogenic evidence:

Oncogenic: The TP53 Y220C missense mutation is described as a "deleterious somatic mutation," indicating its role in tumor development or progression, which aligns with the definition of oncogenic evidence.

Predictive: The study discusses the response of a patient with the TP53 Y220C mutation to the M6620-carboplatin combination therapy, suggesting that this variant may correlate with treatment response, which fits the predictive evidence type.

Diagnostic, Prognostic evidence:

Diagnostic: The study assesses the association between GNA14 expression levels and clinicopathological features, indicating its potential use as a biomarker for diagnosis in hepatocellular carcinoma (HCC).

Prognostic: The study identifies low expression of GNA14 as an independent predictor for survival outcomes in patients with HCC, suggesting its role in prognostic assessment.

Prognostic evidence:

Prognostic: The study indicates that miR-28-5p serves as an independent indicator for overall survival in patients with colon cancer, suggesting a correlation between the variant and disease outcome.

Prognostic evidence:

Prognostic: The study indicates that high HOTTIP expression is associated with worse outcomes in cancer patients, specifically noting a pooled hazard ratio of 2.34 for overall survival, which demonstrates a correlation with disease outcome independent of therapy. Additionally, the findings suggest that elevated HOTTIP expression correlates with advanced clinical stage and lymph node metastasis, further supporting its role as a prognostic marker.

Oncogenic evidence:

Oncogenic: The study discusses how alterations in the SPOP gene significantly co-occur with alterations in the BIN1 gene and how somatic mutations in SPOP derange BIN1 gene expression, indicating that SPOP contributes to tumor development or progression in prostate cancer. Additionally, the increased expression of SPOP is associated with reduced survival, further supporting its role in oncogenesis.

Predictive, Prognostic evidence:

Prognostic: The study reports that various mutations, including RNF43-MT, CREBBP-MT, and others, are associated with longer overall survival (OS) in colorectal cancer patients treated with immune checkpoint inhibitors, indicating a correlation between these variants and disease outcome independent of therapy. The abstract specifically mentions hazard ratios (HR) and confidence intervals (CI) that support this association with survival.

Predictive: The abstract discusses the predictive value of specific gene mutations on the overall survival of colorectal cancer patients treated with immune checkpoint inhibitors, indicating that certain mutations may correlate with treatment response. The mention of "predictive biomarkers" and their influence on survival outcomes in the context of therapy supports this classification.

Prognostic evidence:

Prognostic: The abstract indicates that the gene expression and methylation of SERPINA5 and TIMP1 may serve as prognostic predictors in low-grade gliomas (LGGs), suggesting a correlation with disease outcome independent of therapy.

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Predictive, Oncogenic evidence:

Predictive: The study indicates that the F691L mutation confers moderate resistance to gilteritinib, suggesting a correlation between this variant and treatment response. The mention of "resistance" in relation to gilteritinib treatment highlights its predictive nature regarding therapy outcomes.

Oncogenic: The identification of the F691L mutation as a secondary mutation that contributes to resistance implies its role in tumor progression or development, particularly in the context of FLT3 mutations in acute myeloid leukemia. This supports the classification of F691L as an oncogenic variant due to its involvement in resistance mechanisms.

Predictive evidence:

Predictive: The study identifies PPP2R2A deficiency as a potential new predictive biomarker for patient stratification in the clinical use of ATR and CHK1 inhibitors, indicating that this variant correlates with sensitivity to these therapies. The findings suggest that the presence of PPP2R2A deficiency can influence treatment outcomes with ATR and CHK1 inhibitors in non-small cell lung cancer.

Prognostic evidence:

Prognostic: The study reports that patients with a high mutant/wild-type (wt) ratio of FLT3-ITD mutations had significantly shorter overall and disease-free survival, indicating that this variant correlates with disease outcome independent of therapy. The multivariate analysis further supports the high mutant/wt ratio as a strong independent prognostic factor.

Prognostic evidence:

Prognostic: The abstract indicates that TGFbeta2 expression is significantly correlated with patient outcome in multiple types of cancer, particularly gastric cancer, suggesting its role as a prognostic biomarker. This correlation with outcome, independent of therapy context, supports the classification as prognostic evidence.

