Host genetics and infectious disease: new tools, insights and translational opportunities

Next-generation drug repurposing using human genetics and network biology

(2020) Serguei Nabirotchkin et al.   CURRENT OPINION IN PHARMACOLOGY

Human Inborn Errors of Immunity: 2019 Update of the IUIS Phenotypical Classification

(2020) Aziz Bousfiha et al.   JOURNAL OF CLINICAL IMMUNOLOGY

A brief history of human disease genetics

(2020) Melina Claussnitzer et al.   NATURE

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

A Novel Coronavirus from Patients with Pneumonia in China, 2019

(2020) Na Zhu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Advances in the Evolutionary Understanding of MHC Polymorphism

(2020) Jacek Radwan et al.   TRENDS IN GENETICS

Genetic risk for dengue hemorrhagic fever and dengue fever in multiple ancestries

(2020) Guillaume Pare et al.   EBioMedicine

Lethal Infectious Diseases as Inborn Errors of Immunity: Toward a Synthesis of the Germ and Genetic Theories

(2020) Jean-Laurent Casanova et al.   Annual Review of Pathology-Mechanisms of Disease

A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection

(2020) Jean-Laurent Casanova et al.   CELL

The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic

(2020)   EUROPEAN JOURNAL OF HUMAN GENETICS

Human leukocyte antigen susceptibility map for SARS-CoV-2

(2020) Austin Nguyen et al.   JOURNAL OF VIROLOGY

Viral and host factors related to the clinical outcome of COVID-19

(2020) Xiaonan Zhang et al.   NATURE

Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study

(2020) Annemarie B Docherty et al.   BMJ-British Medical Journal

Dexamethasone in Hospitalized Patients with Covid-19 — Preliminary Report

(2020)   NEW ENGLAND JOURNAL OF MEDICINE

Genomewide Association Study of Severe Covid-19 with Respiratory Failure

(2020) David Ellinghaus et al.   NEW ENGLAND JOURNAL OF MEDICINE

The major genetic risk factor for severe COVID-19 is inherited from Neanderthals

(2020) Hugo Zeberg et al.   NATURE

Inborn errors of type I IFN immunity in patients with life-threatening COVID-19

(2020) Qian Zhang et al.   SCIENCE

Autoantibodies against type I IFNs in patients with life-threatening COVID-19

(2020) Paul Bastard et al.   SCIENCE

Dual RNA-Seq of Human Leprosy Lesions Identifies Bacterial Determinants Linked to Host Immune Response

(2019) Dennis J. Montoya et al.   Cell Reports

Ataxia‐telangiectasia: A review of clinical features and molecular pathology

(2019) Parisa Amirifar et al.   PEDIATRIC ALLERGY AND IMMUNOLOGY

PheWAS uncovers a pathological role of coagulation Factor X during Acinetobacter baumannii infection

(2019) Jacob E. Choby et al.   INFECTION AND IMMUNITY

Human Immunology through the Lens of Evolutionary Genetics

(2019) Lluis Quintana-Murci   CELL

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

Defining the genetic and evolutionary architecture of alternative splicing in response to infection

(2019) Maxime Rotival et al.   Nature Communications

Severe influenza pneumonitis in children with inherited TLR3 deficiency

(2019) Hye Kyung Lim et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Inherited IFNAR1 deficiency in otherwise healthy patients with adverse reaction to measles and yellow fever live vaccines

(2019) Nicholas Hernandez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Association Between Single-Nucleotide Polymorphisms in HLA Alleles and Human Immunodeficiency Virus Type 1 Viral Load in Demographically Diverse, Antiretroviral Therapy–Naive Participants From the Strategic Timing of AntiRetroviral Treatment Trial

(2019) Christina Ekenberg et al.   JOURNAL OF INFECTIOUS DISEASES

Genetic analyses of diverse populations improves discovery for complex traits

(2019) Genevieve L. Wojcik et al.   NATURE

Exome sequencing of Finnish isolates enhances rare-variant association power

(2019) Adam E. Locke et al.   NATURE

A genetics-led approach defines the drug target landscape of 30 immune-related traits

(2019) Hai Fang et al.   NATURE GENETICS

CCR5AS lncRNA variation differentially regulates CCR5, influencing HIV disease outcome

(2019) Smita Kulkarni et al.   NATURE IMMUNOLOGY

Mapping the drivers of within-host pathogen evolution using massive data sets

(2019) Duncan S. Palmer et al.   Nature Communications

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

(2019) John A. Lees et al.   Nature Communications

Common Genetic Variations Associated with the Persistence of Immunity following Childhood Immunization

(2019) Daniel O’Connor et al.   Cell Reports

Solving the missing heritability problem

(2019) Alexander I. Young   PLoS Genetics

Coagulation factors VII, IX and X are effective antibacterial proteins against drug-resistant Gram-negative bacteria

(2019) Jinwu Chen et al.   CELL RESEARCH

Analysis of the B cell receptor repertoire in six immune-mediated diseases

(2019) R. J. M. Bashford-Rogers et al.   NATURE

Major subpopulations of Plasmodium falciparum in sub-Saharan Africa

(2019) Alfred Amambua-Ngwa et al.   SCIENCE

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

(2019) Virginia M. Howick et al.   SCIENCE

Genetics of leprosy: today and beyond

(2019) Vinicius M. Fava et al.   HUMAN GENETICS

Complement deficiencies and dysregulation: Pathophysiological consequences, modern analysis, and clinical management

(2019) Jutta Schröder-Braunstein et al.   MOLECULAR IMMUNOLOGY

Early progression to active tuberculosis is a highly heritable trait driven by 3q23 in Peruvians

(2019) Yang Luo et al.   Nature Communications

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

(2019) Kathrin Näpflin et al.   PeerJ

Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium whole genome sequences improves imputation quality and detection of rare variant associations in admixed African and Hispanic/Latino populations

(2019) Madeline H. Kowalski et al.   PLoS Genetics

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

(2018) Etienne Patin et al.   NATURE IMMUNOLOGY

The personal and clinical utility of polygenic risk scores

(2018) Ali Torkamani et al.   NATURE REVIEWS GENETICS

ElevatedHLA-Aexpression impairs HIV control through inhibition of NKG2A-expressing cells

(2018) Veron Ramsuran et al.   SCIENCE

BiallelicRIPK1mutations in humans cause severe immunodeficiency, arthritis, and intestinal inflammation

(2018) Delphine Cuchet-Lourenço et al.   SCIENCE

Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4

(2018) James J. Gilchrist et al.   Nature Communications

An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease

(2018) Liuyang Wang et al.   Cell Host & Microbe

Mendelian susceptibility to mycobacterial disease: 2014-2018 update

(2018) Jérémie Rosain et al.   IMMUNOLOGY AND CELL BIOLOGY

Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency

(2018) Nicholas Hernandez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Ancient hepatitis B viruses from the Bronze Age to the Medieval period

(2018) Barbara Mühlemann et al.   NATURE

Disruption of an antimycobacterial circuit between dendritic and helper T cells in human SPPL2a deficiency

(2018) Xiao-Fei Kong et al.   NATURE IMMUNOLOGY

Genome-wide association study identifies two risk loci for tuberculosis in Han Chinese

(2018) Ruijuan Zheng et al.   Nature Communications

Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines

(2018) Petar Scepanovic et al.   Genome Medicine

Transcriptomic Signatures in Sepsis and a Differential Response to Steroids: From the VANISH Randomized Trial

(2018) David B Antcliffe et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Very low depth whole genome sequencing in complex trait association studies

(2018) Arthur Gilly et al.   BIOINFORMATICS

The hyper IgM syndromes: Epidemiology, pathogenesis, clinical manifestations, diagnosis and management

(2018) Reza Yazdani et al.   CLINICAL IMMUNOLOGY

Multi-Ancestry Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus

(2018) Candelaria Vergara et al.   GASTROENTEROLOGY

Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017

(2018) Jeffrey D Stanaway et al.   LANCET

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Human RIPK1 deficiency causes combined immunodeficiency and inflammatory bowel diseases

(2018) Yue Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A homozygous loss-of-function mutation leading to CYBC1 deficiency causes chronic granulomatous disease

(2018) Gudny A. Arnadottir et al.   Nature Communications

Discovery of susceptibility loci associated with tuberculosis in Han Chinese

(2017) Hui Qi et al.   HUMAN MOLECULAR GENETICS

Mendelian Randomization

(2017) Connor A. Emdin et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

A novel kindred with inherited STAT2 deficiency and severe viral illness

(2017) Leen Moens et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Recurrent rhinovirus infections in a child with inherited MDA5 deficiency

(2017) Ian T. Lamborn et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genetic diversity of the African malaria vector Anopheles gambiae

