Challenging popular tools for the annotation of genetic variations with a real case, pathogenic mutations of lysosomal alpha-galactosidase

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

SDM: a server for predicting effects of mutations on protein stability

(2017) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

Ten quick tips for machine learning in computational biology

(2017) Davide Chicco   BioData Mining

In Vitro Enzyme Measurement to Test Pharmacological Chaperone Responsiveness in Fabry and Pompe Disease

(2017) Jan Lukas et al.   Jove-Journal of Visualized Experiments

The validation of pharmacogenetics for the identification of Fabry patients to be treated with migalastat

(2016) Elfrida R. Benjamin et al.   GENETICS IN MEDICINE

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

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity

(2016) Karthik A Jagadeesh et al.   NATURE GENETICS

Treatment of Fabry’s Disease with the Pharmacologic Chaperone Migalastat

(2016) Dominique P. Germain et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification of an Allosteric Binding Site on Human Lysosomal Alpha-Galactosidase Opens the Way to New Pharmacological Chaperones for Fabry Disease

(2016) Valentina Citro et al.   PLoS One

Taming molecular flexibility to tackle rare diseases

(2015) Maria Vittoria Cubellis et al.   BIOCHIMIE

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

X-chromosome inactivation in female patients with Fabry disease

(2015) L. Echevarria et al.   CLINICAL GENETICS

Functional and Clinical Consequences of Novel α-Galactosidase A Mutations in Fabry Disease

(2015) Jan Lukas et al.   HUMAN MUTATION

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Drug repositioning can accelerate discovery of pharmacological chaperones

(2015) Bruno Hay Mele et al.   Orphanet Journal of Rare Diseases

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

(2015) Qiongshi Lu et al.   Scientific Reports

Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

(2015) C. Dong et al.   HUMAN MOLECULAR GENETICS

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

A thermodynamic assay to test pharmacological chaperones for Fabry disease

(2013) Giuseppina Andreotti et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

(2013) Hannah Carter et al.   BMC GENOMICS

A Phase 2 study of migalastat hydrochloride in females with Fabry disease: Selection of population, safety and pharmacodynamic effects

(2013) R. Giugliani et al.   MOLECULAR GENETICS AND METABOLISM

Fabry_CEP: a tool to identify Fabry mutations responsive to pharmacological chaperones

(2013) Marco Cammisa et al.   Orphanet Journal of Rare Diseases

Long term enzyme replacement therapy for Fabry disease: effectiveness on kidney, heart and brain

(2013) Saskia M Rombach et al.   Orphanet Journal of Rare Diseases

Functional Characterisation of Alpha-Galactosidase A Mutations as a Basis for a New Classification System in Fabry Disease

(2013) Jan Lukas et al.   PLoS Genetics

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

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

wANNOVAR: annotating genetic variants for personal genomes via the web

(2012) Xiao Chang et al.   JOURNAL OF MEDICAL GENETICS

Agalsidase Benefits Renal Histology in Young Patients with Fabry Disease

(2012) C. Tondel et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

The Molecular Basis of Pharmacological Chaperoning in Human α-Galactosidase

(2011) Abigail I. Guce et al.   CHEMISTRY & BIOLOGY

A pharmacogenetic approach to identify mutant forms of α-galactosidase a that respond to a pharmacological chaperone for Fabry disease

(2011) Xiaoyang Wu et al.   HUMAN MUTATION

Fabry-database.org: database of the clinical phenotypes, genotypes and mutant α-galactosidase A structures in Fabry disease

(2011) Seiji Saito et al.   JOURNAL OF HUMAN GENETICS

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Therapy of Fabry disease with pharmacological chaperones: from in silico predictions to in vitro tests

(2011) Giuseppina Andreotti et al.   Orphanet Journal of Rare Diseases

Prediction of the clinical phenotype of Fabry disease based on protein sequential and structural information

(2010) Seiji Saito et al.   JOURNAL OF HUMAN GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Single-nucleotide evolutionary constraint scores highlight disease-causing mutations

(2010) Gregory M Cooper et al.   NATURE METHODS

Prediction of the responsiveness to pharmacological chaperones: lysosomal human alpha-galactosidase, a case of study

(2010) Giuseppina Andreotti et al.   Orphanet Journal of Rare Diseases

Fabry disease

(2010) Dominique P Germain   Orphanet Journal of Rare Diseases

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

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

Effects of pH and Iminosugar Pharmacological Chaperones on Lysosomal Glycosidase Structure and Stability

(2009) Raquel L. Lieberman et al.   BIOCHEMISTRY

Functional studies of new GLA gene mutations leading to conformational fabry disease

(2009) C. Filoni et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Effects of a chemical chaperone on genetic mutations in α-galactosidase A in Korean patients with Fabry disease

(2009) Jung-Young Park et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Identification of deleterious mutations within three human genomes

(2009) S. Chun et al.   GENOME RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Catalytic Mechanism of Human α-Galactosidase

(2009) Abigail I. Guce et al.   JOURNAL OF BIOLOGICAL CHEMISTRY