Aortic dissection typically presents acutely with sudden, severe tearing chest or back pain, often described as lancinating in quality. [5-6] Approximately 50% of patients with thoracic aortic aneurysm may progress to dissection without timely intervention. [5] In contrast, thoracic aortic aneurysm is usually asymptomatic and discovered incidentally during physical examination or imaging for other indications. [5]

[Paper-level Aggregated] PMCID: PMC12221223

Evidence Type(s): Diagnostic

Summary: Mutation: C>T | Summary: The C>T mutation is characterized as a well-established feature defining cutaneous melanoma, indicating its role in classifying the disease.

Gene→Variant (gene-first): NF1(4763):C>T

Genes: NF1(4763)

Variants: C>T

[Paragraph-level] PMCID: PMC12221223 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: C>T | Summary: The C>T mutation is characterized as a well-established feature defining cutaneous melanoma, indicating its role in classifying the disease. Evidence Type: Oncogenic | Mutation: C>T | Summary: The C>T mutation contributes to tumor development in the context of NF1Mut melanomas, supporting its classification as an oncogenic variant.

Gene→Variant (gene-first): 4763:C>T

Genes: 4763

Variants: C>T

[Paper-level Aggregated] PMCID: PMC10527017

Evidence Type(s): Diagnostic

Summary: Mutation: H1047R | Summary: The H1047R mutation is used to classify tumors into specific subtypes, such as Luminal A and B, based on PAM50 classification, indicating its role in defining disease characteristics.

Gene→Variant (gene-first): PIK3CA(5290):H1047R

Genes: PIK3CA(5290)

Variants: H1047R

[Paragraph-level] PMCID: PMC10527017 Section: RESULTS PassageIndex: 25

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: H1047R | Summary: The H1047R mutation in PIK3CA is associated with tumor development and progression, as indicated by its presence in samples from patients with specific cancer subtypes. Evidence Type: Diagnostic | Mutation: H1047R | Summary: The H1047R mutation is used to classify tumors into specific subtypes, such as Luminal A and B, based on PAM50 classification, indicating its role in defining disease characteristics.

Gene→Variant (gene-first): 5290:H1047R

Genes: 5290

Variants: H1047R

[Paper-level Aggregated] PMCID: PMC10082285

Evidence Type(s): Diagnostic

Summary: Mutation: L858R | Summary: The presence of the L858R mutation is used to classify and confirm the diagnosis of EGFR-mutated NSCLC, supporting its role as a diagnostic marker.

Evidence Type: Diagnostic

Gene→Variant (gene-first): EGFR(1956):L858R

Genes: EGFR(1956)

Variants: L858R

[Paragraph-level] PMCID: PMC10082285 Section: ABSTRACT PassageIndex: 5

Evidence Type(s): Predictive, Diagnostic

Summary: Evidence Type: Predictive | Mutation: L858R | Summary: The L858R mutation is associated with response to osimertinib therapy in patients with EGFR-mutated NSCLC, indicating its predictive value for treatment sensitivity. Evidence Type: Diagnostic | Mutation: L858R | Summary: The presence of the L858R mutation is used to classify and confirm the diagnosis of EGFR-mutated NSCLC, supporting its role as a diagnostic marker.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paper-level Aggregated] PMCID: PMC10015977

Evidence Type(s): Diagnostic

Summary: Mutation: K700E | Summary: The K700E mutation in SF3B1 is important for diagnostic classification in myelodysplastic syndromes (MDS). It is used to refine sub-classification and risk assessment criteria, helping to define disease characteristics and classify patients based on specific clinico-pathologic features and cytogenetic aberrations. The presence of K700E aids in distinguishing between different subtypes of MDS and correlates with certain clinical features, such as a higher percentage of ring sideroblasts and ANC.

Gene→Variant (gene-first): SF3B1(23451):K700E

Genes: SF3B1(23451)

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 12

Evidence Type(s): Prognostic, Diagnostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with lower comprehensive cytogenetic scoring system (CCSS) scores, indicating a potential correlation with disease outcome in patients. Evidence Type: Diagnostic | Mutation: K700E | Summary: The presence of the K700E mutation helps classify patients into different categories based on their cytogenetic aberrations, distinguishing them from non-K700E MDS patients.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 10

Evidence Type(s): Diagnostic, Prognostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: K700E | Summary: The K700E mutation is associated with specific clinico-pathologic features that help classify and define the subtype of MDS in patients. Evidence Type: Prognostic | Mutation: K700E | Summary: The presence of the K700E mutation correlates with certain clinical features, such as a higher percentage of ring sideroblasts and ANC, which may indicate disease outcome independent of therapy. Evidence Type: Oncogenic | Mutation: K700E | Summary: The K700E mutation contributes to the development and progression of MDS, as indicated by its association with specific clinical features and classifications.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 9

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: K700E | Summary: The comparison between SF3B1 K700E and non-K700E mutated MDS suggests that the K700E variant may be used to classify or define a subtype of myelodysplastic syndromes (MDS).

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: RESULTS PassageIndex: 7

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: K700E | Summary: The K700E mutation is mentioned in the context of defining and classifying subtypes of MDS, indicating its role in diagnostic criteria.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 12

Evidence Type(s): Prognostic, Diagnostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with a favorable prognosis in myelodysplastic syndromes, indicating its relevance in predicting disease outcomes. Evidence Type: Diagnostic | Mutation: K700E | Summary: The K700E mutation is used to refine the sub-classification and risk assessment criteria for myelodysplastic syndromes, highlighting its role in defining disease characteristics.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 10

Evidence Type(s): Prognostic, Diagnostic

Summary: Evidence Type: Prognostic | Mutation: K700E | Summary: The K700E mutation in SF3B1 is associated with significantly better overall survival (OS) in patients with myelodysplastic syndromes (MDS) compared to non-K700E mutations, indicating its prognostic value. Evidence Type: Diagnostic | Mutation: K700E | Summary: The presence of the K700E mutation in SF3B1 is important for risk-assessment in myelodysplastic syndromes (MDS), suggesting its role in classifying the disease.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paragraph-level] PMCID: PMC10015977 Section: ABSTRACT PassageIndex: 4

Evidence Type(s): Diagnostic, Prognostic

Summary: Evidence Type: Diagnostic | Mutation: K700E | Summary: The passage discusses the analysis of clinical-pathologic features and outcomes in MDS patients, indicating that K700E is used to explore differences in disease characteristics, which supports its role in diagnostic classification. Evidence Type: Prognostic | Mutation: K700E | Summary: The mention of outcomes in the context of K700E suggests that this variant may correlate with disease outcomes, supporting its prognostic significance in treatment-naive MDS patients.

Gene→Variant (gene-first): 23451:K700E

Genes: 23451

Variants: K700E

[Paper-level Aggregated] PMCID: PMC10011885

Evidence Type(s): Diagnostic

Summary: Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to classify patients with selected cancers, confirming their mutation-positive status. It is also utilized to define and classify patients based on the presence of mutant ctDNA in plasma, indicating its role in diagnosing the disease.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC10011885 Section: RESULTS PassageIndex: 15

Evidence Type(s): Diagnostic, Prognostic, Predictive

Summary: Evidence Type: Diagnostic | Mutation: V600E | Summary: The BRAF V600E mutation is used to define and classify patients based on the presence of mutant ctDNA in plasma, indicating its role in diagnosing the disease. Evidence Type: Prognostic | Mutation: V600E | Summary: Higher levels of ctDNA for the BRAF V600E mutation at baseline are associated with inferior progression-free survival (PFS) and overall survival (OS), indicating its prognostic significance. Evidence Type: Predictive | Mutation: V600E | Summary: The presence of the BRAF V600E mutation correlates with clinical benefit, as patients with lower ctDNA levels achieved better outcomes, suggesting its predictive value for treatment response.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC10011885 Section: RESULTS PassageIndex: 3

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is associated with tumor development or progression in various cancers, including non-colorectal cancers. Evidence Type: Diagnostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to classify patients with selected cancers, confirming their mutation-positive status.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC9365372

Evidence Type(s): Diagnostic

Summary: Mutation: T790M | Summary: The T790M mutation is used to classify patients as T790M-negative, which is a significant reason for exclusion from treatment in the study.

Gene→Variant (gene-first): EGFR(1956):T790M

Genes: EGFR(1956)

Variants: T790M

[Paragraph-level] PMCID: PMC9365372 Section: RESULTS PassageIndex: 3

Evidence Type(s): Predictive, Diagnostic

Summary: Evidence Type: Predictive | Mutation: T790M | Summary: The T790M mutation is associated with screening failure for treatment, indicating its role in predicting resistance to therapy in NSCLC patients. Evidence Type: Diagnostic | Mutation: T790M | Summary: The T790M mutation is used to classify patients as T790M-negative, which is a significant reason for exclusion from treatment in the study.

Gene→Variant (gene-first): 1956:T790M

Genes: 1956

Variants: T790M

[Paper-level Aggregated] PMCID: PMC9338780

Evidence Type(s): Diagnostic

Summary: Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to define and classify anaplastic thyroid cancer and confirm the diagnosis of advanced thyroid cancer, supporting its role as a diagnostic marker for this disease subtype.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC9338780 Section: RESULTS PassageIndex: 2

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is confirmed in a significant portion of patients with advanced thyroid cancer, indicating its role in tumor development or progression. Evidence Type: Diagnostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to confirm the diagnosis of advanced thyroid cancer in the patient cohort.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC9338780 Section: ABSTRACT PassageIndex: 2

Evidence Type(s): Predictive, Diagnostic, Oncogenic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation is associated with response to combined therapy with dabrafenib and trametinib in anaplastic thyroid cancer, indicating its predictive value for treatment efficacy. Evidence Type: Diagnostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to define and classify anaplastic thyroid cancer, supporting its role as a diagnostic marker for this disease subtype. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation contributes to tumor development and progression in anaplastic thyroid cancer, indicating its oncogenic potential.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC8881279

Evidence Type(s): Diagnostic

Summary: Mutation: E401G | Summary: The ERBB2 E401G variant is detected in a patient with cancer of unknown primary (CUP), suggesting its role in defining or classifying the disease.

Gene→Variant (gene-first): FANCC(2176):E401G

Genes: FANCC(2176)

Variants: E401G

[Paragraph-level] PMCID: PMC8881279 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: E401G | Summary: The ERBB2 E401G variant is detected in a patient with cancer of unknown primary (CUP), suggesting its role in defining or classifying the disease.

Gene→Variant (gene-first): 2176:E401G

Genes: 2176

Variants: E401G

[Paper-level Aggregated] PMCID: PMC8700411

Evidence Type(s): Diagnostic

Summary: Mutation: G770 | Summary: The G770 mutation is associated with advanced lung cancers and is used to classify or define a specific subtype of lung cancer related to EGFR Exon 20 insertion mutations.

