The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities, Am J Hum Genet, vol.97, pp.199-215, 2015. ,
Disease-targeted sequencing: a cornerstone in the clinic, Nat Rev Genet, vol.14, pp.295-300, 2013. ,
Evolving health care through personal genomics, Nature Reviews Genetics, vol.18, pp.259-67, 2017. ,
Clinical whole-exome sequencing for the diagnosis of mendelian disorders, N Engl J Med, vol.369, pp.1502-1513, 2013. ,
The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases, Genet Med, vol.14, pp.51-60, 2012. ,
Paediatric genomics: diagnosing rare disease in children, Nature Reviews Genetics, vol.19, pp.253-68, 2018. ,
Guidelines for investigating causality of sequence variants in human disease, Nature, vol.508, pp.469-76, 2014. ,
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, Genetics in Medicine, vol.17, pp.405-428, 2015. ,
ClinVar: public archive of relationships among sequence variation and human phenotype, Nucleic Acids Res, pp.980-985, 2014. ,
Targeted capture and massively parallel sequencing of 12 human exomes, Nature, vol.461, pp.272-278, 2009. ,
Exome sequencing identifies the cause of a mendelian disorder, Nature Genetics, vol.42, pp.30-35, 2010. ,
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data, Nature Reviews Genetics, vol.12, pp.628-668, 2011. ,
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nat Protoc, vol.4, pp.1073-81, 2009. ,
A method and server for predicting damaging missense mutations, Nat Methods, vol.7, pp.248-257, 2010. ,
Identifying Mendelian disease genes with the variant effect scoring tool, BMC Genomics, vol.14, 2013. ,
Performance of mutation pathogenicity prediction methods on missense variants, Hum Mutat, vol.32, pp.358-68, 2011. ,
The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity, Human Mutation, vol.36, pp.513-536, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01246688
Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel, Am J Hum Genet, vol.88, pp.440-449, 2011. ,
A general framework for estimating the relative pathogenicity of human genetic variants, Nat Genet, vol.46, pp.310-315, 2014. ,
Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies, Hum Mol Genet, vol.24, pp.2125-2162, 2015. ,
FATHMM-XF: accurate prediction of pathogenic point mutations via extended features, Bioinformatics, vol.34, pp.511-514, 2018. ,
A spectral approach integrating functional genomic annotations for coding and noncoding variants, Nature Genetics, vol.48, pp.214-234, 2016. ,
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants, Am J Hum Genet, vol.99, pp.877-85, 2016. ,
M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity, Nature Genetics, vol.48, pp.1581-1587, 2016. ,
ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants, The American Journal of Human Genetics, vol.103, pp.474-83, 2018. ,
Predicting the clinical impact of human mutation with deep neural networks, Nature Genetics, vol.50, p.30038395, 2018. ,
Learning binary relations using weighted majority voting, Mach Learn, vol.20, pp.245-71, 1995. ,
Random Forests, Machine Learning, vol.45, pp.5-32, 2001. ,
Logistic Regression, AdaBoost and Bregman Distances, Machine Learning, vol.48, pp.253-85, 2002. ,
Analysis of protein-coding genetic variation in 60,706 humans, Nature, vol.536, pp.285-91, 2016. ,
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes, Genome Res, vol.15, pp.1034-50, 2005. ,
Detection of nonneutral substitution rates on mammalian phylogenies, Genome Res, vol.20, pp.110-131, 2010. ,
Identifying novel constrained elements by exploiting biased substitution patterns, Bioinformatics, vol.25, pp.54-62, 2009. ,
A map of constrained coding regions in the human genome, Nature Genetics, vol.51, p.88, 2019. ,
Regional missense constraint improves variant deleteriousness prediction. preprint. Genomics, 2017. ,
AAindex: amino acid index database, Nucleic Acids Res, vol.28, p.374, 2000. ,
The Ensembl Variant Effect Predictor, Genome Biol, vol.17, p.27268795, 2016. ,
Vcfanno: fast, flexible annotation of genetic variants, Genome Biol, vol.17, p.27250555, 2016. ,
0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs, Hum Mutat, vol.37, pp.235-276, 2016. ,
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine, Hum Genet, vol.133, p.24077912, 2014. ,
DoCM: a database of curated mutations in cancer, Nat Methods, vol.13, pp.806-813, 2016. ,
The UK10K project identifies rare variants in health and disease, Nature, vol.526, pp.82-90, 2015. ,
Cohort Profile: the 'children of the 90s'-the index offspring of the Avon Longitudinal Study of Parents and Children, Int J Epidemiol, vol.42, pp.111-138, 2013. ,
The UK Adult Twin Registry (TwinsUK Resource), Twin Res Hum Genet, vol.16, pp.144-153, 2013. ,
SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population, European Journal of Human Genetics, vol.25, pp.1253-60, 2017. ,
Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics, Sci Rep, vol.8, pp.1-30, 2018. ,
Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa, BMC Genomics, vol.15, p.963, 2014. ,
An integrated map of genetic variation from 1,092 human genomes, Genomes Project Consortium, vol.491, pp.56-65, 2012. ,
Integrated analysis of the large-scale sequencing project "Myocapture" to identify novel genes for myopathies, Neuromuscular Disorders, vol.27, p.195, 2017. ,
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, 2013. ,
From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline, Curr Protoc Bioinformatics, vol.43, pp.11-21, 2013. ,
An Introduction to Statistical Learning, 2013. ,
How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis, BMC Genomics, vol.13, 2012. ,
A new substitution matrix for protein sequence searches based on contact frequencies in protein structures, Protein Eng, vol.6, pp.267-78, 1993. ,