Prognostic evidence:

Prognostic: The study reports a significant correlation between high EID3 expression and poor overall survival (OS) in glioblastoma multiforme (GBM) patients, indicating that EID3 expression can serve as an independent factor for predicting prognosis. The multivariate Cox regression analysis further supports this association with a specific hazard ratio (HR = 1.41), emphasizing its relevance to disease outcome.

Predictive, Oncogenic evidence:

Predictive: The study indicates that the D816 V mutant c-kit does not respond to STI571, suggesting that this variant correlates with resistance to this specific therapy. The mention of STI571's ineffectiveness against the D816 V variant highlights its predictive nature regarding treatment response.

Oncogenic: The D816 V mutation is implicated in systemic mastocytosis, indicating that it contributes to tumor development or progression. The context of the variant being associated with a disease characterized by abnormal mast cell accumulation supports its classification as oncogenic.

Predictive, Diagnostic evidence:

Predictive: The study suggests that NRG1 and ERBB3 expression may serve as biomarkers for response to SINE treatment, indicating a correlation between these variants and sensitivity to therapy. The mention of the antitumor effect of SINE being influenced by NRG1 and ERBB3 highlights their potential role in predicting treatment outcomes.

Diagnostic: The findings indicate that NRG1 and ERBB3 expression levels can classify ovarian cancer cell lines based on their response to SINE treatment, suggesting their use as biomarkers for identifying SINE-resistant cancers. This classification aligns with the diagnostic evidence type as it relates to defining a subtype of cancer based on variant expression.

Predictive, Prognostic, Oncogenic evidence:

Prognostic: The study indicates that EPS8L3 is associated with poor prognosis in liver cancer, as evidenced by the statement that high expression of EPS8L3 yields poor prognosis in Chinese liver cancer patients.

Oncogenic: The results suggest that EPS8L3 has pivotal oncogenic functions in liver cancer, as it is shown to contribute to cell proliferation and migration, and its knockdown inhibits these processes, indicating its role in tumor development.

Predictive: The findings demonstrate that EPS8L3 expression can substantially increase the efficacy of low dosage Sorafenib treatment, suggesting a correlation between EPS8L3 levels and response to this specific therapy.

Prognostic, Oncogenic evidence:

Oncogenic: The study indicates that CDCA2 acts as an oncogene, as it is overexpressed in prostate cancer and its silencing represses tumor growth, suggesting its role in tumor development and progression.

Prognostic: The abstract mentions that CDCA2 correlates with poor prognosis and patient survival, indicating its potential as a prognostic biomarker in multiple cancer types.

Prognostic evidence:

Prognostic: The study indicates that HHLA2 levels were positively correlated with survival rates in kidney clear cell carcinoma (KIRC), suggesting that it may serve as a prognostic marker for patient outcomes independent of therapy. The mention of "predicts a favorable survival outcome" further supports this classification.

Predictive, Oncogenic evidence:

Oncogenic: The study indicates that Rab18 functions as an oncoprotein in human head and neck squamous cell carcinoma (HNSCC), suggesting that it contributes to tumor development and progression. The mention of Rab18's role in regulating cell proliferation and invasion further supports its oncogenic potential.

Predictive: The abstract states that Rab18 influences cisplatin sensitivity in HNSCC, indicating a correlation between the variant and response to a specific therapy. This suggests that Rab18 may play a role in determining how well patients respond to cisplatin treatment.

Predictive evidence:

Predictive: The abstract indicates that RBM17 is a potential therapeutic target for HCC treatment, suggesting a correlation between the variant and response to therapy. This implies that the variant may influence treatment outcomes, fitting the predictive evidence type.

Prognostic evidence:

Prognostic: The study indicates that PALB2 deletion is significantly associated with shorter disease-free survival (DFS) and overall survival (OS) in colorectal cancer (CRC) patients, suggesting that it serves as an independent prognostic factor for poor outcomes. The multivariate analysis further supports this by confirming that both PALB2 deletion and low mRNA expression are independent prognostic factors of poor OS.

Prognostic evidence:

Prognostic: The abstract mentions a "significant association of higher expression of the COL6A3 E5-E6 junction... with better overall survival," indicating that this variant correlates with disease outcome independent of therapy.