Gene→Variant (gene-first): EGFR(1956):G770

Genes: EGFR(1956)

Variants: G770

[Paragraph-level] PMCID: PMC8700411 Section: RESULTS PassageIndex: 9

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: G770 | Summary: The passage discusses advanced lung cancers harboring EGFR Exon 20 insertion mutations, indicating that the G770 mutation contributes to tumor development or progression. Evidence Type: Diagnostic | Mutation: G770 | Summary: The mention of advanced lung cancers associated with EGFR Exon 20 insertion mutations suggests that the G770 mutation is used to classify or define a specific subtype of lung cancer.

Gene→Variant (gene-first): 1956:G770

Genes: 1956

Variants: G770

[Paper-level Aggregated] PMCID: PMC8307492

Evidence Type(s): Diagnostic

Summary: Mutation: L858R | Summary: The L858R mutation is used to classify and confirm the presence of a specific EGFR mutation in patients, aiding in the diagnosis of the disease.

Gene→Variant (gene-first): EGFR(1956):L858R

Genes: EGFR(1956)

Variants: L858R

[Paragraph-level] PMCID: PMC8307492 Section: RESULTS PassageIndex: 11

Evidence Type(s): Prognostic, Diagnostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: L858R | Summary: The L858R mutation is associated with treatment and survival data, indicating a correlation with disease outcome independent of therapy. Evidence Type: Diagnostic | Mutation: L858R | Summary: The L858R mutation is used to classify and confirm the presence of a specific EGFR mutation in patients, aiding in the diagnosis of the disease. Evidence Type: Oncogenic | Mutation: L858R | Summary: The L858R mutation is a somatic variant that contributes to tumor development and progression in patients with EGFR mutations.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paper-level Aggregated] PMCID: PMC8033310

Evidence Type(s): Diagnostic

Summary: Mutation: E545K | Summary: The E545K mutation is associated with the diagnosis of invasive cancer in patients with PIK3CA mutations, as indicated by its presence in the cohort studied.

Evidence Type: Diagnostic Mutation: H1047R | Summary: The H1047R mutation is also linked to the diagnosis of invasive cancer in patients with PIK3CA mutations, as observed in the cohort analyzed.

Gene→Variant (gene-first): PIK3CA(5290):E545K PIK3CA(5290):H1047R

Genes: PIK3CA(5290)

Variants: E545K H1047R

[Paragraph-level] PMCID: PMC8033310 Section: RESULTS PassageIndex: 11

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: E545K | Summary: The E545K mutation is associated with the diagnosis of invasive cancer in patients with PIK3CA mutations, as indicated by its presence in the cohort studied. Evidence Type: Diagnostic | Mutation: H1047R | Summary: The H1047R mutation is also linked to the diagnosis of invasive cancer in patients with PIK3CA mutations, as observed in the cohort analyzed.

Gene→Variant (gene-first): 5290:E545K 5290:H1047R

Genes: 5290

Variants: E545K H1047R

[Paper-level Aggregated] PMCID: PMC7612117

Evidence Type(s): Diagnostic

Summary: Mutation: L1363P | Summary: The presence of the KB1(L1363P)P mutation helps define and classify the tumors as carcinosarcomas, distinguishing them from adenocarcinomas based on their histological characteristics.

Gene→Variant (gene-first): TP53BP1(7158):L1363P

Genes: TP53BP1(7158)

Variants: L1363P

[Paragraph-level] PMCID: PMC7612117 Section: RESULTS PassageIndex: 13

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: L1363P | Summary: The KB1(L1363P)P mutation is associated with the development of carcinosarcomas, indicating its contribution to tumor progression and classification as an oncogenic variant. Evidence Type: Diagnostic | Mutation: L1363P | Summary: The presence of the KB1(L1363P)P mutation helps define and classify the tumors as carcinosarcomas, distinguishing them from adenocarcinomas based on their histological characteristics.

Gene→Variant (gene-first): 7158:L1363P 7158:p.L1363P

Genes: 7158

Variants: L1363P p.L1363P

[Paper-level Aggregated] PMCID: PMC7611203

Evidence Type(s): Diagnostic

Summary: Mutation: c.185delAG | Summary: The BRCA1:c.185delAG mutation is mentioned as a pathogenic mutation used to classify patients in the dataset, indicating its role in defining a disease subtype.

Evidence Type: Diagnostic Mutation: c.5946delT | Summary: The BRCA2:c.5946delT mutation is identified as a common founder mutation in multiple patients, supporting its use in disease classification.

Evidence Type: Diagnostic Mutation: c.6174delT | Summary: The BRCA2:c.6174delT mutation is noted as a pathogenic mutation represented by multiple patients, indicating its role in defining a disease subtype.

Gene→Variant (gene-first): BRCA1(672):c.185delAG BRCA2(675):c.5946delT BRCA2(675):c.6174delT

Genes: BRCA1(672) BRCA2(675)

Variants: c.185delAG c.5946delT c.6174delT

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 7

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: c.185delAG | Summary: The BRCA1:c.185delAG mutation is mentioned as a pathogenic mutation used to classify patients in the dataset, indicating its role in defining a disease subtype. Evidence Type: Diagnostic | Mutation: c.5946delT | Summary: The BRCA2:c.5946delT mutation is identified as a common founder mutation in multiple patients, supporting its use in disease classification. Evidence Type: Diagnostic | Mutation: c.6174delT | Summary: The BRCA2:c.6174delT mutation is noted as a pathogenic mutation represented by multiple patients, indicating its role in defining a disease subtype.

Gene→Variant (gene-first): 672:c.185delAG 672:c.5266dupC 675:c.5946delT 675:c.6174delT 672:c.68_69delAG

Genes: 672 675

Variants: c.185delAG c.5266dupC c.5946delT c.6174delT c.68_69delAG

[Paper-level Aggregated] PMCID: PMC7294133

Evidence Type(s): Diagnostic

Summary: Mutation: V871I | Summary: The EPHB4-V871I mutation is identified in neuroblastoma (NB) patients, suggesting its role in defining or classifying the disease.

Gene→Variant (gene-first): EPHB4(2050):V871I

Genes: EPHB4(2050)

Variants: V871I

[Paragraph-level] PMCID: PMC7294133 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: V871I | Summary: The EPHB4-V871I mutation is identified in neuroblastoma (NB) patients, suggesting its role in defining or classifying the disease.

Gene→Variant (gene-first): 2050:V871I

Genes: 2050

Variants: V871I

[Paper-level Aggregated] PMCID: PMC7211323

Evidence Type(s): Diagnostic

Summary: Mutation: 1309-1310delAA | Summary: The mutation 1309-1310delAA is associated with the MSI-H subtype of gastric cancers, indicating its role in classifying the disease.

Evidence Type: Diagnostic Mutation: c.1310delA | Summary: The mutation c.1310delA is linked to the MSI-H subtype of gastric cancers, supporting its use in disease classification.

Evidence Type: Diagnostic Mutation: c.285delA | Summary: The mutation c.285delA is associated with the MSI-H subtype of gastric cancers, indicating its relevance in disease classification.

Gene→Variant (gene-first): ACVR2A(92):1309-1310delAA ACVR2A(92):c.1310delA ACVR2A(92):c.285delA

Genes: ACVR2A(92)

Variants: 1309-1310delAA c.1310delA c.285delA

[Paragraph-level] PMCID: PMC7211323 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: 1309-1310delAA | Summary: The mutation 1309-1310delAA is associated with the MSI-H subtype of gastric cancers, indicating its role in classifying the disease. Evidence Type: Diagnostic | Mutation: c.1310delA | Summary: The mutation c.1310delA is linked to the MSI-H subtype of gastric cancers, supporting its use in disease classification. Evidence Type: Diagnostic | Mutation: c.285delA | Summary: The mutation c.285delA is associated with the MSI-H subtype of gastric cancers, indicating its relevance in disease classification.

Gene→Variant (gene-first): 92:1309-1310delAA 92:c.1310delA 92:c.285delA

Genes: 92

Variants: 1309-1310delAA c.1310delA c.285delA

[Paper-level Aggregated] PMCID: PMC7068240

Evidence Type(s): Diagnostic

Summary: Mutation: V600E | Summary: The BRAF V600E mutation is associated with colorectal cancers (CRCs) and is used to classify and define subtypes of colorectal cancer based on their mutational profiles and MSI status.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 3

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is associated with tumor development or progression in colorectal cancer (CRC) specimens, indicating its role as an oncogenic variant. Evidence Type: Diagnostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to classify and define subtypes of colorectal cancer based on their mutational profiles and MSI status.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: V600E | Summary: The BRAF V600E mutation is associated with colorectal cancers (CRCs), indicating its role in defining or classifying this subtype of cancer. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation contributes to tumor development or progression in colorectal cancers.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC5822176

Evidence Type(s): Diagnostic

Summary: Mutation: K27M | Summary: The K27M mutation is associated with the diagnosis and classification of various grades of astrocytoma, as indicated by the correlation with MIB-1 labeling indices prior to testing.

Gene→Variant (gene-first): IDH1(3417):K27M

Genes: IDH1(3417)

Variants: K27M

[Paragraph-level] PMCID: PMC5822176 Section: RESULTS PassageIndex: 6

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: K27M | Summary: The K27M mutation is associated with the diagnosis and classification of various grades of astrocytoma, as indicated by the correlation with MIB-1 labeling indices prior to testing.

Gene→Variant (gene-first): 3417:K27M

Genes: 3417

Variants: K27M

[Paper-level Aggregated] PMCID: PMC5355930

Evidence Type(s): Diagnostic

Summary: Mutation: H1047R | Summary: The H1047R mutation is used to define patient subgroups based on PIK3CA mutations in the context of treatment analysis.

Evidence Type: Diagnostic Mutation: E545K | Summary: The E545K mutation is used to define patient subgroups based on PIK3CA mutations in the context of treatment analysis.

Evidence Type: Diagnostic Mutation: E542K | Summary: The E542K mutation is used to define patient subgroups based on PIK3CA mutations in the context of treatment analysis.

Gene→Variant (gene-first): PIK3CA(5290):H1047R PIK3CA(5290):E545K PIK3CA(5290):E542K

Genes: PIK3CA(5290)

Variants: H1047R E545K E542K

[Paragraph-level] PMCID: PMC5355930 Section: ABSTRACT PassageIndex: 4

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: H1047R | Summary: The H1047R mutation is used to define patient subgroups based on PIK3CA mutations in the context of treatment analysis. Evidence Type: Diagnostic | Mutation: E545K | Summary: The E545K mutation is used to define patient subgroups based on PIK3CA mutations in the context of treatment analysis. Evidence Type: Diagnostic | Mutation: E542K | Summary: The E542K mutation is used to define patient subgroups based on PIK3CA mutations in the context of treatment analysis.

