Applications of artificial intelligence in clinical laboratory genomics

Finding the sweet spot: a qualitative study exploring patients’ acceptability of chatbots in genetic service delivery

(2023) Stephanie Luca et al.   HUMAN GENETICS

Improving variant calling using population data and deep learning

(2023) Nae-Chyun Chen et al.   BMC BIOINFORMATICS

Generation and multi-dimensional profiling of a childhood cancer cell line atlas defines new therapeutic opportunities

(2023) Claire Xin Sun et al.   CANCER CELL

Evaluation of an automated genome interpretation model for rare disease routinely used in a clinical genetic laboratory

(2023) Linyan Meng et al.   GENETICS IN MEDICINE

Germline Genetic Testing After Cancer Diagnosis

(2023) Allison W. Kurian et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

A draft human pangenome reference

(2023) Wen-Wei Liao et al.   NATURE

Cue: a deep-learning framework for structural variant discovery and genotyping

(2023) Victoria Popic et al.   NATURE METHODS

Variant calling and benchmarking in an era of complete human genome sequences

(2023) Nathan D. Olson et al.   NATURE REVIEWS GENETICS

Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland

(2023) Caroline F. Wright et al.   NEW ENGLAND JOURNAL OF MEDICINE

The landscape of tolerated genetic variation in humans and primates

(2023) Hong Gao et al.   SCIENCE

Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning

(2023) Bennet Peterson et al.   Genome Medicine

Comparing Physician and Artificial Intelligence Chatbot Responses to Patient Questions Posted to a Public Social Media Forum

(2023) John W. Ayers et al.   JAMA Internal Medicine

Comprehensive transcriptomic analysis to identify biological and clinical differences in cholangiocarcinoma

(2023) Marco Silvestri et al.   Cancer Medicine

An Open Dataset of Annotated Metaphase Cell Images for Chromosome Identification

(2023) Jenn-Jhy Tseng et al.   Scientific Data

The Impact of Artificial Intelligence in the Odyssey of Rare Diseases

(2023) Anna Visibelli et al.   Biomedicines

PhenomeCentral: 7 years of rare disease matchmaking

(2022) Matthew Osmond et al.   HUMAN MUTATION

GestaltMatcher facilitates rare disease matching using facial phenotype descriptors

(2022) Tzung-Chien Hsieh et al.   NATURE GENETICS

AI in health and medicine

(2022) Pranav Rajpurkar et al.   NATURE MEDICINE

Is there a way to reduce the inequity in variant interpretation on the basis of ancestry?

(2022) Paul S. Appelbaum et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Scoping review and classification of deep learning in medical genetics

(2022) Suzanna E. Ledgister Hanchard et al.   GENETICS IN MEDICINE

Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking

(2022) Kym M. Boycott et al.   HUMAN MUTATION

Use of a chatbot to increase uptake of cascade genetic testing

(2022) Tara Schmidlen et al.   Journal of Genetic Counseling

The Human Pangenome Project: a global resource to map genomic diversity

(2022) Ting Wang et al.   NATURE

Polishing copy number variant calls on exome sequencing data via deep learning

(2022) Furkan Özden et al.   GENOME RESEARCH

An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases

(2022) Mallory J. Owen et al.   Nature Communications

Assessing the clinical utility of protein structural analysis in genomic variant classification: experiences from a diagnostic laboratory

(2022) Richard C. Caswell et al.   Genome Medicine

ChromoEnhancer: An Artificial-Intelligence-Based Tool to Enhance Neoplastic Karyograms as an Aid for Effective Analysis

(2022) Yahya Bokhari et al.   Cells

Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma

(2022) Almudena Espín-Pérez et al.   npj Precision Oncology

A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases

(2022) Stephen F. Kingsmore et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Using deep learning and electronic health records to detect Noonan syndrome in pediatric patients

(2022) Zeyu Yang et al.   GENETICS IN MEDICINE

SVision: a deep learning approach to resolve complex structural variants

(2022) Jiadong Lin et al.   NATURE METHODS

Calibration of computational tools for missense variant pathogenicity classification and ClinGen recommendations for PP3/BP4 criteria

(2022) Vikas Pejaver et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Integrative analysis of multi-omics data for liquid biopsy

(2022) Geng Chen et al.   BRITISH JOURNAL OF CANCER

A Systematic Method for Detecting Abnormal mRNA Splicing and Assessing Its Clinical Impact in Individuals Undergoing Genetic Testing for Hereditary Cancer Syndromes

(2022) Nick Kamps-Hughes et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Insights on variant analysis in silico tools for pathogenicity prediction

(2022) Felipe Antonio de Oliveira Garcia et al.   Frontiers in Genetics

PhenoTagger: A Hybrid Method for Phenotype Concept Recognition using Human Phenotype Ontology

(2021) Ling Luo et al.   BIOINFORMATICS

Artificial intelligence and pathology: From principles to practice and future applications in histomorphology and molecular profiling

(2021) Albrecht Stenzinger et al.   SEMINARS IN CANCER BIOLOGY

One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation

(2021) Stephen E. Lincoln et al.   GENETICS IN MEDICINE

Artificial intelligence–assisted phenotype discovery of fragile X syndrome in a population-based sample

(2021) Arezoo Movaghar et al.   GENETICS IN MEDICINE

The Role of Electronic Health Records in Advancing Genomic Medicine

(2021) Jodell E. Linder et al.   Annual Review of Genomics and Human Genetics

Artificial intelligence in early drug discovery enabling precision medicine

(2021) Fabio Boniolo et al.   Expert Opinion on Drug Discovery

Racial and ethnic disparities in diagnostic efficacy of comprehensive genetic testing for sensorineural hearing loss

(2021) Michelle M. Florentine et al.   HUMAN GENETICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

How artificial intelligence might disrupt diagnostics in hematology in the near future

(2021) Wencke Walter et al.   ONCOGENE

Can artificial intelligence save medical genetics?

