Cancer driver mutations: predictions and reality
D Ostroverkhova, TM Przytycka… - Trends in Molecular …, 2023 - cell.com
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of
them drive cancer progression, termed driver mutations. Driver mutations may vary between …
them drive cancer progression, termed driver mutations. Driver mutations may vary between …
Genome interpretation using in silico predictors of variant impact
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …
personalized therapeutic opportunities. Clinical associations and laboratory experiments …
Disease variant prediction with deep generative models of evolutionary data
Quantifying the pathogenicity of protein variants in human disease-related genes would
have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of …
have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of …
Proteingym: Large-scale benchmarks for protein fitness prediction and design
Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …
understanding genetic disease to designing novel proteins to address our most pressing …
The landscape of tolerated genetic variation in humans and primates
H Gao, T Hamp, J Ede, JG Schraiber, J McRae… - Science, 2023 - science.org
Personalized genome sequencing has revealed millions of genetic differences between
individuals, but our understanding of their clinical relevance remains largely incomplete. To …
individuals, but our understanding of their clinical relevance remains largely incomplete. To …
dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs
Whole exome sequencing has been increasingly used in human disease studies.
Prioritization based on appropriate functional annotations has been used as an …
Prioritization based on appropriate functional annotations has been used as an …
Updated benchmarking of variant effect predictors using deep mutational scanning
BJ Livesey, JA Marsh - Molecular systems biology, 2023 - embopress.org
The assessment of variant effect predictor (VEP) performance is fraught with biases
introduced by benchmarking against clinical observations. In this study, building on our …
introduced by benchmarking against clinical observations. In this study, building on our …
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations
BJ Livesey, JA Marsh - Molecular systems biology, 2020 - embopress.org
To deal with the huge number of novel protein‐coding variants identified by genome and
exome sequencing studies, many computational variant effect predictors (VEPs) have been …
exome sequencing studies, many computational variant effect predictors (VEPs) have been …
Longitudinal dynamics of clonal hematopoiesis identifies gene-specific fitness effects
NA Robertson, E Latorre-Crespo… - Nature medicine, 2022 - nature.com
Clonal hematopoiesis of indeterminate potential (CHIP) increases rapidly in prevalence
beyond age 60 and has been associated with increased risk for malignancy, heart disease …
beyond age 60 and has been associated with increased risk for malignancy, heart disease …
[HTML][HTML] Analysis of missense variants in the human genome reveals widespread gene-specific clustering and improves prediction of pathogenicity
We used a machine learning approach to analyze the within-gene distribution of missense
variants observed in hereditary conditions and cancer. When applied to 840 genes from the …
variants observed in hereditary conditions and cancer. When applied to 840 genes from the …