Gene→Variant (gene-first): 5290:E542K 5290:E545K 5290:H1047R

Genes: 5290

Variants: E542K E545K H1047R

[Paper-level Aggregated] PMCID: PMC5122709

Evidence Type(s): Diagnostic

Summary: Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to confirm the diagnosis of melanoma, serving as a diagnostic marker for the disease.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC5122709 Section: RESULTS PassageIndex: 3

Evidence Type(s): Predictive, Diagnostic, Oncogenic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation is associated with treatment response to BRAF inhibitors, indicating its predictive value for therapy outcomes in melanoma patients. Evidence Type: Diagnostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to confirm the diagnosis of melanoma, serving as a diagnostic marker for the disease. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is known to contribute to tumor development and progression in melanoma, classifying it as an oncogenic variant.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC5111006

Evidence Type(s): Diagnostic

Summary: Mutation: rs757110 | Summary: The variant rs757110 in ABCC8 is associated with diabetes or insulin secretion, indicating its role in defining or classifying a disease.

Evidence Type: Diagnostic Mutation: rs5215 | Summary: The variant rs5215 in KCNJ11 is associated with diabetes or insulin secretion, indicating its role in defining or classifying a disease.

Evidence Type: Diagnostic Mutation: rs5219 | Summary: The variant rs5219 in KCNJ11 is associated with diabetes or insulin secretion, indicating its role in defining or classifying a disease.

Evidence Type: Diagnostic Mutation: rs2468844 | Summary: The variant rs2468844 in SAA2 is associated with carotid intima media thickness, indicating its role in defining or classifying a disease.

Evidence Type: Diagnostic Mutation: rs11703684 | Summary: The variant rs11703684 in PIWIL3 is associated with oligospermia, indicating its role in defining or classifying a disease.

Gene→Variant (gene-first): ABCC8(6833):rs757110 KCNJ11(3767):rs5215 KCNJ11(3767):rs5219 SAA2(6289):rs2468844 PIWIL3(440822):rs11703684

Genes: ABCC8(6833) KCNJ11(3767) SAA2(6289) PIWIL3(440822)

Variants: rs757110 rs5215 rs5219 rs2468844 rs11703684

[Paragraph-level] PMCID: PMC5111006 Section: RESULTS PassageIndex: 18

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: rs757110 | Summary: The variant rs757110 in ABCC8 is associated with diabetes or insulin secretion, indicating its role in defining or classifying a disease. Evidence Type: Diagnostic | Mutation: rs5215 | Summary: The variant rs5215 in KCNJ11 is associated with diabetes or insulin secretion, indicating its role in defining or classifying a disease. Evidence Type: Diagnostic | Mutation: rs5219 | Summary: The variant rs5219 in KCNJ11 is associated with diabetes or insulin secretion, indicating its role in defining or classifying a disease. Evidence Type: Diagnostic | Mutation: rs2468844 | Summary: The variant rs2468844 in SAA2 is associated with carotid intima media thickness, indicating its role in defining or classifying a disease. Evidence Type: Diagnostic | Mutation: rs11703684 | Summary: The variant rs11703684 in PIWIL3 is associated with oligospermia, indicating its role in defining or classifying a disease.

Gene→Variant (gene-first): 440822:rs11703684 6289:rs2468844 3767:rs5215 3767:rs5219 6833:rs757110

Genes: 440822 6289 3767 6833

Variants: rs11703684 rs2468844 rs5215 rs5219 rs757110

[Paper-level Aggregated] PMCID: PMC5019182

Evidence Type(s): Diagnostic

Summary: Mutation: p.Glu542Lys | Summary: The p.Glu542Lys mutation is associated with developmental pediatric disorders, indicating its role in defining or classifying a disease subtype.

Evidence Type: Diagnostic Mutation: p.Glu545Lys | Summary: The p.Glu545Lys mutation is frequently observed in pediatric disorders, supporting its use in defining or classifying a disease subtype.

Evidence Type: Diagnostic Mutation: p.His1047Arg | Summary: The p.His1047Arg mutation is highly recurrent in developmental pediatric disorders, suggesting its role in defining or classifying a disease subtype.

Evidence Type: Diagnostic Mutation: p.Glu726Lys | Summary: The p.Glu726Lys mutation is associated with classic features of MCAP, which helps in defining and classifying the disease.

Gene→Variant (gene-first): PIK3CA(5290):p.Glu542Lys PIK3CA(5290):p.Glu545Lys PIK3CA(5290):p.His1047Arg PIK3CA(5290):p.Glu726Lys

Genes: PIK3CA(5290)

Variants: p.Glu542Lys p.Glu545Lys p.His1047Arg p.Glu726Lys

[Paragraph-level] PMCID: PMC5019182 Section: RESULTS PassageIndex: 14

Evidence Type(s): Diagnostic, Predisposing, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: p.Glu726Lys | Summary: The p.Glu726Lys mutation is associated with classic features of MCAP, which helps in defining and classifying the disease. Evidence Type: Predisposing | Mutation: p.Glu726Lys | Summary: The presence of the p.Glu726Lys mutation in patients indicates a potential inherited risk for developing MCAP and its associated features. Evidence Type: Oncogenic | Mutation: p.Glu726Lys | Summary: The p.Glu726Lys mutation in PIK3CA is implicated in tumor development and progression, contributing to the oncogenic characteristics observed in patients with MCAP.

Gene→Variant (gene-first): 5290:p.Glu726Lys

Genes: 5290

Variants: p.Glu726Lys

[Paragraph-level] PMCID: PMC5019182 Section: RESULTS PassageIndex: 9

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: p.Glu542Lys | Summary: The p.Glu542Lys mutation is associated with developmental pediatric disorders, indicating its role in defining or classifying a disease subtype. Evidence Type: Diagnostic | Mutation: p.Glu545Lys | Summary: The p.Glu545Lys mutation is frequently observed in pediatric disorders, supporting its use in defining or classifying a disease subtype. Evidence Type: Diagnostic | Mutation: p.His1047Arg | Summary: The p.His1047Arg mutation is highly recurrent in developmental pediatric disorders, suggesting its role in defining or classifying a disease subtype.

Gene→Variant (gene-first): 5290:p.Glu542Lys 5290:p.Glu545Lys 5290:p.Glu726Lys 5290:p.Gly914Arg 5290:p.His1047Arg

Genes: 5290

Variants: p.Glu542Lys p.Glu545Lys p.Glu726Lys p.Gly914Arg p.His1047Arg

[Paper-level Aggregated] PMCID: PMC4999563

Evidence Type(s): Diagnostic

Summary: Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to classify and confirm the subtype of tumors in which it is found, indicating its diagnostic relevance.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC4999563 Section: RESULTS PassageIndex: 4

Evidence Type(s): Diagnostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: V600E | Summary: The presence of the BRAF V600E mutation is used to classify and confirm the subtype of tumors in which it is found, indicating its diagnostic relevance. Evidence Type: Oncogenic | Mutation: V600E | Summary: The BRAF V600E mutation is known to contribute to tumor development and progression, supporting its classification as an oncogenic variant.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC4748120

Evidence Type(s): Diagnostic

Summary: Mutation: A66dup | Summary: The presence of the A66dup mutation in K-Ras has diagnostic implications, as it is associated with an atypical myeloproliferative neoplasm in the patient described.

Gene→Variant (gene-first): PIK3R1(5295):A66dup

Genes: PIK3R1(5295)

Variants: A66dup

[Paragraph-level] PMCID: PMC4748120 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Functional, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: A66dup | Summary: The A66dup mutation in K-Ras is associated with tumor development and progression, as it transforms the growth of primary myeloid progenitors and Ba/F3 cells, indicating its oncogenic potential. Evidence Type: Functional | Mutation: A66dup | Summary: The A66dup mutation alters the molecular function of K-Ras by reducing intrinsic GTP hydrolysis rates and impairing PI3 kinase binding, demonstrating its impact on biochemical activity. Evidence Type: Diagnostic | Mutation: A66dup | Summary: The presence of the A66dup mutation in K-Ras has diagnostic implications, as it is associated with an atypical myeloproliferative neoplasm in the patient described.

Gene→Variant (gene-first): 5295:A66dup

Genes: 5295

Variants: A66dup

[Paper-level Aggregated] PMCID: PMC4654747

Evidence Type(s): Diagnostic

Summary: Mutation: K27M | Summary: The K27M mutation is used to classify and define specific tumor subtypes, particularly in H3.1 and H3.3 tumors, and is associated with the proneural-glioblastoma multiforme subtype, indicating its role in disease classification. It can be accurately detected by immunohistochemistry (IHC).

Gene→Variant (gene-first): H3-3B(3021):K27M

Genes: H3-3B(3021)

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 11

Evidence Type(s): Diagnostic, Prognostic, Functional

Summary: Evidence Type: Diagnostic | Mutation: K27M | Summary: The K27M mutation is associated with the proneural-glioblastoma multiforme subtype, indicating its role in classifying and defining this specific disease subtype. Evidence Type: Prognostic | Mutation: K27M | Summary: The presence of the K27M mutation correlates with disease outcome, as indicated by the clinico-radiological follow-up of DIPG patients showing a significant association with metastatic relapse. Evidence Type: Functional | Mutation: K27M | Summary: The K27M mutation is linked to alterations in molecular functions, specifically affecting adhesion properties and deregulating genes related to migration and invasion in tumors.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 9

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation is associated with specific tumor subgroups (H3.1 and H3.3) and is implicated in tumor development, particularly in the context of DIPG and pHGG. Evidence Type: Diagnostic | Mutation: K27M | Summary: The K27M mutation is used to classify and define specific tumor subtypes, particularly in H3.1 and H3.3 tumors, indicating its role in disease classification.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 4

Evidence Type(s): Diagnostic, Oncogenic, Functional

Summary: Evidence Type: Diagnostic | Mutation: K27M | Summary: The H3-K27M mutation is used to classify and define a subtype of tumors, as it can be accurately detected by immunohistochemistry (IHC). Evidence Type: Oncogenic | Mutation: K27M | Summary: The H3-K27M mutation contributes to tumor development or progression, as indicated by its presence in tumor cells. Evidence Type: Functional | Mutation: K27I | Summary: The K27I mutation results in a loss of H3K27me3 immunoexpression, indicating an alteration in molecular function. Evidence Type: Functional | Mutation: 83A>T | Summary: The nucleotide change 83A>T is part of the K27I mutation and contributes to the alteration in molecular function. Evidence Type: Functional | Mutation: 84G>T | Summary: The nucleotide change 84G>T is part of the K27I mutation and contributes to the alteration in molecular function.

Gene→Variant (gene-first): 7157:83A>T 4613:84G>T 3021:K27I 3021:K27M 126961:lysine-to-isoleucine

Genes: 7157 4613 3021 126961

Variants: 83A>T 84G>T K27I K27M lysine-to-isoleucine

[Paper-level Aggregated] PMCID: PMC4477877

Evidence Type(s): Diagnostic

Summary: Mutation: 415 T>C | Summary: The variant 415 T>C is associated with the diagnosis of thrombocytopenia and/or ALL, as it co-segregates with affected individuals in the family.