(2017) Alistair Miles et al.   NATURE

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

(2017) M Azim Ansari et al.   NATURE GENETICS

Identification of sequence variants influencing immunoglobulin levels

(2017) Stefan Jonsson et al.   NATURE GENETICS

Tissue dual RNA-seq allows fast discovery of infection-specific functions and riboregulators shaping host–pathogen transcriptomes

(2017) Aaron M. Nuss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resistance to malaria through structural variation of red blood cell invasion receptors

(2017) Ellen M. Leffler et al.   SCIENCE

Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants

(2017) Jason H. Karnes et al.   Science Translational Medicine

Genome-wide association and HLA region fine-mapping studies identify susceptibility loci for multiple common infections

(2017) Chao Tian et al.   Nature Communications

Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania

(2017) Tom Parks et al.   Nature Communications

A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa

(2017) Rafal S. Sobota et al.   PLoS Genetics

Classification of patients with sepsis according to blood genomic endotype: a prospective cohort study

(2017) Brendon P Scicluna et al.   Lancet Respiratory Medicine

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

(2016) Yohann Nédélec et al.   CELL

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

(2016) Hélène Quach et al.   CELL

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans

(2016) Yang Li et al.   CELL

A genome-wide association study of pulmonary tuberculosis in Morocco

(2016) A. V. Grant et al.   HUMAN GENETICS

X-linked Agammaglobulinemia

(2016) Deepti Suri et al.   INDIAN JOURNAL OF PEDIATRICS

Severe Early-Onset Combined Immunodeficiency due to Heterozygous Gain-of-Function Mutations in STAT1

(2016) Safa Baris et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

(2016) Alexander J. Westermann et al.   NATURE

Reference-based phasing using the Haplotype Reference Consortium panel

(2016) Po-Ru Loh et al.   NATURE GENETICS

HLA class II sequence variants influence tuberculosis risk in populations of European ancestry

(2016) Gardar Sveinbjornsson et al.   NATURE GENETICS

A large-scale genome-wide association and meta-analysis identified four novel susceptibility loci for leprosy

(2016) Zhenzhen Wang et al.   Nature Communications

Genome-wide association study identifies 8p21.3 associated with persistent hepatitis B virus infection among Chinese

(2016) Yuanfeng Li et al.   Nature Communications

Genomic landscape of the individual host response and outcomes in sepsis: a prospective cohort study

(2016) Emma E Davenport et al.   Lancet Respiratory Medicine

A novel presentation of homozygous loss-of-function STAT-1 mutation in an infant with hyperinflammation—A case report and review of the literature

(2016) Charlotte Burns et al.   Journal of Allergy and Clinical Immunology-In Practice

International Consensus Document (ICON): Common Variable Immunodeficiency Disorders

(2016) Francisco A. Bonilla et al.   Journal of Allergy and Clinical Immunology-In Practice

Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common Viruses

(2015) Christian Hammer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Severe combined immunodeficiency: recent developments and guidance on clinical management

(2015) Lizzy Rivers et al.   ARCHIVES OF DISEASE IN CHILDHOOD

The Genetic Architecture of the Human Immune System: A Bioresource for Autoimmunity and Disease Pathogenesis

(2015) Mario Roederer et al.   CELL

Genome-wide association study identifies SNPs in the MHC class II loci that are associated with self-reported history of whooping cough

(2015) George McMahon et al.   HUMAN MOLECULAR GENETICS

Use of ruxolitinib to successfully treat chronic mucocutaneous candidiasis caused by gain-of-function signal transducer and activator of transcription 1 (STAT1) mutation

(2015) Eleanor Higgins et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

A novel locus of resistance to severe malaria in a region of ancient balancing selection

(2015)   NATURE

Susceptibility to tuberculosis is associated with variants in the ASAP1 gene encoding a regulator of dendritic cell migration

(2015) James Curtis et al.   NATURE GENETICS

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy

(2015) Hong Liu et al.   NATURE GENETICS

The impact of host genetic variation on infection with HIV-1

(2015) Paul J McLaren et al.   NATURE IMMUNOLOGY

Searching for the human genetic factors standing in the way of universally effective vaccines

(2015) A. J. Mentzer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

(2015) Paul J. McLaren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency

(2015) M. J. Ciancanelli et al.   SCIENCE

Human IFNAR2 deficiency: Lessons for antiviral immunity

(2015) Christopher J. A. Duncan et al.   Science Translational Medicine

Genomic modulators of gene expression in human neutrophils

(2015) Vivek Naranbhai et al.   Nature Communications

Genome-Wide Association Studies of HIV-1 Host Control in Ethnically Diverse Chinese Populations

