nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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
nan evidence:
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nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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
nan evidence:
Missing abstract
nan
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.
nan
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
nan evidence:
Missing abstract
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
nan evidence:
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nan
nan evidence:
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nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
nan evidence:
Missing abstract
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
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).
nan
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.
nan
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.
nan
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.
nan
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.
nan
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.
nan
Oncogenic, Functional evidence:
Oncogenic: The study demonstrates that IL-33 significantly increases glioma cell invasion and migration, indicating its role in tumor progression. This suggests that IL-33 contributes to the development or progression of glioma, aligning with the definition of an oncogenic variant.
Functional: The findings show that IL-33 alters molecular functions by upregulating matrix metalloproteinases (MMP2 and MMP9) and increasing the phosphorylation of NF-kappaB, which are indicative of changes in biochemical activity related to glioma cell behavior. This supports the classification of IL-33 as having functional evidence.
nan
Prognostic evidence:
Prognostic: The study indicates that elevated IL-33 mRNA levels are associated with inferior survival in glioblastoma patients, suggesting that IL-33 may correlate with disease outcome independent of therapy. This aligns with the definition of prognostic evidence, as it discusses survival outcomes related to the variant.
nan
Diagnostic, Prognostic evidence:
Diagnostic: The study indicates that IL-33 has diagnostic value in gliomas, as it is associated with the clinicopathological features of the disease and can be used as a biomarker for detection.
Prognostic: The results show that high IL-33 expression correlates with shorter progression-free survival and overall survival in glioma patients, indicating its role as an independent factor of poor prognosis.
nan
Predictive, Oncogenic evidence:
Oncogenic: The study discusses the role of beta-catenin signaling in gastric cancer, indicating that dysregulation of this pathway contributes to tumor development and progression, particularly through its interaction with CCL28 and Treg cells.
Predictive: The findings suggest that inhibition of beta-catenin/TCF activity leads to reduced CCL28 expression and Treg cell infiltration, which correlates with tumor progression, indicating that targeting this pathway may influence treatment response in gastric cancer.
nan
Predictive, Diagnostic evidence:
Predictive: The study discusses the correlation between BRD levels, particularly BRD4, and sensitivity to BET degraders like ZBC260, indicating that these levels can predict the response to therapy. The mention of "correlated positively with high sensitivity to BET degraders" supports the classification as predictive evidence regarding treatment response.
Diagnostic: The study identifies molecular markers, specifically BRD levels, that determine cell sensitivity to BET degraders, suggesting that these markers can be used to classify or define a subtype of lung cancer that may respond to specific therapies. This aligns with the diagnostic evidence type as it relates to the identification of disease characteristics.
nan
Predictive, Oncogenic evidence:
Predictive: The abstract discusses how comprehensive genomic profiling can identify genomic alterations that direct treatment targeted therapy, indicating a correlation between the BRAF V600E variant and response to specific therapies. Additionally, the results mention that treatment with dabrafenib in BRAF V600E mutated melanoma can significantly improve overall survival, highlighting the predictive nature of this variant in treatment response.
Oncogenic: The mention of BRAF V600E in the context of metastatic melanoma suggests that this somatic variant contributes to tumor development or progression, as it is associated with a specific cancer type and treatment response. The reference to trials for BRAF V600E further supports its role in oncogenesis.
nan
Diagnostic, Prognostic evidence:
Diagnostic: The study indicates that the expression profile of miRNAs can differentiate between astrocytoma tumors and normal brain tissues, suggesting their potential use as diagnostic markers in defining the signature of astrocytomas.
Prognostic: The results show that low expression of specific miRNAs (hsa-miR-181b and hsa-miR-106a) and high expression of another (hsa-miR-21) are significantly associated with poor patient survival, indicating that these miRNAs can serve as prognostic markers independent of other clinicopathological factors.
nan
Predictive, Oncogenic, Functional evidence:
Oncogenic: The abstract states that Acvr1G328V cooperates with other mutations to induce diffuse gliomas in mice, indicating that this variant contributes to tumor development. This aligns with the definition of an oncogenic variant, as it demonstrates a role in the progression of cancer.
Functional: The abstract mentions that Acvr1G328V upregulates transcription factors to block oligodendroglial cell differentiation, suggesting that this variant alters molecular function. This indicates a change in biochemical activity related to cell differentiation processes.
Predictive: The abstract notes that E6201, a covalent MEK1/2 inhibitor, can inhibit ACVR1 and reduce the growth of ACVR1 mutant glioma xenografts, implying that the presence of the G328V variant may correlate with response to this specific therapy. This suggests a predictive relationship between the variant and treatment response.
nan
Predictive, Diagnostic evidence:
Predictive: The study evaluates the response of mismatch repair-deficient (dMMR) rectal cancer to neoadjuvant chemotherapy, indicating that the variant correlates with resistance to this specific therapy, as evidenced by the progression of disease in 29% of patients receiving chemotherapy.
Diagnostic: The identification of dMMR rectal tumors through IHC and microsatellite instability analysis suggests that the variant is used to classify and confirm the presence of a specific subtype of rectal cancer, particularly in relation to Lynch syndrome.
nan
Predictive, Diagnostic evidence:
Predictive: The study discusses how ATM loss in prostate cancer models does not significantly increase sensitivity to PARP inhibitors but does sensitize tumors to ATR inhibitors, indicating a correlation between the variant and response to specific therapies. This suggests that patients with ATM alterations may benefit more from ATR inhibitor therapy than from PARP inhibitors.
Diagnostic: The abstract mentions that ATM alterations are present in approximately 5% of advanced prostate tumors, indicating its association with a specific subtype of cancer, which supports its use as a biomarker for identifying patients with these alterations.
nan
Diagnostic, Prognostic evidence:
Diagnostic: The abstract states that "SPATS2 expression could be a novel diagnostic biomarker in liver cancer," indicating that the variant is used to classify or define a disease.
Prognostic: The abstract also mentions that SPATS2 expression could serve as a prognostic biomarker, suggesting a correlation with disease outcome independent of therapy.
nan
Prognostic evidence:
Prognostic: The abstract indicates that TUBA1C may serve as a potential prognostic marker for PDAC therapy, suggesting a correlation with disease outcome independent of therapy.
nan
Predisposing, Functional evidence:
Predisposing: The study discusses "germline CHEK2 missense alleles detected in familial breast cancer patients," indicating that these variants are inherited and confer a predisposition to cancer.
Functional: The development of a yeast-based assay to assess "in vivo CHEK2-mediated response to DNA damage" demonstrates that the study evaluates how these variants alter the molecular function of the CHEK2 protein in response to DNA damage.
nan
Predisposing, Functional evidence:
Predisposing: The study discusses germline mutations in CHEK2 as a multiple cancer-predisposing gene that increases breast cancer risk, indicating that these variants confer inherited risk for developing the disease.
Functional: The research developed a complementation assay to quantify CHK2-specific phosphorylation of endogenous protein KAP1, demonstrating that certain variants alter molecular function, specifically in relation to their deleterious effects on protein activity.
nan
Predictive evidence:
Predictive: The study discusses how increased iNOS/NO signaling in tumor cells, influenced by CAFs after radiotherapy, affects the effectiveness of radiotherapy in treating PDAC tumors. This indicates a correlation between the variant's activity and the response to therapy, suggesting that targeting iNOS/NO signaling may improve treatment outcomes.
nan
Predictive, Diagnostic evidence:
Predictive: The study discusses how patients with acquired MET alterations may derive clinical benefit from therapies that target both ALK and MET, indicating a correlation between the presence of these alterations and response to treatment. This suggests that MET amplification is associated with resistance to ALK inhibitors and that targeting MET can improve treatment outcomes.
Diagnostic: The abstract mentions that MET amplification was detected in 15% of tumor biopsies from patients relapsing on next-generation ALK inhibitors, which indicates that MET alterations can be used to classify or confirm a specific subtype of resistance in ALK-positive lung cancer. This association highlights the role of MET amplification as a biomarker for identifying patients who may experience ALK-independent resistance.
nan
Prognostic evidence:
Prognostic: The study indicates that alterations to the p53 tumor suppressor gene are associated with more aggressive disease in breast cancer, evidenced by shortened survival of patients with mutations. Specifically, mutations within exon 4 and those causing denaturation of the protein structure were linked to poor prognosis, highlighting their impact on overall patient survival.
nan
Prognostic, Functional evidence:
Prognostic: The abstract states that mutations at the Arg248 position are significantly associated with shorter patient survival, indicating a correlation between this variant and disease outcome.
Functional: The abstract mentions that ectopic expression of the p53 mutant R282W significantly upregulated CYP3A4 mRNA and protein levels, demonstrating that this variant alters molecular function related to drug metabolism.
nan
Predictive, Prognostic evidence:
Prognostic: The study reports that TP53 mutations are associated with shorter survival and a shorter time to relapse, indicating that these mutations correlate with disease outcomes independent of therapy. This is supported by the statistical significance (P<0.001) mentioned in the results.
Predictive: The abstract discusses how the presence of RAS pathway mutations and JAK2 mutations correlates with shorter survival and higher risks of relapse and death without relapse, suggesting that these mutations may predict clinical outcomes after allogeneic hematopoietic stem-cell transplantation. The specific mention of these associations with transplantation outcomes supports this classification.
nan
Diagnostic, Prognostic evidence:
Diagnostic: The study assesses the frequency of TP53 alterations in acute myeloid leukemia with complex karyotype (CK-AML) and correlates these alterations with other genetic changes, indicating that TP53 mutations are used to classify and define the disease.
Prognostic: The results indicate that patients with TP53 alterations had significantly lower complete remission rates and inferior overall survival, demonstrating that these alterations correlate with disease outcome independent of therapy.
nan
Prognostic evidence:
Prognostic: The study discusses the SNP rs2305089 in relation to local recurrence and overall survival in spinal column chordoma, indicating that this variant correlates with disease outcomes independent of therapy.
nan
Predictive, Prognostic evidence:
Prognostic: The study reports that TP53 mutation is strongly associated with a poor prognosis for overall survival in patients with glioblastoma, indicating that the presence of this variant correlates with disease outcome independent of therapy.
Predictive: The findings suggest that mutant TP53 decreases the chemosensitivity of glioblastoma to temozolomide, indicating a correlation between the variant and resistance to this specific therapy.
nan
Prognostic, Oncogenic evidence:
Oncogenic: The study indicates that mutations in the ARID2 gene are commonly found in hepatocellular carcinoma (HCC) and that ARID2 plays a significant role in cancer development, particularly in relation to metastasis. The evidence of ARID2 knockout promoting pulmonary metastasis in HCC mouse models supports the notion that ARID2 mutations contribute to tumor progression.
Prognostic: The abstract mentions a positive association between ARID2 expression and survival of HCC patients, indicating that lower levels of ARID2 correlate with poorer outcomes. This suggests that ARID2 may serve as a prognostic marker for HCC, as its expression levels are linked to disease progression and patient survival.
nan
Prognostic evidence:
Prognostic: The abstract states that YAP1 is an important prognostic biomarker for pancreatic cancer, indicating a correlation with disease outcome independent of therapy. This suggests that the presence of the variant may be associated with survival or progression in patients with pancreatic cancer.
nan
Predictive, Diagnostic, Prognostic evidence:
Predictive: The study indicates that high APOBEC3B expression is associated with improved progression-free survival and sensitivity to cisplatin and carboplatin, suggesting that it may serve as a predictive biomarker for therapeutic response to platinum-based chemotherapy.
Prognostic: The results show that high APOBEC3B expression correlates with improved progression-free survival and moderately with overall survival, indicating its potential role as a prognostic factor independent of therapy.
Diagnostic: The study identifies APOBEC3B as a candidate biomarker for detection and intervention in clear cell ovarian carcinoma, suggesting its use in classifying or confirming the disease.
nan
Predictive, Prognostic evidence:
Prognostic: The abstract states that "IL-6 was significantly associated with poor prognosis in patients with esophageal cancer," indicating that the variant correlates with disease outcome independent of therapy.
Predictive: The mention of "treatment resistance" in the context of targeting IL-6 suggests that this variant may correlate with resistance to specific therapies, indicating its predictive value for treatment response.
nan
Predictive, Prognostic evidence:
Predictive: The study found that preoperative plasma levels of IL-6 and IL-6sR were independent predictors of lymphovascular invasion, metastases to lymph nodes, disease recurrence, and disease-specific survival, indicating their potential role in predicting treatment outcomes.
Prognostic: The results indicated that high levels of IL-6 and IL-6sR predicted disease-specific survival, demonstrating their correlation with disease outcomes independent of therapy.
nan
Prognostic evidence:
Prognostic: The study identifies high levels of serum IL-6 as an independent adverse prognostic variable for overall survival in patients with hormone-refractory metastatic breast cancer, indicating a correlation between IL-6 levels and poor survival outcomes.
nan
Prognostic, Oncogenic evidence:
Prognostic: The study indicates that low BAP1 mRNA levels are associated with overall survival (OS) in cutaneous melanoma (CM) patients, with specific hazard ratios provided (HR = 0.73), suggesting a correlation between the variant and disease outcome independent of therapy.
Oncogenic: The presence of BAP1 point mutations, including E30K and P30, is discussed in the context of their unknown significance in tumors, indicating that these somatic variants may contribute to tumor development or progression, although they were not associated with overall survival in CM.
nan
Predictive, Prognostic evidence:
Prognostic: The abstract states that "all three genes were associated with a poor prognosis in human patients," indicating that the variants correlate with disease outcome independent of therapy. This suggests that the presence of these proteins is linked to survival rates in patients with pancreatic ductal adenocarcinoma (PDAC).
Predictive: The abstract mentions that "precise interventions targeting cancer cell-derived matrisome proteins, such as AGRN, SERPINB5, and CSTB, may represent preferred potential therapeutic targets," which implies that these variants could influence treatment response or resistance, thus providing predictive evidence regarding their role in therapy.
nan
nan evidence:
Missing abstract
nan
Prognostic evidence:
Prognostic: The study reports that glioma patients with higher expression of KIF3C had longer survival time, indicating a correlation between KIF3C expression and disease outcome independent of therapy. This is further supported by subgroup analysis showing that higher KIF3C expression predicted longer survival time in the low-grade glioma group.
nan
Predictive, Oncogenic evidence:
Predictive: The study discusses how ATRX mutations lead to increased sensitivity to the WEE1 inhibitor AZD1775, indicating a correlation between the ATRX variant and response to this specific therapy. This suggests that targeting WEE1 could be a therapeutic strategy for ATRX-deficient cancers, highlighting the predictive nature of the variant in relation to treatment response.
Oncogenic: The abstract mentions that ATRX is frequently mutated in tumors, including gliomas and liver cancers, and that these mutations contribute to tumor growth and survival, which aligns with the definition of oncogenic variants that drive tumor development or progression. The identification of ATRX mutations as a target for therapeutic intervention further supports its role in oncogenesis.
nan
Predictive, Prognostic, Oncogenic evidence:
Prognostic: The abstract states that "Low levels of ARID1A were associated with a poor prognosis," indicating that the variant correlates with disease outcome independent of therapy.
Oncogenic: The abstract mentions that "Depletion of ARID1A activated an oncogenic transcriptome that drove SCC progression," suggesting that the variant contributes to tumor development or progression.
Predictive: The abstract discusses the potential of parthenolide as a treatment for patients with low ARID1A expression, indicating that the variant's status may correlate with response to this specific therapy.
nan
Predictive, Oncogenic evidence:
Predictive: The study discusses the use of KRASG12C inhibitors and their effects on signaling and viability, indicating a correlation with treatment response and resistance mechanisms. The mention of "adaptive feedback" and "enhance efficacy" suggests that the variant's presence influences the effectiveness of specific therapies targeting KRASG12C.
Oncogenic: The abstract describes KRAS as the most commonly mutated oncogene and discusses the KRASG12C mutation in the context of tumor development and progression, indicating that this somatic variant contributes to cancer biology. The focus on the KRASG12C mutation and its role in signaling pathways further supports its classification as oncogenic.
nan
Oncogenic, Functional evidence:
Oncogenic: The study describes a partial duplication of the switch 2 domain of K-Ras in a patient with juvenile myelomonocytic leukaemia, indicating that this somatic variant contributes to tumor development or progression, as it is associated with a myeloproliferative neoplasm characterized by driver Ras pathway mutations.
Functional: The variant is shown to result in a protein with altered electrophoretic mobility, suggesting that the duplication affects the molecular function of K-Ras, specifically its conformation and possibly its interaction with other proteins, as indicated by the immunoblot analysis.
nan
Predictive, Prognostic, Oncogenic evidence:
Prognostic: The study indicates that KRAS mutation is significantly associated with worse overall survival (OS) and disease-free survival (DFS) in early stage resected NSCLC, suggesting that the presence of this mutation correlates with poorer disease outcomes.
Predictive: The findings also show that KRAS mutation is associated with inferior outcomes of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) treatment and chemotherapy, indicating that this variant may predict resistance to these therapies.
Oncogenic: The paper discusses KRAS as the most frequently mutated oncogene in NSCLC, which implies that mutations in this gene contribute to tumor development and progression, supporting its classification as an oncogenic variant.
nan
Oncogenic, Functional evidence:
Oncogenic: The study investigates the effect of the C118S mutation on tumorigenesis, demonstrating that KrasC118S alleles impede urethane-induced lung tumorigenesis, indicating that this somatic variant contributes to tumor development.
Functional: The abstract discusses how the thiol residue of cysteine 118 (C118) is crucial for the activation of Ras proteins through redox-dependent reactions, suggesting that the C118S mutation alters the molecular function of Ras, impacting its activation and subsequent signaling pathways.