Diagnostic, Predisposing evidence:

Predisposing: The abstract describes Wiedemann-Steiner Syndrome (WSS) as an autosomal dominant disorder, indicating that the KMT2A mutations are inherited and confer a risk for developing this syndrome. The mention of "de novo KMT2A missense mutation" suggests a genetic predisposition to the disorder.

Diagnostic: The identification of heterozygous KMT2A mutations as the molecular defect underlying WSS indicates that these mutations are used to define and classify the disorder, supporting their role as a diagnostic marker for the syndrome.

Predictive, Prognostic evidence:

Prognostic: The study reports that patients with MPC1 deletion tumors have worse overall survival compared to those with MPC1 intact tumors, indicating a correlation between the variant and disease outcome independent of therapy.

Predictive: The results indicate that MPC1 deletion is associated with a poor response to temozolomide (TMZ) chemotherapy in glioblastoma patients, suggesting that the variant may influence treatment sensitivity.

nan evidence:

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Predictive, Oncogenic evidence:

Predictive: The study discusses the treatment of patients with tumors harboring FGFR aberrations with the FGFR inhibitor AZD4547, indicating a correlation between the presence of these variants and the response to therapy, as evidenced by the reported response rates and progression-free survival metrics.

Oncogenic: The abstract mentions that different FGFR somatic alterations may confer varying levels of signaling potency and oncogene dependence, suggesting that these variants contribute to tumor development or progression.

Predictive, Oncogenic evidence:

Predictive: The study discusses the treatment of patients with tumors harboring FGFR aberrations with the FGFR inhibitor AZD4547, indicating a correlation between the presence of these variants and the response to therapy, as evidenced by the reported response rates and progression-free survival metrics.

Oncogenic: The abstract mentions that different FGFR somatic alterations may confer varying levels of signaling potency and oncogene dependence, suggesting that these variants contribute to tumor development or progression.

Predictive, Oncogenic evidence:

Predictive: The study discusses how the loss of the RB tumor suppressor correlates with increased drug sensitivity to specific therapies, particularly CHK inhibitors, indicating a potential for targeted treatment in RB-deficient triple-negative breast cancers (TNBCs). The mention of "therapeutic effects were robust and selective for RB loss of function" further supports this classification.

Oncogenic: The abstract indicates that approximately 30% of TNBCs exhibit functional loss of the RB tumor suppressor, suggesting that this loss contributes to tumor development and progression, particularly through the mechanisms of checkpoint functions and increased sensitivity to therapies. The context of RB loss being a target for precision intervention implies its role in oncogenesis.

Predisposing, Functional evidence:

Predisposing: The study discusses germline variants of WWP1, including K740N, which are associated with a hereditary predisposition to multiple types of cancer, indicating that these variants confer inherited risk for developing disease.

Functional: The results indicate that the prioritized WWP1 variants, including K740N, resulted in gain-of-function effects that led to aberrant enzymatic activation and consequent PTEN inactivation, demonstrating an alteration in molecular function.

Predictive, Oncogenic evidence:

Predictive: The study discusses how KRAS mutations, specifically G12D and G12V, correlate with increased sensitivity to metformin treatment in colorectal cancer (CRC) cell lines, indicating that these variants may predict a better therapeutic response to this drug.

Oncogenic: The presence of KRAS mutations (G12D and G12V) is implicated in enhancing the tumor cells' sensitivity to metformin, suggesting that these somatic variants contribute to tumor development or progression by altering the response to therapy.

Oncogenic evidence:

Oncogenic: The abstract discusses how the E542K mutation, along with other PI3-kinase mutations, induces oncogenic transformation in chicken embryo fibroblasts, demonstrating its role in tumor development. The evidence of elevated catalytic activity and constitutive phosphorylation of key signaling proteins further supports its oncogenic potential.

Predictive, Diagnostic, Oncogenic, Functional evidence:

Predictive: The study provides evidence that somatic mutations in the EGFR gene's TK domain are associated with sensitivity to gefitinib and erlotinib, as indicated by the significant differences in mutation presence between gefitinib-sensitive and refractory tumors. This correlation suggests that the presence of these mutations can predict the response to these specific therapies.

Diagnostic: The abstract mentions that most mutation-positive tumors were adenocarcinomas from never smokers, indicating that these mutations can be used to classify a specific subtype of lung cancer. This association supports the use of EGFR mutations as a diagnostic marker for identifying a distinct subset of lung cancers.

Oncogenic: The presence of somatic mutations in the EGFR TK domain is implicated in the development of lung cancer, as the study discusses the mutations found in tumors and their association with sensitivity to targeted therapies. This suggests that these mutations contribute to tumor development or progression in the context of lung cancer.

Functional: The study describes how specific mutations in the EGFR TK domain alter the molecular function of the protein, as evidenced by the differences in phosphotyrosine levels and drug sensitivity in the mutant forms compared to the wild-type. This indicates that the mutations have a direct impact on the biochemical activity of the EGFR protein.

Oncogenic, Functional evidence:

Oncogenic: The study demonstrates that PHGDH knockdown significantly inhibited cell viability, colony formation, and tumor growth in thyroid cancer cell lines and in vivo models, indicating that PHGDH contributes to tumor development and progression in papillary thyroid cancer.

Functional: The results show that PHGDH inhibition affects the expression of embryonic cancer stemness markers and alters cell viability and colony formation, suggesting that the variant alters molecular function related to tumorigenesis in thyroid cancer.

Diagnostic, Functional evidence:

Diagnostic: The abstract mentions that mutated ACVR2A is significantly associated with MSI-H in gastric cancer (GC), indicating its potential use as a biomarker for classification or diagnosis of this subtype.

Functional: The results section describes the generation of stable cell lines overexpressing ACVR2A and its mutants, which implies that the variants, including c.1310delA, are being studied for their molecular function and effects on protein expression.

Predictive, Oncogenic evidence:

Predictive: The study investigates how mutations in the AXL receptor, specifically tyrosine 821, contribute to resistance against cetuximab and radiation treatment in head and neck squamous cell carcinoma (HNSCC). The findings suggest that targeting AXL and c-ABL can overcome this resistance, indicating a correlation between the variant and treatment response.

Oncogenic: The research highlights that the signaling of AXL, particularly through the mutation of tyrosine 821, plays a role in the development of resistance in HNSCC, suggesting that this variant contributes to tumor progression and behavior in the context of cancer treatment.

Prognostic, Oncogenic evidence:

Prognostic: The study reports that high mRNA levels of HOXA2, HOXA3, and HOXA13, as well as low levels of HOXA7, predict poor overall survival (OS) of KIRC patients, indicating a correlation between these variants and disease outcome independent of therapy.

Oncogenic: The findings suggest that HOXA13 functions as a novel oncogene in KIRC, as the knockdown of HOXA13 significantly suppressed cell proliferation in vitro, demonstrating its role in tumor development or progression.

Predictive evidence:

Predictive: The study discusses the administration of gemtuzumab ozogamycin (mylotarg) in patients with untreated acute promyelocytic leukemia (APL) and reports a complete remission (CR) rate of 84%, indicating that the variant correlates with response to this specific therapy. The mention of treatment response and the effectiveness of mylotarg in achieving CR supports this classification.

Predictive, Oncogenic evidence:

Predictive: The study discusses how patients with KRAS G12C-mutant non-small cell lung cancer (NSCLC) experience clinical benefit from selective KRAS G12C inhibition, indicating a correlation between the variant and response to therapy. Additionally, it highlights the resistance mechanisms in colorectal cancer, suggesting that the variant's presence influences treatment outcomes.

Oncogenic: The variant KRAS G12C is implicated in tumor development, as the study examines its role in colorectal cancer cell lines and discusses the effects of KRAS G12C inhibition, which is indicative of its contribution to cancer progression. The findings suggest that KRAS G12C is a driver mutation in these cancer types.

Prognostic evidence:

Prognostic: The abstract states that "STAT1 has been identified to have prognostic value in patients with solid cancer," indicating that the variant correlates with disease outcome independent of therapy. Additionally, the mention of "predict prognosis in cancer patients based on their tumor types" further supports its prognostic significance.

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.

nan evidence:

Missing abstract

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.

nan evidence:

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.