(2021) Benjamin D. Solomon   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

PheneBank: a literature-based database of phenotypes

(2021) Mohammad Taher Pilehvar et al.   BIOINFORMATICS

Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms

(2021) Andrew Cox et al.   BIOINFORMATICS

Knowledge-based approaches to drug discovery for rare diseases

(2021) Vinicius M. Alves et al.   DRUG DISCOVERY TODAY

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

Patient Interactions With an Automated Conversational Agent Delivering Pretest Genetics Education: Descriptive Study

(2021) Daniel Chavez-Yenter et al.   JOURNAL OF MEDICAL INTERNET RESEARCH

Disease variant prediction with deep generative models of evolutionary data

(2021) Jonathan Frazer et al.   NATURE

Hereditary Cancer Risk Using a Genetic Chatbot Before Routine Care Visits

(2021) Shivani Nazareth et al.   OBSTETRICS AND GYNECOLOGY

Ask Rosa – The making of a digital genetic conversation tool, a chatbot, about hereditary breast and ovarian cancer

(2021) Elen Siglen et al.   PATIENT EDUCATION AND COUNSELING

Artificial intelligence in the embryology laboratory: a review

(2021) Irene Dimitriadis et al.   REPRODUCTIVE BIOMEDICINE ONLINE

Classification of fluorescent R-Band metaphase chromosomes using a convolutional neural network is precise and fast in generating karyograms of hematologic neoplastic cells

(2021) Beate Vajen et al.   Cancer Genetics

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

Virtual genetic diagnosis for familial hypercholesterolemia powered by machine learning

(2020) Ana Pina et al.   European Journal of Preventive Cardiology

Clinical versus automated assessments of morphological variants in twins with and without neurodevelopmental disorders

(2020) Lynnea Myers et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

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

(2020) Konrad J. Karczewski et al.   NATURE

Reaching the End-Game for GWAS: Machine Learning Approaches for the Prioritization of Complex Disease Loci

(2020) Hannah L. Nicholls et al.   Frontiers in Genetics

Democratizing genomics: Leveraging software to make genetics an integral part of routine care

(2020) Moran Snir et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

An online compendium of treatable genetic disorders

(2020) David Bick et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Chatbots & artificial intelligence to scale genetic information delivery

(2020) Shivani Nazareth et al.   Journal of Genetic Counseling

The Human Phenotype Ontology in 2021

(2020) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing–Detected Variants with an Orthogonal Method in Clinical Genetic Testing

(2019) Stephen E. Lincoln et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

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

(2019) Johannes Birgmeier et al.   GENETICS IN MEDICINE

Patient assessment of chatbots for the scalable delivery of genetic counseling

(2019) Tara Schmidlen et al.   Journal of Genetic Counseling

The Impact of Genetic Variants on PTEN Molecular Functions and Cellular Phenotypes

(2019) Nicholas Hasle et al.   Cold Spring Harbor Perspectives in Medicine

A Deep Learning Approach for Detecting Copy Number Variation in Next-Generation Sequencing Data

(2019) Tom Hill et al.   G3-Genes Genomes Genetics

The DisGeNET knowledge platform for disease genomics: 2019 update

(2019) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

(2019) Kent A Shefchek et al.   NUCLEIC ACIDS RESEARCH

Improving Copy Number Variant Detection from Sequencing Data with a Combination of Programs and a Predictive Model

(2019) Salla Välipakka et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

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

Prevalence and properties of intragenic copy-number variation in Mendelian disease genes

(2018) Rebecca Truty et al.   GENETICS IN MEDICINE

Biomedical informatics and machine learning for clinical genomics

(2018) James A Diao et al.   HUMAN MOLECULAR GENETICS

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Mutational processes shape the landscape of TP53 mutations in human cancer

(2018) Andrew O. Giacomelli et al.   NATURE GENETICS

Identifying facial phenotypes of genetic disorders using deep learning

(2018) Yaron Gurovich et al.   NATURE MEDICINE

Genomic and Phenomic Research in the 21st Century

(2018) Scott Hebbring   TRENDS IN GENETICS

Artificial intelligence in healthcare

(2018) Kun-Hsing Yu et al.   Nature Biomedical Engineering

Rules and tools to predict the splicing effects of exonic and intronic mutations

(2017) Kinji Ohno et al.   Wiley Interdisciplinary Reviews-RNA

Rapid identification of familial hypercholesterolemia from electronic health records: The SEARCH study

(2016) Maya S. Safarova et al.   Journal of Clinical Lipidology

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

(2015) Sue Richards et al.   GENETICS IN MEDICINE

GenomeConnect: Matchmaking Between Patients, Clinical Laboratories, and Researchers to Improve Genomic Knowledge

(2015) Brianne E. Kirkpatrick et al.   HUMAN MUTATION

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

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

In silico tools for splicing defect prediction: a survey from the viewpoint of end users

(2013) Xueqiu Jian et al.   GENETICS IN MEDICINE

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

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

FindZebra: A search engine for rare diseases

(2013) Radu Dragusin et al.   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

Complex effects of nucleotide variants in a mammalian cis-regulatory element

(2012) J. C. Kwasnieski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo 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

The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease

(2008) Peter N. Robinson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes

(2008) Elliott H. Margulies et al.   NATURE REVIEWS GENETICS