Neoantigens: promising targets for cancer therapy

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DJ Schaid, W Chen, NB Larson - Nature Reviews Genetics, 2018 - nature.com
Advancing from statistical associations of complex traits with genetic markers to
understanding the functional genetic variants that influence traits is often a complex process …

Accurate proteome-wide missense variant effect prediction with AlphaMissense

J Cheng, G Novati, J Pan, C Bycroft, A Žemgulytė… - Science, 2023 - science.org
The vast majority of missense variants observed in the human genome are of unknown
clinical significance. We present AlphaMissense, an adaptation of AlphaFold fine-tuned on …

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 …

Disease variant prediction with deep generative models of evolutionary data

J Frazer, P Notin, M Dias, A Gomez, JK Min, K Brock… - Nature, 2021 - nature.com
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 …

Rare variant associations with plasma protein levels in the UK Biobank

RS Dhindsa, OS Burren, BB Sun, BP Prins, D Matelska… - Nature, 2023 - nature.com
Integrating human genomics and proteomics can help elucidate disease mechanisms,
identify clinical biomarkers and discover drug targets,,–. Because previous proteogenomic …

Language models enable zero-shot prediction of the effects of mutations on protein function

J Meier, R Rao, R Verkuil, J Liu… - Advances in neural …, 2021 - proceedings.neurips.cc
Modeling the effect of sequence variation on function is a fundamental problem for
understanding and designing proteins. Since evolution encodes information about function …

The genomic landscape of pediatric acute lymphoblastic leukemia

SW Brady, KG Roberts, Z Gu, L Shi, S Pounds, D Pei… - Nature …, 2022 - nature.com
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Here, using
whole-genome, exome and transcriptome sequencing of 2,754 childhood patients with ALL …

Rare variant contribution to human disease in 281,104 UK Biobank exomes

Q Wang, RS Dhindsa, K Carss, AR Harper, A Nag… - Nature, 2021 - nature.com
Genome-wide association studies have uncovered thousands of common variants
associated with human disease, but the contribution of rare variants to common disease …