Author: sciencedock


[PMID: 28977528] [Nucleic Acids Research]

MAPPIN: a method for annotating, predicting pathogenicity and mode of inheritance for nonsynonymous variants

“a prediction method which utilizes a random forest algorithm to distinguish between nsSNVs with dominant, recessive, and benign effects.” “MAPPIN outperforms CADD and Eigen in predicting disease inheritance modes for all validation datasets. “


Bi-allelic Variants and HRD

[PMID: 29021619] [Nature Communications]

Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes

“over 5% of all cancers harbor bi-allelic pathogenic mutations in HR-related genes” “bi-allelic alterations in HR DNA repair-related genes occur across cancer types, are mutually exclusive, and are associated with genomics features consistent with lack of competent HR DNA repair” mono-allelic alterations are not associated with HDR.

De Novo Pathway-based Tumor Subtyping

[PMID: 28934488] [Nucleic Acids Research]

De novo pathway-based biomarker identification

“prediction models built upon single-gene (SG) features show poor stability and performance on independent datasets. Attempts to mitigate these drawbacks have led to the development of network-based approaches that integrate pathway information to produce meta-gene (MG) features. ” “a novel MG approach based on de novo pathways, which for the first time have been used as features in a multi-class setting to predict cancer subtypes”