The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation …

PD Stenson, M Mort, EV Ball, K Evans, M Hayden… - Human genetics, 2017 - Springer
Abstract The Human Gene Mutation Database (HGMD®) constitutes a comprehensive
collection of published germline mutations in nuclear genes that underlie, or are closely …

Advances and challenges in targeting FGFR signalling in cancer

IS Babina, NC Turner - Nature Reviews Cancer, 2017 - nature.com
Fibroblast growth factors (FGFs) and their receptors (FGFRs) regulate numerous cellular
processes. Deregulation of FGFR signalling is observed in a subset of many cancers …

Proteingym: Large-scale benchmarks for protein fitness prediction and design

P Notin, A Kollasch, D Ritter… - Advances in …, 2023 - proceedings.neurips.cc
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 …

Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria

V Pejaver, AB Byrne, BJ Feng, KA Pagel… - The American Journal of …, 2022 - cell.com
Summary Recommendations from the American College of Medical Genetics and Genomics
and the Association for Molecular Pathology (ACMG/AMP) for interpreting sequence variants …

Learning protein fitness models from evolutionary and assay-labeled data

C Hsu, H Nisonoff, C Fannjiang, J Listgarten - Nature biotechnology, 2022 - nature.com
Abstract Machine learning-based models of protein fitness typically learn from either
unlabeled, evolutionarily related sequences or variant sequences with experimentally …

Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer

M Wong, C Mayoh, LMS Lau, DA Khuong-Quang… - Nature medicine, 2020 - nature.com
Abstract The Zero Childhood Cancer Program is a precision medicine program to benefit
children with poor-outcome, rare, relapsed or refractory cancer. Using tumor and germline …

dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

X Liu, C Li, C Mou, Y Dong, Y Tu - Genome medicine, 2020 - Springer
Whole exome sequencing has been increasingly used in human disease studies.
Prioritization based on appropriate functional annotations has been used as an …

Association analysis identifies 65 new breast cancer risk loci

K Michailidou, S Lindström, J Dennis, J Beesley, S Hui… - Nature, 2017 - nature.com
Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as
BRCA1, and many common, mostly non-coding variants. However, much of the genetic …

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

K Yizhak, F Aguet, J Kim, JM Hess, K Kübler, J Grimsby… - Science, 2019 - science.org
INTRODUCTION Cancer genome studies have contributed to the analysis and discovery of
somatic mutations that drive cancer growth. However, studying the genetic makeup of a …

REVEL: an ensemble method for predicting the pathogenicity of rare missense variants

NM Ioannidis, JH Rothstein, V Pejaver… - The American Journal of …, 2016 - cell.com
The vast majority of coding variants are rare, and assessment of the contribution of rare
variants to complex traits is hampered by low statistical power and limited functional data …