[Paper-level Aggregated] PMCID: PMC7611203

Evidence Type(s): Oncogenic, Predictive, Predisposing

Justification: Oncogenic: The text discusses multiple pathogenic mutations, including BRCA1 and BRCA2 variants, which are known to be associated with an increased risk of breast and ovarian cancer, indicating their oncogenic potential. Predictive: The mention of neoantigens derived from pathogenic mutations being likely presented by HLA class I complexes suggests that these mutations can be used to predict immune responses, which is a predictive aspect in the context of cancer treatment. Predisposing: The identification of common founder mutations such as BRCA1:c.185delAG and BRCA2:c.6174delT indicates that these variants predispose individuals to developing certain cancers, thus classifying them as predisposing mutations.

Gene→Variant (gene-first): BRCA1(672):c.185delAG BRCA1(672):c.5266dupC BRCA2(675):c.5946delT BRCA2(675):c.6174delT BRCA1(672):c.68_69delAG BRCA1(672):p.C61S BRCA1(672):p.M1I

Genes: BRCA1(672) BRCA2(675)

Variants: c.185delAG c.5266dupC c.5946delT c.6174delT c.68_69delAG p.C61S p.M1I

[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: 8

Evidence Type(s): None

Justification: Not enough information in this passage.

Gene→Variant (gene-first): 675:c.7355delA

Genes: 675

Variants: c.7355delA

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

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of specific pathogenic mutations in patients, indicating their association with disease, which supports the use of these variants for classification and diagnosis. Oncogenic: The mention of pathogenic mutations suggests that these variants contribute to tumor development or progression, particularly in the context of BRCA1 and BRCA2 mutations associated with cancer.

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

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

Evidence Type(s): Diagnostic, Oncogenic

Justification: Diagnostic: The passage discusses the presence of specific pathogenic mutations in patients, indicating their association with disease, which supports the use of these variants for classification and diagnosis. Oncogenic: The mention of pathogenic mutations suggests that these variants contribute to tumor development or progression, particularly in the context of BRCA1 and BRCA2 mutations associated with cancer.

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