Phenotype-aware prioritisation of rare Mendelian disease variants

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases

(2022) Xiao Yuan et al.   BRIEFINGS IN BIOINFORMATICS

Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics

(2022) Alistair Ward et al.   Journal of Personalized Medicine

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases

(2022) Julius O B Jacobsen et al.   BRIEFINGS IN BIOINFORMATICS

From variant to function in human disease genetics

(2021) Tuuli Lappalainen et al.   SCIENCE

Artificial intelligence (AI)-assisted exome reanalysis greatly aids in the identification of new positive cases and reduces analysis time in a clinical diagnostic laboratory

(2021) Timothy D. O’Brien et al.   GENETICS IN MEDICINE

Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial

(2021) Sarah E. Hunt et al.   HUMAN MUTATION

100,000 Genomes Pilot on Rare-Disease Diagnosis in Health Care — Preliminary Report

(2021) et al.   NEW ENGLAND JOURNAL OF MEDICINE

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

(2021) Francisco M. De La Vega et al.   Genome Medicine

Genomic Data Sharing for Novel Mendelian Disease Gene Discovery: The Matchmaker Exchange

(2020) Danielle R. Azzariti et al.   Annual Review of Genomics and Human Genetics

VarFish: comprehensive DNA variant analysis for diagnostics and research

(2020) Manuel Holtgrewe et al.   NUCLEIC ACIDS RESEARCH

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature

(2020) Johannes Birgmeier et al.   Science Translational Medicine

An Improved Phenotype-Driven Tool for Rare Mendelian Variant Prioritization: Benchmarking Exomiser on Real Patient Whole-Exome Data

(2020) Valentina Cipriani et al.   Genes

Interpretable Clinical Genomics with a Likelihood Ratio Paradigm

(2020) Peter N. Robinson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Diagnostic yield and clinical utility of whole exome sequencing using an automated variant prioritization system, EVIDENCE

(2020) Go Hun Seo et al.   CLINICAL GENETICS

VINYL: Variant prIoritizatioN bY survivaL analysis

(2020) Matteo Chiara et al.   BIOINFORMATICS

The Human Phenotype Ontology in 2021

(2020) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

Rapid and accurate interpretation of clinical exomes using Phenoxome: a computational phenotype-driven approach

(2019) Chao Wu et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis

(2019) Qigang Li et al.   GENETICS IN MEDICINE

DeepPVP: phenotype-based prioritization of causative variants using deep learning

(2019) Imane Boudellioua et al.   BMC BIOINFORMATICS

PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease

(2019) Zixiu Li et al.   BIOINFORMATICS

eDiVA—Classification and prioritization of pathogenic variants for clinical diagnostics

(2019) Mattia Bosio et al.   HUMAN MUTATION

MutationDistiller: user-driven identification of pathogenic DNA variants

(2019) Daniela Hombach et al.   NUCLEIC ACIDS RESEARCH

Doc2Hpo: a web application for efficient and accurate HPO concept curation

(2019) Cong Liu et al.   NUCLEIC ACIDS RESEARCH

VarSight: prioritizing clinically reported variants with binary classification algorithms

(2019) James M. Holt et al.   BMC BIOINFORMATICS

Personalised analytics for rare disease diagnostics

(2019) Denise Anderson et al.   Nature Communications

VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants

(2019) Eddie Ip et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes

(2018) Jung Hoon Son et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases

(2018) Daniel Koile et al.   BMC BIOINFORMATICS

Clinical sequencing: From raw data to diagnosis with lifetime value

(2018) S.M. Caspar et al.   CLINICAL GENETICS

Paediatric genomics: diagnosing rare disease in children

(2018) Caroline F. Wright et al.   NATURE REVIEWS GENETICS

VarAFT: a variant annotation and filtration system for human next generation sequencing data

(2018) Jean-Pierre Desvignes et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis

(2018) Cole A. Deisseroth et al.   GENETICS IN MEDICINE

VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data

(2017) Heiko Müller et al.   NUCLEIC ACIDS RESEARCH

Semantic prioritization of novel causative genomic variants

(2017) Imane Boudellioua et al.   PLoS Computational Biology

VarElect: the phenotype-based variation prioritizer of the GeneCards Suite

(2016) Gil Stelzer et al.   BMC GENOMICS

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

(2016) Regis A. James et al.   Genome Medicine

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency

(2015) William P. Bone et al.   GENETICS IN MEDICINE

wKGGSeq: A Comprehensive Strategy-Based and Disease-Targeted Online Framework to Facilitate Exome Sequencing Studies of Inherited Disorders

(2015) Mulin Jun Li et al.   HUMAN MUTATION

The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery

(2015) Anthony A. Philippakis et al.   HUMAN MUTATION

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

Next-generation diagnostics and disease-gene discovery with the Exomiser

(2015) Damian Smedley et al.   Nature Protocols

Phevor Combines Multiple Biomedical Ontologies for Accurate Identification of Disease-Causing Alleles in Single Individuals and Small Nuclear Families

(2014) Marc V. Singleton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Jannovar: A Java Library for Exome Annotation

(2014) Marten Jäger et al.   HUMAN MUTATION

Phen-Gen: combining phenotype and genotype to analyze rare disorders

(2014) Asif Javed et al.   NATURE METHODS

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies

(2014) Alejandro Alemán et al.   NUCLEIC ACIDS RESEARCH

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

(2014) T. Zemojtel et al.   Science Translational Medicine

Improved exome prioritization of disease genes through cross-species phenotype comparison

(2013) P. N. Robinson et al.   GENOME RESEARCH

PhenoDB: A New Web-Based Tool for the Collection, Storage, and Analysis of Phenotypic Features

(2013) Ada Hamosh et al.   HUMAN MUTATION

PhenoTips: Patient Phenotyping Software for Clinical and Research Use

(2013) Marta Girdea et al.   HUMAN MUTATION

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS