Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations

Identification of two novel TPK1 gene mutations in a Chinese patient with thiamine pyrophosphokinase deficiency undergoing whole exome sequencing

(2019) Lina Zhu et al.   JOURNAL OF PEDIATRIC ENDOCRINOLOGY & METABOLISM

The role of protein complexes in human genetic disease

(2019) L. Therese Bergendahl et al.   PROTEIN SCIENCE

Recurrent heterozygous PAX6 missense variants cause severe bilateral microphthalmia via predictable effects on DNA–protein interaction

(2019) Kathleen A. Williamson et al.   GENETICS IN MEDICINE

A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships

(2018) Taylor L. Mighell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Calmodulin Mutations Associated with Congenital Cardiac Disease Display Novel Biophysical and Biochemical Characteristics

(2018) Michail Nomikos et al.   BIOPHYSICAL JOURNAL

Multiplex assessment of protein variant abundance by massively parallel sequencing

(2018) Kenneth A. Matreyek et al.   NATURE GENETICS

Differential strengths of molecular determinants guide environment specific mutational fates

(2018) Rohan Dandage et al.   PLoS Genetics

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data

(2018) Vanessa E. Gray et al.   Cell Systems

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

(2018) Juhye M. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Representativeness of variation benchmark datasets

(2018) Gerard C. P. Schaafsma et al.   BMC BIOINFORMATICS

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Human Calmodulin Mutations

(2018) Helene H. Jensen et al.   Frontiers in Molecular Neuroscience

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4

(2017) Qifang Xu et al.   HUMAN MUTATION

Reports from CAGI: The Critical Assessment of Genome Interpretation

(2017) Roger A Hoskins et al.   HUMAN MUTATION

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI

(2017) Marco Carraro et al.   HUMAN MUTATION

A framework for exhaustively mapping functional missense variants

(2017) Jochen Weile et al.   Molecular Systems Biology

DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins

(2017) Daniele Raimondi et al.   NUCLEIC ACIDS RESEARCH

Deconstruction of the Ras switching cycle through saturation mutagenesis

(2017) Pradeep Bandaru et al.   eLife

A Restricted Repertoire of De Novo Mutations in ITPR1 Cause Gillespie Syndrome with Evidence for Dominant-Negative Effect

(2016) Meriel McEntagart et al.   AMERICAN JOURNAL OF HUMAN GENETICS

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex

(2016) Daniel T. Harris et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

(2016) Michael Doud et al.   Viruses-Basel

Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture

(2016) Hugh K. Haddox et al.   PLoS Pathogens

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

(2015) Dominik G. Grimm et al.   HUMAN MUTATION

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

(2015) Nicholas C. Wu et al.   PLoS Genetics

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features

(2014) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expanding the clinical and molecular spectrum of thiamine pyrophosphokinase deficiency: A treatable neurological disorder caused by TPK1 mutations

(2014) Siddharth Banka et al.   MOLECULAR GENETICS AND METABOLISM

Large-scale discovery of novel genetic causes of developmental disorders

(2014) T. W. Fitzgerald et al.   NATURE

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

OMICtools: an informative directory for multi-omic data analysis

(2014) V. J. Henry et al.   Database-The Journal of Biological Databases and Curation

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation

(2013) Emidio Capriotti et al.   BMC GENOMICS

Calmodulin Mutations Associated With Recurrent Cardiac Arrest in Infants

(2013) Lia Crotti et al.   CIRCULATION

De novo mutations in epileptic encephalopathies

(2013) et al.   NATURE

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Deep Sequencing of Systematic Combinatorial Libraries Reveals β-Lactamase Sequence Constraints at High Resolution

(2012) Zhifeng Deng et al.   JOURNAL OF MOLECULAR BIOLOGY

Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study

(2012) Anita Rauch et al.   LANCET

Patterns and rates of exonic de novo mutations in autism spectrum disorders

(2012) Benjamin M. Neale et al.   NATURE

Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability

(2012) Joep de Ligt et al.   NEW ENGLAND JOURNAL OF MEDICINE

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Protein Model Discrimination Using Mutational Sensitivity Derived from Deep Sequencing

(2012) Bharat V. Adkar et al.   STRUCTURE

Improving the prediction of disease-related variants using protein three-dimensional structure

(2011) Emidio Capriotti et al.   BMC BIOINFORMATICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS