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

MVP predicts the pathogenicity of missense variants by deep learning

(2021) Hongjian Qi et al.   Nature Communications

Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

(2021) Daniel Taliun et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

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

Whole-genome sequencing of patients with rare diseases in a national health system

(2020) Ernest Turro et al.   NATURE

Partially automated whole-genome sequencing reanalysis of previously undiagnosed pediatric patients can efficiently yield new diagnoses

(2020) Kiely N. James et al.   npj Genomic Medicine

Exome sequencing and characterization of 49,960 individuals in the UK Biobank

(2020) Cristopher V. Van Hout et al.   NATURE

A state-based approach to genomics for rare disease and population screening

(2020) Kelly M. East et al.   GENETICS IN MEDICINE

Spatially clustering de novo variants in CYFIP2, encoding the cytoplasmic FMRP interacting protein 2, cause intellectual disability and seizures

(2019) Markus Zweier et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation

(2019) Michelle M. Clark et al.   Science Translational Medicine

Partial loss of USP9X function leads to a male neurodevelopmental and behavioural disorder converging on TGFβ signalling

(2019) Brett V. Johnson et al.   BIOLOGICAL PSYCHIATRY

Two additional males with X-linked, syndromic mental retardation carry de novo mutations in HNRNPH2

(2019) Wayne M. Jepsen et al.   CLINICAL GENETICS

Reanalysis of Clinical Exome Sequencing Data

(2019) Pengfei Liu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mendelian Gene Discovery: Fast and Furious with No End in Sight

(2019) Michael J. Bamshad et al.   AMERICAN JOURNAL OF HUMAN GENETICS

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature

(2019) Johannes Birgmeier et al.   GENETICS IN MEDICINE

Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation

(2019) Thomas A Sasani et al.   eLife

A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants

(2019) Stephen F. Kingsmore et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A missense mutation in the catalytic domain of O ‐GlcNAc transferase links perturbations in protein O ‐GlcNAcylation to X‐linked intellectual disability

(2019) Veronica M. Pravata et al.   FEBS LETTERS

Artificial intelligence in clinical and genomic diagnostics

(2019) Raquel Dias et al.   Genome Medicine

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

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

Mutations inSRP54gene cause severe congenital neutropenia as well as Shwachman-Diamond-like syndrome

(2018) Christine Bellanné-Chantelot et al.   BLOOD

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

(2018) Steven Flygare et al.   BMC BIOINFORMATICS

Genomic sequencing identifies secondary findings in a cohort of parent study participants

(2018) Michelle L Thompson et al.   GENETICS IN MEDICINE

Rapid whole-genome sequencing decreases infant morbidity and cost of hospitalization

(2018) Lauge Farnaes et al.   npj Genomic Medicine

Meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases

(2018) Michelle M. Clark et al.   npj Genomic Medicine

The Clinical Sequencing Evidence-Generating Research Consortium: Integrating Genomic Sequencing in Diverse and Medically Underserved Populations

(2018) Laura M. Amendola et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Compound heterozygous mutations in IL10RA combined with a complement factor properdin mutation in infantile-onset inflammatory bowel disease

(2018) Eun Suk Jung et al.   EUROPEAN JOURNAL OF GASTROENTEROLOGY & HEPATOLOGY

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

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

Clinical Decision Support in the Era of Artificial Intelligence

(2018) Edward H. Shortliffe et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Automated Clinical Exome Reanalysis Reveals Novel Diagnoses

(2018) Samuel W. Baker et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

High-performance medicine: the convergence of human and artificial intelligence

(2018) Eric J. Topol   NATURE MEDICINE

Mutations in signal recognition particle SRP54 cause syndromic neutropenia with Shwachman-Diamond–like features

(2017) Raphael Carapito et al.   JOURNAL OF CLINICAL INVESTIGATION

Settling the score: variant prioritization and Mendelian disease

(2017) Karen Eilbeck et al.   NATURE REVIEWS GENETICS

Compelling Reasons for Repairing Human Germlines

(2017) George Church   NEW ENGLAND JOURNAL OF MEDICINE

Genomic diagnosis for children with intellectual disability and/or developmental delay

(2017) Kevin M. Bowling et al.   Genome Medicine

Novel autosomal dominant TNNT1 mutation causing nemaline myopathy

(2017) Chamindra G. Konersman et al.   Molecular Genetics & Genomic Medicine

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants

(2016) Nilah M. Ioannidis et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers

(2016) Aaron M. Wenger et al.   GENETICS IN MEDICINE

The Geisinger MyCode community health initiative: an electronic health record–linked biobank for precision medicine research

(2016) David J. Carey et al.   GENETICS IN MEDICINE

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

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

(2015) Tudor Groza et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond

(2015) Sungmin Lee et al.   BRIEFINGS IN BIOINFORMATICS

Congenital secretory diarrhoea caused by activating germline mutations inGUCY2C

(2015) Thomas Müller et al.   GUT

Reduced sodium/proton exchanger NHE3 activity causes congenital sodium diarrhea

(2015) Andreas R. Janecke et al.   HUMAN MOLECULAR GENETICS

Leiomodin-3 dysfunction results in thin filament disorganization and nemaline myopathy

(2015) Michaela Yuen et al.   JOURNAL OF CLINICAL INVESTIGATION

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases

(2015) Hui Yang et al.   NATURE METHODS

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

(2015) Damian Smedley et al.   Nature Protocols

ClinVar: public archive of interpretations of clinically relevant variants

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

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

Early-onset Crohn’s disease and autoimmunity associated with a variant in CTLA-4

(2014) Sebastian Zeissig et al.   GUT

XIAP variants in male Crohn's disease

(2014) Yvonne Zeissig et al.   GUT

Mutation Update: The Spectra of Nebulin Variants and Associated Myopathies

(2014) Vilma-Lotta Lehtokari et al.   HUMAN MUTATION

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

A framework for the interpretation of de novo mutation in human disease

(2014) Kaitlin E Samocha et al.   NATURE GENETICS

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

(2014) Desirée Schubert et al.   NATURE MEDICINE

Mutations in KLHL40 Are a Frequent Cause of Severe Autosomal-Recessive Nemaline Myopathy

(2013) Gianina Ravenscroft et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

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

Method of the Year 2013

(2013)   NATURE METHODS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders

(2012) G. J. Swaminathan et al.   HUMAN MOLECULAR GENETICS

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

(2012)   NATURE

Loss-of-function mutations in HINT1 cause axonal neuropathy with neuromyotonia

(2012) Magdalena Zimoń et al.   NATURE GENETICS

A probabilistic disease-gene finder for personal genomes

(2011) M. Yandell et al.   GENOME RESEARCH

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

A copy number variation morbidity map of developmental delay

(2011) Gregory M Cooper et al.   NATURE GENETICS

Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

(2010) David T. Miller et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Mutations and polymorphisms of the skeletal muscle α-actin gene (ACTA1)

(2009) Nigel G. Laing et al.   HUMAN MUTATION