Gene→Variant (gene-first): IKZF1(10320):415 T>C

Genes: IKZF1(10320)

Variants: 415 T>C

[Paragraph-level] PMCID: PMC4477877 Section: RESULTS PassageIndex: 5

Evidence Type(s): Diagnostic, Oncogenic, Functional

Summary: Evidence Type: Diagnostic | Mutation: 415 T>C | Summary: The variant 415 T>C is associated with the diagnosis of thrombocytopenia and/or ALL, as it co-segregates with affected individuals in the family. Evidence Type: Oncogenic | Mutation: 415 T>C | Summary: The 415 T>C variant is a somatic mutation that contributes to tumor development, as it is present in all affected family members tested. Evidence Type: Functional | Mutation: L349P | Summary: The L349P mutation results in a substitution that alters the molecular function of the ETV6 protein, impacting its role in cellular processes.

Gene→Variant (gene-first): 10320:415 T>C 2120:L349P 2120:c. T1046C 2120:proline for leucine at codon 349

Genes: 10320 2120

Variants: 415 T>C L349P c. T1046C proline for leucine at codon 349

[Paper-level Aggregated] PMCID: PMC4411002

Evidence Type(s): Diagnostic

Summary: Mutation: c.241 G>A; p.E81K | Summary: The presence of the c.241 G>A [p.E81K] mutation was confirmed in biopsies, indicating its use in defining or confirming a disease or subtype.

Evidence Type: Diagnostic

Gene→Variant (gene-first): PIK3CA(5290):c.241 G>A PIK3CA(5290):p.E81K

Genes: PIK3CA(5290)

Variants: c.241 G>A p.E81K

[Paragraph-level] PMCID: PMC4411002 Section: RESULTS PassageIndex: 15

Evidence Type(s): Diagnostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: c.241 G>A; p.E81K | Summary: The presence of the c.241 G>A [p.E81K] mutation was confirmed in biopsies, indicating its use in defining or confirming a disease or subtype. Evidence Type: Oncogenic | Mutation: c.241 G>A; p.E81K | Summary: The mutation is present in tumor biopsies, suggesting it contributes to tumor development or progression.

Gene→Variant (gene-first): 5290:c.241 G>A 5290:p.E81K

Genes: 5290

Variants: c.241 G>A p.E81K

[Paper-level Aggregated] PMCID: PMC4320693

Evidence Type(s): Diagnostic

Summary: Mutation: p.His1047Arg | Summary: The p.His1047Arg (H1047R) mutation is associated with a significant proportion of patients and is linked to phenotypes such as FAO, Hemihyperplasia- Multiple Lipomatosis (HHML), or macrodactyly, indicating its potential role in defining or classifying these conditions.

Evidence Type: Diagnostic Mutation: p.His1047Leu | Summary: The p.His1047Leu (H1047L) mutation is present in a notable percentage of patients and is linked to phenotypes consistent with FAO, Hemihyperplasia- Multiple Lipomatosis (HHML), or macrodactyly, suggesting its relevance in the diagnosis or classification of these conditions.

Evidence Type: Diagnostic Mutation: p.Glu545Lys | Summary: The p.Glu545Lys (E545K) mutation is found in a smaller subset of patients and is associated with the CLOVES syndrome phenotype, supporting its role in defining or classifying this condition.

Evidence Type: Diagnostic Mutation: p.Glu542Lys | Summary: The p.Glu542Lys (E542K) mutation occurs in a minority of patients and is found in individuals with phenotypes consistent with CLOVES syndrome, indicating its potential use in the diagnosis or classification of this condition.

Evidence Type: Diagnostic Mutation: p.Cys420Arg | Summary: The p.Cys420Arg (C420R) mutation, although less common, is identified in patients with CLOVES syndrome, indicating its relevance in defining or classifying this condition.

Gene→Variant (gene-first): PIK3CA(5290):p.His1047Arg PIK3CA(5290):p.His1047Leu PIK3CA(5290):p.Glu545Lys PIK3CA(5290):p.Glu542Lys PIK3CA(5290):p.Cys420Arg

Genes: PIK3CA(5290)

Variants: p.His1047Arg p.His1047Leu p.Glu545Lys p.Glu542Lys p.Cys420Arg

[Paragraph-level] PMCID: PMC4320693 Section: RESULTS PassageIndex: 4

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: p.His1047Arg | Summary: The mutation p.His1047Arg is associated with phenotypes such as FAO, Hemihyperplasia- Multiple Lipomatosis (HHML), or macrodactyly, indicating its role in defining or classifying these conditions. Evidence Type: Diagnostic | Mutation: p.His1047Leu | Summary: The mutation p.His1047Leu is linked to phenotypes consistent with FAO, Hemihyperplasia- Multiple Lipomatosis (HHML), or macrodactyly, suggesting its use in disease classification. Evidence Type: Diagnostic | Mutation: p.Glu542Lys | Summary: The mutation p.Glu542Lys is found in patients with phenotypes consistent with CLOVES syndrome, indicating its role in defining or classifying this condition. Evidence Type: Diagnostic | Mutation: p.Glu545Lys | Summary: The mutation p.Glu545Lys is associated with the CLOVES syndrome phenotype, supporting its use in disease classification. Evidence Type: Diagnostic | Mutation: p.Cys420Arg | Summary: The mutation p.Cys420Arg is identified in patients with CLOVES syndrome, indicating its relevance in defining or classifying this condition.

Gene→Variant (gene-first): 5290:p.Cys420Arg 5290:p.Glu542Lys 5290:p.Glu545Lys 5290:p.His1047Arg 5290:p.His1047Leu

Genes: 5290

Variants: p.Cys420Arg p.Glu542Lys p.Glu545Lys p.His1047Arg p.His1047Leu

[Paragraph-level] PMCID: PMC4320693 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: p.His1047Arg | Summary: The p.His1047Arg (H1047R) mutation is associated with a significant proportion of patients, indicating its potential role in defining or classifying a disease or subtype. Evidence Type: Diagnostic | Mutation: p.His1047Leu | Summary: The p.His1047Leu (H1047L) mutation is present in a notable percentage of patients, suggesting its relevance in the diagnosis or classification of a disease or subtype. Evidence Type: Diagnostic | Mutation: p.Glu545Lys | Summary: The p.Glu545Lys (E545K) mutation is found in a smaller subset of patients, which may indicate its role in defining or classifying a disease or subtype. Evidence Type: Diagnostic | Mutation: p.Glu542Lys | Summary: The p.Glu542Lys (E542K) mutation occurs in a minority of patients, suggesting its potential use in the diagnosis or classification of a disease or subtype. Evidence Type: Diagnostic | Mutation: p.Cys420Arg | Summary: The p.Cys420Arg (C420R) mutation, although less common, may still play a role in defining or classifying a disease or subtype based on its occurrence in patients.

Gene→Variant (gene-first): 5290:C420R 5290:E542K 5290:E545K 5290:H1047L 5290:H1047R 5290:p.Cys420Arg 5290:p.Glu542Lys 5290:p.Glu545Lys 5290:p.His1047Arg 5290:p.His1047Leu

Genes: 5290

Variants: C420R E542K E545K H1047L H1047R p.Cys420Arg p.Glu542Lys p.Glu545Lys p.His1047Arg p.His1047Leu

[Paper-level Aggregated] PMCID: PMC4159563

Evidence Type(s): Diagnostic

Summary: Mutation: K27M | Summary: The presence of the K27M-H3 mutation is used to classify and define the histological subtype of astrocytomas in DIPG cases. It is associated with specific histological features that can help in tumor classification, serving as a diagnostic marker for tumors in DIPG patients.

Gene→Variant (gene-first): ACVR1(90):K27M

Genes: ACVR1(90)

Variants: K27M

[Paragraph-level] PMCID: PMC4159563 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic, Diagnostic, Oncogenic

Summary: Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M mutation in histone H3 is associated with worse overall survival in DIPG patients compared to those without histone mutations, indicating its prognostic significance. Evidence Type: Diagnostic | Mutation: K27M | Summary: The presence of the K27M mutation in histone H3 is used to classify and define the subtype of tumors in DIPG patients, serving as a diagnostic marker. Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation in histone H3 contributes to tumor development and progression in DIPG, indicating its oncogenic potential.

Gene→Variant (gene-first): 90:K27M

Genes: 90

Variants: K27M

[Paragraph-level] PMCID: PMC4159563 Section: RESULTS PassageIndex: 8

Evidence Type(s): Diagnostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: K27M | Summary: The K27M mutation is associated with specific histological features, which can be used to classify or define certain types of tumors. Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation contributes to tumor development and progression, indicating its role as an oncogenic variant.

Gene→Variant (gene-first): 90:K27M

Genes: 90

Variants: K27M

[Paragraph-level] PMCID: PMC4159563 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Diagnostic, Prognostic

Summary: Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M-H3 mutation is associated with high-grade astrocytomas and contributes to tumor development in diffuse intrinsic pontine glioma (DIPG). Evidence Type: Diagnostic | Mutation: K27M | Summary: The presence of the K27M-H3 mutation is used to classify and define the histological subtype of astrocytomas in DIPG cases. Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M-H3 mutation correlates with disease behavior and outcome in pediatric brainstem gliomas, indicating that it may not predict outcomes accurately according to the current WHO grading scheme.

Gene→Variant (gene-first): 90:K27M

Genes: 90

Variants: K27M

[Paper-level Aggregated] PMCID: PMC3997489

Evidence Type(s): Diagnostic

Summary: Mutation: K27M | Summary: The presence of the K27M mutation is used to classify and define the molecular subgroup of Diffuse Intrinsic Pontine Glioma (DIPG), aiding in the understanding of its genetic drivers.

Gene→Variant (gene-first): H3-3B(3021):K27M

Genes: H3-3B(3021)

Variants: K27M

[Paragraph-level] PMCID: PMC3997489 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M mutation is associated with the development and progression of Diffuse Intrinsic Pontine Glioma (DIPG), contributing to the tumor's oncogenic characteristics. Evidence Type: Diagnostic | Mutation: K27M | Summary: The presence of the K27M mutation is used to classify and define the molecular subgroup of DIPG, aiding in the understanding of its genetic drivers.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paper-level Aggregated] PMCID: PMC3542862

Evidence Type(s): Diagnostic

Summary: Mutation: R115P | Summary: The R115P mutation in PIK3CA is suggested as a likely candidate for macrodactyly, indicating its role in defining or classifying a disease.

Evidence Type: Diagnostic

Gene→Variant (gene-first): PDK1(5163):R115P

Genes: PDK1(5163)

Variants: R115P

[Paragraph-level] PMCID: PMC3542862 Section: RESULTS PassageIndex: 5

Evidence Type(s): Diagnostic, Oncogenic

Summary: Evidence Type: Diagnostic | Mutation: R115P | Summary: The R115P mutation in PIK3CA is suggested as a likely candidate for macrodactyly, indicating its role in defining or classifying a disease. Evidence Type: Oncogenic | Mutation: R115L | Summary: The R115L mutation is associated with a squamous cell carcinoma, suggesting that mutations at p.Arg115 contribute to tumor development or progression. Evidence Type: Oncogenic | Mutation: p.Arg115 | Summary: The annotation of mutations at p.Arg115 in the context of cancer indicates their potential role in oncogenesis.

Gene→Variant (gene-first): 5290:R115L 5163:R115P 5290:p.Arg115

Genes: 5290 5163

Variants: R115L R115P p.Arg115

[Paper-level Aggregated] PMCID: PMC3422615

Evidence Type(s): Diagnostic

Summary: Mutation: K27M | Summary: The K27M-H3.3 mutation is used to define clinically and biologically distinct subgroups in pediatric glioblastomas, supporting its role in diagnostic testing.

Gene→Variant (gene-first): H3-3B(3021):K27M

Genes: H3-3B(3021)

Variants: K27M

[Paragraph-level] PMCID: PMC3422615 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Prognostic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: K27M | Summary: The K27M-H3.3 mutation is prevalent in pediatric glioblastomas and contributes to tumor development, defining clinically and biologically distinct subgroups. Evidence Type: Prognostic | Mutation: K27M | Summary: The K27M-H3.3 mutation is universally associated with short survival in DIPG, indicating its prognostic significance in disease outcome. Evidence Type: Diagnostic | Mutation: K27M | Summary: The K27M-H3.3 mutation is used to define clinically and biologically distinct subgroups in pediatric glioblastomas, supporting its role in diagnostic testing.

Gene→Variant (gene-first): 3021:G34V 3021:G34V/R 3021:K27M

Genes: 3021

Variants: G34V G34V/R K27M

[Paper-level Aggregated] PMCID: PMC2736831

Evidence Type(s): Diagnostic

Summary: Mutation: V600E | Summary: The assessment of the BRAF V600E mutation can aid in defining and classifying patients for treatment, indicating its diagnostic utility in patient selection.

Gene→Variant (gene-first): BRAF(673):V600E

Genes: BRAF(673)

Variants: V600E

[Paragraph-level] PMCID: PMC2736831 Section: ABSTRACT PassageIndex: 8

Evidence Type(s): Predictive, Diagnostic

Summary: Evidence Type: Predictive | Mutation: V600E | Summary: The BRAF V600E mutation may correlate with response to anti-EGFR monoclonal antibodies, suggesting its role in optimizing patient selection for therapy. Evidence Type: Diagnostic | Mutation: V600E | Summary: The assessment of the BRAF V600E mutation can aid in defining and classifying patients for treatment, indicating its diagnostic utility in patient selection.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paper-level Aggregated] PMCID: PMC2570525

Evidence Type(s): Diagnostic

Summary: Mutation: AKT1 E17K | Summary: The AKT1 E17K mutation is mentioned in the context of detection in melanoma, suggesting its role in defining or classifying the disease.

Gene→Variant (gene-first): AKT1(207):AKT1 E17K

Genes: AKT1(207)

Variants: AKT1 E17K

[Paragraph-level] PMCID: PMC2570525 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: AKT1 E17K | Summary: The AKT1 E17K mutation is mentioned in the context of detection in melanoma, suggesting its role in defining or classifying the disease.

Gene→Variant (gene-first): 207:AKT1 E17K 207:E17K

Genes: 207

Variants: AKT1 E17K E17K

[Paper-level Aggregated] PMCID: PMC2360265

Evidence Type(s): Diagnostic

Summary: Mutation: L858R | Summary: The presence of the L858R mutation is used to classify patients within the 'classical mutations' group, indicating its role in defining or confirming a subtype of disease.

Gene→Variant (gene-first): EGFR(1956):L858R

Genes: EGFR(1956)

Variants: L858R

[Paragraph-level] PMCID: PMC2360265 Section: RESULTS PassageIndex: 7

Evidence Type(s): Oncogenic, Diagnostic

Summary: Evidence Type: Oncogenic | Mutation: L858R | Summary: The L858R mutation is classified as a 'classical mutation' and is associated with tumor development or progression in patients, particularly in the context of adenocarcinomas and smoking status. Evidence Type: Diagnostic | Mutation: L858R | Summary: The presence of the L858R mutation is used to classify patients within the 'classical mutations' group, indicating its role in defining or confirming a subtype of disease.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paper-level Aggregated] PMCID: PMC1952070

Evidence Type(s): Diagnostic

Summary: Mutation: G/A; rs10251977 | Summary: The variant rs10251977 is mentioned as a single nucleotide polymorphism, which can be used to classify or define a disease or subtype.

Evidence Type: Diagnostic Mutation: T/C; rs17290643 | Summary: The variant rs17290643 is mentioned as a single nucleotide polymorphism, which can be used to classify or define a disease or subtype.

Gene→Variant (gene-first): TXK(7294):G/A NA:rs10251977 NA:T/C NA:rs17290643

Genes: TXK(7294) NA

Variants: G/A rs10251977 T/C rs17290643

[Paragraph-level] PMCID: PMC1952070 Section: RESULTS PassageIndex: 8

Evidence Type(s): Diagnostic, Predictive

Summary: Evidence Type: Diagnostic | Mutation: G/A; rs10251977 | Summary: The variant rs10251977 is mentioned as a single nucleotide polymorphism, which can be used to classify or define a disease or subtype. Evidence Type: Diagnostic | Mutation: T/C; rs17290643 | Summary: The variant rs17290643 is mentioned as a single nucleotide polymorphism, which can be used to classify or define a disease or subtype. Evidence Type: Predictive | Mutation: G/A; rs10251977 | Summary: There was no correlation between the G/A SNP rs10251977 and gefitinib response, indicating it does not predict therapy response. Evidence Type: Predictive | Mutation: T/C; rs17290643 | Summary: There was no correlation between the T/C SNP rs17290643 and gefitinib response, indicating it does not predict therapy response.

Gene→Variant (gene-first): 7294:G/A NA:rs10251977 NA:rs17290643

Genes: 7294 NA

Variants: G/A rs10251977 rs17290643

[Paper-level Aggregated] PMCID: PMC1702556

Evidence Type(s): Diagnostic

Summary: Mutation: R108K | Summary: The R108K mutation is associated with defining the presence of EGFR missense mutations in gliomas, indicating its role in classifying the disease.

Evidence Type: Diagnostic Mutation: T263P | Summary: The T263P mutation is part of the common amino acid changes in EGFR missense mutations, contributing to the classification of gliomas.

Evidence Type: Diagnostic Mutation: A289V | Summary: The A289V mutation is identified as one of the common amino acid changes in EGFR missense mutations, aiding in the diagnosis of gliomas.

Evidence Type: Diagnostic Mutation: G598V | Summary: The G598V mutation is included among the common amino acid changes in EGFR missense mutations, which helps in the diagnostic classification of gliomas.

Gene→Variant (gene-first): EGFR(1956):R108K EGFR(1956):T263P EGFR(1956):A289V EGFR(1956):G598V

Genes: EGFR(1956)

Variants: R108K T263P A289V G598V

[Paragraph-level] PMCID: PMC1702556 Section: RESULTS PassageIndex: 5

Evidence Type(s): Diagnostic

Summary: Evidence Type: Diagnostic | Mutation: R108K | Summary: The R108K mutation is associated with defining the presence of EGFR missense mutations in gliomas, indicating its role in classifying the disease. Evidence Type: Diagnostic | Mutation: T263P | Summary: The T263P mutation is part of the common amino acid changes in EGFR missense mutations, contributing to the classification of gliomas. Evidence Type: Diagnostic | Mutation: A289V | Summary: The A289V mutation is identified as one of the common amino acid changes in EGFR missense mutations, aiding in the diagnosis of gliomas. Evidence Type: Diagnostic | Mutation: G598V | Summary: The G598V mutation is included among the common amino acid changes in EGFR missense mutations, which helps in the diagnostic classification of gliomas.

Gene→Variant (gene-first): 1956:A289V 1956:G598V 1956:R108K 1956:T263P

Genes: 1956

Variants: A289V G598V R108K T263P

[Paragraph-level] PMCID: PMC2736831 Section: ABSTRACT PassageIndex: 8

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The mention of BRAF V600E mutations in the context of optimizing patient selection for anti-EGFR monoclonal antibodies indicates a correlation with treatment response. Diagnostic: The assessment of BRAF V600E mutations suggests its role in defining or classifying patients for treatment, indicating its use as a biomarker in the context of disease.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC2736831 Section: ABSTRACT PassageIndex: 4

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage discusses the role of the BRAF V600E mutation in predicting resistance to cetuximab plus irinotecan, indicating a correlation with treatment response. Diagnostic: The mention of BRAF V600E mutations in the context of a specific cohort of KRAS wild-type patients suggests its use in classifying or defining a subset of patients for treatment.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC2736831 Section: ABSTRACT PassageIndex: 2

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The BRAF V600E mutation is mentioned in the context of predicting resistance to anti-EGFR monoclonal antibodies in metastatic colorectal cancer. Diagnostic: The BRAF V600E mutation is associated with resistance, indicating its role in defining or classifying a specific disease context (metastatic colorectal cancer).

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC2570525 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the identification of the E17K mutation in clinical specimens, indicating its association with melanoma and its presence in metastatic lesions, which supports its use in defining or classifying the disease. Oncogenic: The E17K mutation is described as being present in metastatic lesions, suggesting that it contributes to tumor development or progression in melanoma.

Gene→Variant (gene-first): 207:E17K

Genes: 207

Variants: E17K

[Paragraph-level] PMCID: PMC2570525 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage mentions the detection of AKT1 E17K mutations in melanoma, indicating that the variant is associated with a specific disease (melanoma). Oncogenic: The mention of AKT1 E17K mutations in the context of melanoma suggests that this somatic variant may contribute to tumor development or progression.

Gene→Variant (gene-first): 207:AKT1 E17K 207:E17K

Genes: 207

Variants: AKT1 E17K E17K

[Paragraph-level] PMCID: PMC2570525 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Diagnostic, Oncogenic, Functional

Justification: Diagnostic: The passage discusses the identification of the AKT1 (E17K) mutation in various cancer types, indicating its association with melanoma and suggesting its role in defining the presence of this mutation in cancer specimens. Oncogenic: The passage states that the AKT1 E17K mutation is an activating mutation that contributes to tumor development, as evidenced by its identification in melanoma specimens and cell lines, indicating its role in cancer progression. Functional: The passage mentions that the AKT3 E17K mutation results in the activation of AKT when expressed in human melanoma cells, demonstrating a change in molecular function related to the variant.

Gene→Variant (gene-first): 207:AKT1 (E17K 207:E17K

Genes: 207

Variants: AKT1 (E17K E17K

[Paragraph-level] PMCID: PMC7211323 Section: RESULTS PassageIndex: 9

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the mutation rate of ACVR2A in a specific population and identifies specific mutations as frequent occurrences in gastric cancer patients, indicating their association with the disease. Oncogenic: The passage describes nonsynonymous mutations in the ACVR2A gene that lead to protein changes, specifically mentioning frameshift truncating mutations, which contribute to tumor development in gastric cancer.

Gene→Variant (gene-first): 92:1310delA 92:c.1309-1310delAA 92:c.285delA 92:p. D96Tfs*54

Genes: 92

Variants: 1310delA c.1309-1310delAA c.285delA p. D96Tfs*54

[Paragraph-level] PMCID: PMC7211323 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the association of specific mutations (c.1310delA, 1309-1310delAA, c.285delA) with the MSI-H subtype of gastric cancers, indicating their role in defining or classifying the disease. Oncogenic: The variants mentioned are associated with a high mutation frequency and a high MSI score, suggesting their contribution to tumor development or progression in gastric cancer.

Gene→Variant (gene-first): 92:1309-1310delAA 92:c.1310delA 92:c.285delA

Genes: 92

Variants: 1309-1310delAA c.1310delA c.285delA

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 14

Evidence Type(s): Diagnostic, Prognostic, Oncogenic

Justification: Diagnostic: The passage discusses the association of H3.1-K27M tumors with clinical characteristics and outcomes, indicating its role in defining and classifying the disease. Prognostic: The variant K27M is correlated with overall survival outcomes, with H3.1 mutations showing a better prognosis compared to H3.3 mutations, independent of therapy. Oncogenic: The mention of H3.1-K27M tumors suggests that this somatic variant contributes to tumor development or progression, as it is associated with clinical characteristics and outcomes in cancer patients.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 13

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The K27M mutation is associated with disease behavior, indicating a correlation with disease outcome, specifically suggesting a less aggressive behavior in DIPG. Diagnostic: The mention of the K27M mutation being associated with DIPG suggests its role in defining or classifying this specific disease subtype.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 11

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the strong enrichment of the K27M variant in specific tumor subtypes, indicating its association with the proneural-glioblastoma multiforme (GBM) and oligodendrocytic or neural signatures, which helps classify the disease. Oncogenic: The K27M variant is implicated in tumor development, as evidenced by its association with oligodendroglial differentiation and the observation of metastatic relapse in patients with H3F3A mutations, suggesting a role in tumor progression.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 9

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the exclusive presence of the K27M variant in specific tumor subgroups (H3.1-K27M and H3.3-K27M), indicating its role in classifying these tumors. Oncogenic: The K27M variant is associated with specific tumor subgroups and is implicated in tumor development, as indicated by its exclusive presence in H3.1 and H3.3 tumors.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 5

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the identification of specific mutations (H3.3-K27M, H3-G34R/V, H3.1- and H3.2-K27M, H3.3 K27I) in different tumor locations, indicating their association with specific tumor types, which supports their use in defining or classifying disease subtypes. Oncogenic: The mention of mutations being identified in specific tumor types suggests that these variants contribute to tumor development or progression, indicating their oncogenic potential.

Gene→Variant (gene-first): 3196:G34R/V 3021:K27I 3021:K27M

Genes: 3196 3021

Variants: G34R/V K27I K27M

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 4

Evidence Type(s): Diagnostic, Functional

Justification: Diagnostic: The passage discusses the detection of H3-K27M mutations and their association with immunohistochemistry (IHC) staining, indicating the use of these variants to classify or define a subtype of disease. Functional: The passage mentions the loss of H3K27me3 immunoexpression associated with the K27I variant, indicating an alteration in molecular function related to protein activity or modification.

Gene→Variant (gene-first): 7157:83A>T 4613:84G>T 3021:K27I 3021:K27M 126961:lysine-to-isoleucine

Genes: 7157 4613 3021 126961

Variants: 83A>T 84G>T K27I K27M lysine-to-isoleucine

[Paragraph-level] PMCID: PMC4654747 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the correlation of the H3-K27M mutation with the classification of DIPG samples, indicating its role in defining or confirming the disease subtype. Oncogenic: The mention of the H3-K27M mutation in the context of tumor samples suggests that it contributes to tumor development or progression, characteristic of oncogenic variants.

Gene→Variant (gene-first): 3021:K27M 3021:lysine 27

Genes: 3021

Variants: K27M lysine 27

[Paragraph-level] PMCID: PMC6549573 Section: RESULTS PassageIndex: 8

Evidence Type(s): Predictive, Diagnostic, Oncogenic

Justification: Predictive: The passage discusses the response to bortezomib in patients with KRAS G12D-mutant lung adenocarcinomas, indicating a correlation between the variant and treatment response. Diagnostic: The KRAS G12D mutation is identified through molecular profiling as part of the patient's diagnosis, linking the variant to the classification of the disease. Oncogenic: The KRAS G12D mutation is described in the context of tumor development and progression, as it is a known driver mutation in lung adenocarcinomas.

Gene→Variant (gene-first): 3845:G12D

Genes: 3845

Variants: G12D

[Paragraph-level] PMCID: PMC6549573 Section: RESULTS PassageIndex: 4

Evidence Type(s): Predictive, Diagnostic, Oncogenic

Justification: Predictive: The passage discusses the response of patients with KRAS G12D-mutant lung cancers to bortezomib, indicating a correlation between the variant and treatment response. Diagnostic: The mention of KRAS G12D in the context of lung cancers suggests its role in classifying or defining a specific subtype of the disease. Oncogenic: The variant KRAS G12D is implicated in lung cancers, indicating its contribution to tumor development or progression.

Gene→Variant (gene-first): 3845:G12D

Genes: 3845

Variants: G12D

[Paragraph-level] PMCID: PMC6549573 Section: RESULTS PassageIndex: 3

Evidence Type(s): Predictive, Diagnostic, Oncogenic

Justification: Predictive: The passage discusses patients with KRAS G12D-mutant lung cancers treated with bortezomib, indicating a correlation between the variant and response to therapy. Diagnostic: The mention of "KRAS G12D-mutant lung cancers" suggests that the variant is used to classify or define a specific subtype of lung cancer. Oncogenic: The variant KRAS G12D is implicated in the context of lung adenocarcinoma, indicating its role in tumor development or progression.

Gene→Variant (gene-first): 3845:G12D

Genes: 3845

Variants: G12D

[Paragraph-level] PMCID: PMC4320693 Section: RESULTS PassageIndex: 4

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the correlation of specific genotypes with phenotypes, indicating that the variants are associated with defining or classifying certain conditions such as FAO, HHML, or CLOVES syndrome. Oncogenic: The variants mentioned are associated with specific phenotypes that suggest a role in tumor development or progression, particularly in the context of CLOVES syndrome and other related conditions.

Gene→Variant (gene-first): 5290:p.Cys420Arg 5290:p.Glu542Lys 5290:p.Glu545Lys 5290:p.His1047Arg 5290:p.His1047Leu

Genes: 5290

Variants: p.Cys420Arg p.Glu542Lys p.Glu545Lys p.His1047Arg p.His1047Leu

[Paragraph-level] PMCID: PMC4320693 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the frequency of specific mutations in patients, indicating their association with a disease or subtype. Oncogenic: The variants mentioned are likely somatic mutations that contribute to tumor development, as they are described in the context of patient mutations.

Gene→Variant (gene-first): 5290:C420R 5290:E542K 5290:E545K 5290:H1047L 5290:H1047R 5290:p.Cys420Arg 5290:p.Glu542Lys 5290:p.Glu545Lys 5290:p.His1047Arg 5290:p.His1047Leu

Genes: 5290

Variants: C420R E542K E545K H1047L H1047R p.Cys420Arg p.Glu542Lys p.Glu545Lys p.His1047Arg p.His1047Leu

[Paragraph-level] PMCID: PMC7064492 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of MAP2K1 (p.K57N) mutations in patients with auricular AVM, indicating an association with the condition and suggesting its role in defining or confirming the disease. Oncogenic: The presence of the MAP2K1 (p.K57N) mutation in the tissue adjacent to the cartilage suggests that it may contribute to tumor development or progression in the context of the auricular AVM.

Gene→Variant (gene-first): 5604:p.K57N

Genes: 5604

Variants: p.K57N

[Paragraph-level] PMCID: PMC4748120 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Oncogenic, Predictive, Diagnostic

Justification: Oncogenic: The passage describes how the A66dup variant contributes to tumor development by transforming the growth of primary myeloid progenitors and Ba/F3 cells, indicating its role in oncogenesis. Predictive: The passage mentions that K-Ras proteins with the A66dup variant are hypersensitive to MEK inhibition, suggesting a correlation with response to a specific therapy. Diagnostic: The discovery of the A66dup variant in a child with an atypical myeloproliferative neoplasm suggests its potential use in defining or classifying this disease.

Gene→Variant (gene-first): 5295:A66dup

Genes: 5295

Variants: A66dup

[Paragraph-level] PMCID: PMC8033310 Section: RESULTS PassageIndex: 11

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the frequency of PIK3CA mutations, including E545K and H1047R, in patients with triple-negative breast cancer (TNBC), indicating their association with the diagnosis of invasive cancer. Oncogenic: The presence of PIK3CA mutations, specifically E545K and H1047R, in patients with invasive cancer suggests that these somatic variants contribute to tumor development or progression in the context of TNBC.

Gene→Variant (gene-first): 5290:E545K 5290:H1047R

Genes: 5290

Variants: E545K H1047R

[Paragraph-level] PMCID: PMC3422615 Section: RESULTS PassageIndex: 12

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the correlation between the K27M-H3.3 mutation and overall survival in DIPG patients, indicating that patients with this mutation have significantly worse survival outcomes compared to those with wild-type tumors. Diagnostic: The K27M-H3.3 mutation is associated with the classification of DIPG patients, as it is mentioned that 69% of the patients carried this mutation, which is relevant for defining their disease status.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC3422615 Section: RESULTS PassageIndex: 10

Evidence Type(s): Oncogenic, Diagnostic

Justification: Oncogenic: The passage discusses frequent focal copy number alterations in the K27M-H3.3 group, indicating that the K27M variant is associated with tumor development through specific genetic alterations. Diagnostic: The mention of the K27M-H3.3 group suggests that the K27M variant is used to classify or define a specific subtype of tumors, indicating its role in disease classification.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC3422615 Section: RESULTS PassageIndex: 7

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of the K27M variant in DIPG samples and its association with TP53 mutations, indicating its role in classifying or defining a subtype of disease. Oncogenic: The K27M variant is mentioned in the context of mutations found in DIPG samples, suggesting its contribution to tumor development or progression in this specific cancer type.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC3422615 Section: RESULTS PassageIndex: 5

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the association of the K27M-H3.3 mutation with ATRX mutations in DIPG samples, indicating its role in defining or classifying a subtype of disease. Oncogenic: The K27M-H3.3 mutation is mentioned in the context of its presence in GBM samples, suggesting its contribution to tumor development or progression.

Gene→Variant (gene-first): 3021:G34V/R 3021:K27M

Genes: 3021

Variants: G34V/R K27M

[Paragraph-level] PMCID: PMC3422615 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The K27M mutation is identified as being present at diagnosis in DIPG samples, indicating its role in defining the disease subtype. Oncogenic: The K27M mutation contributes to tumor development in DIPG, as it is recurrently found in the samples analyzed, suggesting its role in tumor progression.

Gene→Variant (gene-first): 3021:G34V/R 3021:K27M

Genes: 3021

Variants: G34V/R K27M

[Paragraph-level] PMCID: PMC3422615 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Diagnostic, Prognostic, Oncogenic

Justification: Diagnostic: K27M-H3.3 mutation defines clinically and biologically distinct subgroups in DIPG, indicating its use in classifying the disease. Prognostic: K27M-H3.3 is universally associated with short survival in DIPG, while patients wild-type for H3.3 show improved survival, indicating its correlation with disease outcome. Oncogenic: The K27M-H3.3 mutation contributes to tumor development or progression in pediatric glioblastomas, as indicated by its prevalence in DIPG and association with specific copy number changes.

Gene→Variant (gene-first): 3021:G34V 3021:G34V/R 3021:K27M

Genes: 3021

Variants: G34V G34V/R K27M

[Paragraph-level] PMCID: PMC1952070 Section: RESULTS PassageIndex: 8

Evidence Type(s): Diagnostic, Predictive

Justification: Diagnostic: The passage mentions the detection of single nucleotide polymorphisms (SNPs) and their association with specific exons, indicating their role in defining or classifying genetic variants. Predictive: The passage explicitly states that there was "no correlation between these alleles and gefitinib response," which implies that the variants were evaluated for their predictive value regarding treatment response.

Gene→Variant (gene-first): 7294:G/A NA:rs10251977 NA:rs17290643

Genes: 7294 NA

Variants: G/A rs10251977 rs17290643

[Paragraph-level] PMCID: PMC10524391 Section: RESULTS PassageIndex: 9

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage discusses the presence of the EGFR T790M mutation in patients who had received prior EGFR-directed therapy, indicating a correlation with treatment response or resistance to osimertinib. Diagnostic: The mention of the EGFR T790M mutation being detectable at the time of study enrollment suggests its role in classifying or confirming the disease status in patients undergoing treatment.

Gene→Variant (gene-first): 1956:T790M

Genes: 1956

Variants: T790M

[Paragraph-level] PMCID: PMC10524391 Section: RESULTS PassageIndex: 8

Evidence Type(s): Oncogenic, Diagnostic

Justification: Oncogenic: The passage indicates that the variants L747S, L858R, and T790M are present in tumors, suggesting their role in tumor development or progression. Diagnostic: The presence of specific EGFR mutations, including L747S, L858R, and T790M, is used to classify the tumors, indicating their association with the disease.

Gene→Variant (gene-first): 1956:L747S 1956:L858R 1956:T790M

Genes: 1956

Variants: L747S L858R T790M

[Paragraph-level] PMCID: PMC5615879 Section: ABSTRACT PassageIndex: 6

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of KIT mutations in cases and specifies the types of mutations found in different exons, indicating their association with the disease. Oncogenic: The mention of KIT mutations contributing to tumor development is implied by their prevalence in cases, suggesting a role in cancer progression.

Gene→Variant (gene-first): 3815:Ala-Tyr 3815:c.1509_1510insACCTAT 728378:c.1666C>G 3815:c.1666_1668dupCAG 3815:c.1672_1677delAAGGTTinsAGT 5156:c.1925A>G 3815:p.K558_V559delinsS 728378:p.K642R 728378:p.Q556E 3815:p.Q556dup 3815:p.Y503_F504insTY

Genes: 3815 728378 5156

Variants: Ala-Tyr c.1509_1510insACCTAT c.1666C>G c.1666_1668dupCAG c.1672_1677delAAGGTTinsAGT c.1925A>G p.K558_V559delinsS p.K642R p.Q556E p.Q556dup p.Y503_F504insTY

[Paragraph-level] PMCID: PMC5615879 Section: RESULTS PassageIndex: 16

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses mutations identified in tumors located in the small intestine, indicating a significant association with the disease, which supports the use of these variants in defining or classifying the disease. Oncogenic: The passage describes mutations that contribute to tumor development, specifically mentioning internal tandem duplications and insertions in the context of tumors, indicating their role in oncogenesis.

Gene→Variant (gene-first): 3815:Ala-Tyr 3815:c.1504_1509 dup GCCTAT 3815:c.1509_1510insACCTAT 3815:p.Y503_F504insTY

Genes: 3815

Variants: Ala-Tyr c.1504_1509 dup GCCTAT c.1509_1510insACCTAT p.Y503_F504insTY

[Paragraph-level] PMCID: PMC5615879 Section: RESULTS PassageIndex: 13

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage mentions specific variants and their occurrence in a case, indicating their association with a particular disease or condition. Oncogenic: The variants discussed are likely somatic mutations contributing to tumor development, as they are described in the context of a case study.

Gene→Variant (gene-first): 3815:K580dup 3815:c.1673_1674insTCC 3815:c.1731_1742dupTTATGATCACAA 3815:p.K558delinsBP

Genes: 3815

Variants: K580dup c.1673_1674insTCC c.1731_1742dupTTATGATCACAA p.K558delinsBP

[Paragraph-level] PMCID: PMC5615879 Section: RESULTS PassageIndex: 12

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage provides mutation frequencies for specific variants, indicating their association with a disease or subtype. Oncogenic: The mention of substitution mutations suggests that these variants may contribute to tumor development or progression, as they are likely somatic mutations.

Gene→Variant (gene-first): 3815:p.L576P 3815:p.T574I 3815:p.V559A 3815:p.V559D 3815:p.V560D 3815:p.V560G

Genes: 3815

Variants: p.L576P p.T574I p.V559A p.V559D p.V560D p.V560G

[Paragraph-level] PMCID: PMC5615879 Section: RESULTS PassageIndex: 10

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses mutations in exon 11 and their association with specific cases, indicating that these mutations can be used to classify or define a disease subtype. Oncogenic: The mention of double mutations and their role in the context of tumor development suggests that these somatic variants contribute to tumor progression.

Gene→Variant (gene-first): 728378:c.1666C>G 3815:c.1666_1668dupCAG 3815:c.1672_1677delAAGGTTinsAGT 728378:p.Q556E 3815:p.Q556dup

Genes: 728378 3815

Variants: c.1666C>G c.1666_1668dupCAG c.1672_1677delAAGGTTinsAGT p.Q556E p.Q556dup

[Paragraph-level] PMCID: PMC5615879 Section: RESULTS PassageIndex: 9

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the frequency of specific mutations, including in-frame deletions and substitutions, which are associated with the classification of cases, indicating their role in defining or confirming a disease subtype. Oncogenic: The mention of mutations in exon 11, including specific variants, suggests their contribution to tumor development or progression, as they are described in the context of cancer cases.

Gene→Variant (gene-first): 3815:K558 del 3815:V555del 3815:c.1669_1674delTGGAAG 3815:c.1676T>A 3815:c.1679T>A 3815:p.V559D 3815:p.V560D

Genes: 3815

Variants: K558 del V555del c.1669_1674delTGGAAG c.1676T>A c.1679T>A p.V559D p.V560D

[Paragraph-level] PMCID: PMC9365372 Section: ABSTRACT PassageIndex: 9

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage indicates that the variant T790M is associated with favorable clinical efficacy of the therapy Abivertinib in patients, suggesting a correlation with treatment response. Diagnostic: The mention of patients with EGFR T790M+ NSCLC implies that the T790M variant is used to classify or define a specific subtype of non-small cell lung cancer.

Gene→Variant (gene-first): 1956:T790M

Genes: 1956

Variants: T790M

[Paragraph-level] PMCID: PMC9365372 Section: ABSTRACT PassageIndex: 3

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage discusses the evaluation of safety and efficacy of abivertinib in patients with the T790M mutation, indicating a correlation with treatment response in the context of non-small cell lung cancer. Diagnostic: The mention of the Thr790Met point mutation (T790M) being positive in patients with non-small cell lung cancer suggests its role in defining or classifying the disease subtype.

Gene→Variant (gene-first): 1956:T790M 1956:Thr790Met

Genes: 1956

Variants: T790M Thr790Met

[Paragraph-level] PMCID: PMC10082285 Section: ABSTRACT PassageIndex: 5

Evidence Type(s): Predictive, Diagnostic, Prognostic, Oncogenic

Justification: Predictive: The passage discusses the assignment of patients with EGFR-mutated NSCLC to receive osimertinib, indicating a correlation between the L858R variant and response to this specific therapy. Diagnostic: The mention of patients with EGFR-mutated NSCLC, specifically referencing the L858R variant, suggests its role in defining or classifying the disease subtype. Prognostic: The passage refers to disease-free survival (DFS) and overall survival as endpoints, indicating that the L858R variant may correlate with disease outcomes independent of therapy. Oncogenic: The context of the L858R variant being part of EGFR mutations in NSCLC implies its contribution to tumor development or progression, characteristic of oncogenic variants.

Gene→Variant (gene-first): 1956:L858R

Genes: 1956

Variants: L858R

[Paragraph-level] PMCID: PMC9338780 Section: RESULTS PassageIndex: 4

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage discusses the correlation between the BRAF V600E mutation and the response to treatment, indicating that all patients with confirmed responses had BRAF V600E-mutant disease, which suggests a predictive relationship with therapy response. Diagnostic: The mention of "centrally confirmed BRAF V600E-mutant disease" indicates that the variant is used to classify or confirm a specific disease subtype, supporting its role as a diagnostic marker.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC9338780 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage states that 33 out of 36 patients had the BRAF V600E mutation confirmed, indicating its use in defining or confirming a disease subtype, specifically in the context of ATC (anaplastic thyroid carcinoma). Oncogenic: The BRAF V600E mutation is known to contribute to tumor development or progression, which aligns with the evidence type of oncogenic variants in cancer.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC3483540 Section: RESULTS PassageIndex: 12

Evidence Type(s): Oncogenic, Diagnostic

Justification: Oncogenic: The passage discusses the presence of somatic point mutations, specifically the C > A and T > G transversions, in lung cancers of smokers, indicating their contribution to tumor development or progression. Diagnostic: The differences in mutational spectrums between lung cancers of smokers and never-smokers suggest that these variants can be used to classify or define the disease based on smoking status.

Gene→Variant (gene-first): 2199:C > A 2199:T > G

Genes: 2199

Variants: C > A T > G

[Paragraph-level] PMCID: PMC3483540 Section: RESULTS PassageIndex: 5

Evidence Type(s): Oncogenic, Diagnostic

Justification: Oncogenic: The passage discusses several somatic mutations, including those in EGFR, KRAS, NRAS, PIK3CA, BRAF, CTNNB1, and MET, which are identified as driver mutations contributing to lung adenocarcinoma, indicating their role in tumor development or progression. Diagnostic: The passage mentions that specific mutations in well-known cancer genes are associated with lung adenocarcinoma, suggesting that these variants can be used to classify or define the disease.

Gene→Variant (gene-first): 1499:D32G 22853:E555K 3845:G12C 3845:G12D 3845:G12S 3845:G12V 3845:G13C 3845:G13D 1956:G719A 5290:H1047R 1956:L858R 1499:M1124D 3845:Q61H 4893:Q61K 4893:Q61L 673:V600E

Genes: 1499 22853 3845 1956 5290 4893 673

Variants: D32G E555K G12C G12D G12S G12V G13C G13D G719A H1047R L858R M1124D Q61H Q61K Q61L V600E

[Paragraph-level] PMCID: PMC5873857 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the identification of pathogenic variants in patients with vascular malformations (VMs), indicating that these variants are used to classify or define the clinical phenotype associated with the disease. Oncogenic: The identified variant c.159_173del is described as contributing to the allelic spectrum of variants in the RAS/MAPK pathway, which is known to be involved in tumor development and progression, thus supporting its oncogenic potential.

Gene→Variant (gene-first): 5604:c.159_173del

Genes: 5604

Variants: c.159_173del

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 4

Evidence Type(s): Diagnostic, Prognostic

Justification: Diagnostic: The passage discusses the association of the BRAF V600E mutation with non-MSI tumors, indicating its role in classifying or defining a specific subtype of colorectal cancer. Prognostic: The passage mentions that miR-31 is being focused on as a candidate prognostic biomarker, suggesting a correlation with disease outcome in the context of tumors harboring the BRAF V600E mutation.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 3

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the evaluation of CRC specimens based on their BRAF V600E mutation status, which is used to classify the tumors into different subtypes with distinct genetic and clinical features. Oncogenic: The BRAF V600E mutation is mentioned in the context of tumor specimens, indicating its role in tumor development or progression in colorectal cancer.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: RESULTS PassageIndex: 2

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage indicates that the BRAF V600E mutation is associated with colorectal cancers (CRCs), suggesting its role in defining or classifying a disease subtype. Oncogenic: The mention of the BRAF V600E mutation in the context of colorectal cancers implies that it contributes to tumor development or progression.

Gene→Variant (gene-first): 673:V600E

Genes: 673

Variants: V600E

[Paragraph-level] PMCID: PMC7068240 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Prognostic, Diagnostic

Justification: Prognostic: The passage discusses the association of high miR-31 expression with poorer mortality and shorter median survival time in patients with advanced colorectal cancer, indicating a prognostic relationship. Diagnostic: The study evaluates the potential of miRNAs as biomarkers for colorectal cancer, suggesting that the presence of the BRAF V600E mutation can be used to classify tumors based on miR-31 expression levels.

Gene→Variant (gene-first): 673:V600E 673:serine/threonine

Genes: 673

Variants: V600E serine/threonine

[Paragraph-level] PMCID: PMC5083195 Section: RESULTS PassageIndex: 7

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage discusses trends of the SNPs being associated with drug response (gemcitabine IC50 values) and mentions pharmacogenomic effects on gemcitabine during pancreatic cancer treatment. Diagnostic: The SNPs are described as influencing disease risk in pancreatic cancer, indicating their potential role in classifying or associating with the disease.

Gene→Variant (gene-first): NA:rs10979372 1002:rs1122269 NA:rs1374679 57554:rs7515290

Genes: NA 1002 57554

Variants: rs10979372 rs1122269 rs1374679 rs7515290

[Paragraph-level] PMCID: PMC6333965 Section: RESULTS PassageIndex: 12

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the identification of specific mutations in PIK3CA and CDKN2A, indicating their association with patient populations, which suggests their role in defining or classifying disease subtypes. Oncogenic: The mention of TP53 inactivating mutations (R209Q/W, R243W/Q) causing cell cycle deregulation implies that these somatic variants contribute to tumor development or progression.

Gene→Variant (gene-first): 5290:E545K 7157:R209Q/W 7157:R243W/Q 1029:R58X

Genes: 5290 7157 1029

Variants: E545K R209Q/W R243W/Q R58X

[Paragraph-level] PMCID: PMC6333965 Section: ABSTRACT PassageIndex: 6

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage mentions that PIK3CA E545K and CDKN2A R58X are potentially targetable alterations, indicating their association with specific tumor characteristics or responses, which aligns with diagnostic evidence. Oncogenic: The variants PIK3CA E545K and CDKN2A R58X are described as potentially targetable alterations, suggesting their role in tumor development or progression, which supports oncogenic evidence.

Gene→Variant (gene-first): 5290:E545K 1029:R58X

Genes: 5290 1029

Variants: E545K R58X

[Paragraph-level] PMCID: PMC3997489 Section: ABSTRACT PassageIndex: 1

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the prevalence of the K27M mutation in DIPG, indicating its association with this specific disease, which supports its use as a biomarker for classification. Oncogenic: The K27M mutation is described as part of the unique genetic make-up of DIPG, suggesting its contribution to tumor development or progression in this specific cancer type.

Gene→Variant (gene-first): 3021:K27M

Genes: 3021

Variants: K27M

[Paragraph-level] PMCID: PMC4159563 Section: RESULTS PassageIndex: 9

Evidence Type(s): Prognostic, Diagnostic, Oncogenic

Justification: Prognostic: The passage indicates that patients with the K27M mutation in histone H3 have worse overall survival compared to patients with no histone mutations, suggesting a correlation between the variant and disease outcome. Diagnostic: The K27M mutation is associated with specific tumor histologies and is used to classify patients into different groups based on their histone mutation status, indicating its role in defining disease subtypes. Oncogenic: The K27M mutation in histone H3 is described as contributing to tumor development, as it is found in a significant proportion of tumors and correlates with specific tumor characteristics.

Gene→Variant (gene-first): 90:K27M

Genes: 90

Variants: K27M

[Paragraph-level] PMCID: PMC5652823 Section: RESULTS PassageIndex: 24

Evidence Type(s): Predictive, Diagnostic, Oncogenic, Functional

Justification: Predictive: The passage discusses the T790M mutation in the context of resistance to EGFR-TKI therapy and its correlation with treatment response, particularly with osimertinib. Diagnostic: The T790M mutation is mentioned as a resistance mutation detected in patients with acquired resistance to EGFR-TKI therapy, indicating its role in classifying the disease state. Oncogenic: The T790M mutation is described as a resistance mutation that contributes to tumor progression in patients undergoing treatment, indicating its role in cancer development. Functional: The passage implies that the T790M mutation alters the response to therapy, suggesting a change in molecular function related to drug resistance mechanisms.

Gene→Variant (gene-first): 1956:G719C 1956:T790M 673:V600E 1956:c.2155G>T 1956:p.G719C 7157:p.R248W

Genes: 1956 673 7157

Variants: G719C T790M V600E c.2155G>T p.G719C p.R248W

[Paragraph-level] PMCID: PMC5652823 Section: RESULTS PassageIndex: 11

Evidence Type(s): Diagnostic, Predictive, Oncogenic

Justification: Diagnostic: The variant c.2527G>A; p.V843I is associated with lung cancer, as indicated by its reporting in the COSMIC databank and its presence in a patient with NSCLC. Predictive: The passage states that the mutation does not confer sensitivity to EGFR-TKIs, indicating a lack of response to this specific therapy. Oncogenic: The variant is described as "activating from a biological point of view," suggesting it contributes to tumor development or progression in lung cancer.

Gene→Variant (gene-first): 1956:c.2527G>A 1956:p.V843I

Genes: 1956

Variants: c.2527G>A p.V843I

[Paragraph-level] PMCID: PMC5652823 Section: RESULTS PassageIndex: 10

Evidence Type(s): Predictive, Diagnostic, Oncogenic

Justification: Predictive: The passage indicates that the patient showed stable disease on erlotinib, suggesting a correlation between the variant and response to therapy. Diagnostic: The variant is mentioned in the context of being previously described in lung samples, indicating its association with a specific disease subtype (lung cancer). Oncogenic: The variant is discussed in relation to a patient with stage IV lung cancer, suggesting its potential role in tumor development or progression.

Gene→Variant (gene-first): 1956:c.2543C>T 1956:p.P848L

Genes: 1956

Variants: c.2543C>T p.P848L

[Paragraph-level] PMCID: PMC5652823 Section: ABSTRACT PassageIndex: 7

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage indicates that patients with the EGFR-T790M mutation responded to the 3rd-generation EGFR-TKI osimertinib, suggesting a correlation between the variant and treatment response. Diagnostic: The EGFR-T790M mutation is mentioned as being revealed in re-biopsies at progression, indicating its role in defining or confirming the presence of a specific disease state in patients treated with EGFR-TKIs.

Gene→Variant (gene-first): 1956:T790M

Genes: 1956

Variants: T790M

[Paragraph-level] PMCID: PMC6478919 Section: RESULTS PassageIndex: 7

Evidence Type(s): Predictive, Diagnostic

Justification: Predictive: The passage discusses how the variant rs1801018 correlates with patient resistance to paclitaxel, indicating its predictive value for treatment response. Diagnostic: The variation is associated with the classification of patients based on their treatment response, helping to define which patients are likely to respond to single or multiple lines of therapy.

Gene→Variant (gene-first): 596:T instead of a C 596:rs1801018

Genes: 596

Variants: T instead of a C rs1801018

[Paragraph-level] PMCID: PMC6478919 Section: RESULTS PassageIndex: 5

Evidence Type(s): Diagnostic

Justification: Diagnostic: The variant rs6070697 is discussed in the context of its distribution among treatment groups and its presence in both patients and controls, indicating its association with the study population and suggesting a role in defining or classifying the patient cohort.

Gene→Variant (gene-first): 81027:rs6070697

Genes: 81027

Variants: rs6070697

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 26

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses common founder mutations such as BRCA2:c.5946delT and BRCA1:c.68_69delAG, indicating their association with neopeptides that are likely presented in the population, which relates to defining or classifying a disease. Oncogenic: The mention of pathogenic mutations and their associated neoantigens suggests that these variants contribute to tumor development or progression, as they are described as potential tumor antigens.

Gene→Variant (gene-first): 672:c.5266dupC 675:c.5946delT 672:c.68_69delAG

Genes: 672 675

Variants: c.5266dupC c.5946delT c.68_69delAG

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 16

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of pathogenic missense mutations, specifically mentioning the BRCA1:p.C61S and p.M1I mutations, in the context of their association with disease, indicating their role in defining or confirming a disease subtype. Oncogenic: The passage refers to the BRCA1:p.C61S and p.M1I mutations as pathogenic, suggesting that they contribute to tumor development or progression, which aligns with the definition of oncogenic variants.

Gene→Variant (gene-first): 672:p.C61S 672:p.M1I

Genes: 672

Variants: p.C61S p.M1I

[Paragraph-level] PMCID: PMC7611203 Section: RESULTS PassageIndex: 7

Evidence Type(s): Diagnostic, Oncogenic