(2015) Zejun Wei et al.   Scientific Reports

Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study

(2015) Eric O. Johnson et al.   PLoS One

Advantageous diversity maintained by balancing selection in humans

(2014) Felix M Key et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

XLP: Clinical Features and Molecular Etiology due to Mutations in SH2D1A Encoding SAP

(2014) Stuart G Tangye   JOURNAL OF CLINICAL IMMUNOLOGY

Polymorphisms in HLA-DPB1 Are Associated With Differences in Rubella Virus-Specific Humoral Immunity After Vaccination

(2014) N. D. Lambert et al.   JOURNAL OF INFECTIOUS DISEASES

Host-directed therapy of tuberculosis based on interleukin-1 and type I interferon crosstalk

(2014) Katrin D. Mayer-Barber et al.   NATURE

The African Genome Variation Project shapes medical genetics in Africa

(2014) Deepti Gurdasani et al.   NATURE

Obesity-associated variants within FTO form long-range functional connections with IRX3

(2014) Scott Smemo et al.   NATURE

Variation at HLA-DRB1 is associated with resistance to enteric fever

(2014) Sarah J Dunstan et al.   NATURE GENETICS

Advantages and pitfalls in the application of mixed-model association methods

(2014) Jian Yang et al.   NATURE GENETICS

Reappraisal of known malaria resistance loci in a large multicenter study

(2014) Kirk A Rockett et al.   NATURE GENETICS

Natural selection and infectious disease in human populations

(2014) Elinor K. Karlsson et al.   NATURE REVIEWS GENETICS

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

HLA genotypes and rubella vaccine immune response: Additional evidence

(2014) Inna G. Ovsyannikova et al.   VACCINE

Genome-Wide Association Study of Spontaneous Resolution of Hepatitis C Virus Infection: Data From Multiple Cohorts

(2013) Priya Duggal et al.   ANNALS OF INTERNAL MEDICINE

Major Histocompatibility Complex Genomics and Human Disease

(2013) John Trowsdale et al.   Annual Review of Genomics and Human Genetics

KIR3DS1/L1 and HLA-Bw4-80I are associated with HIV disease progression among HIV typical progressors and long-term nonprogressors

(2013) Yongjun Jiang et al.   BMC INFECTIOUS DISEASES

Monitoring the immune response in sepsis: a rational approach to administration of immunoadjuvant therapies

(2013) Fabienne Venet et al.   CURRENT OPINION IN IMMUNOLOGY

Combined immunodeficiency presenting with vaccine-associated paralytic poliomyelitis: a case report and narrative review of literature

(2013) Mohammadreza Shaghaghi et al.   IMMUNOLOGICAL INVESTIGATIONS

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

(2013) Joshua C Denny et al.   NATURE BIOTECHNOLOGY

New loci associated with chronic hepatitis B virus infection in Han Chinese

(2013) Zhibin Hu et al.   NATURE GENETICS

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Deep Dermatophytosis and Inherited CARD9 Deficiency

(2013) Fanny Lanternier et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA-DQB1*03 Confers Susceptibility to Chronic Hepatitis C in Japanese: A Genome-Wide Association Study

(2013) Daiki Miki et al.   PLoS One

Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

(2013) E. M. Leffler et al.   SCIENCE

Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta

(2013) E. K. Karlsson et al.   Science Translational Medicine

Meningococcal disease and the complement system

(2013) Lisa A Lewis et al.   Virulence

Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls

(2013) Paul J. McLaren et al.   PLoS Pathogens

Genome-wide association study indicates two novel resistance loci for severe malaria

(2012) Christian Timmann et al.   NATURE

Common variants at 11p13 are associated with susceptibility to tuberculosis

(2012) Thorsten Thye et al.   NATURE GENETICS

Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles

(2012) Benjamin P Fairfax et al.   NATURE GENETICS

Human genetic susceptibility to infectious disease

(2012) Stephen J. Chapman et al.   NATURE REVIEWS GENETICS

A genome-wide association study of hepatitis B vaccine response in an Indonesian population reveals multiple independent risk variants in the HLA region

(2011) E. Png et al.   HUMAN MOLECULAR GENETICS

Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy

(2011) Furen Zhang et al.   NATURE GENETICS

Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1

(2011) Chiea Chuen Khor et al.   NATURE GENETICS

Hemoglobins S and C Interfere with Actin Remodeling in Plasmodium falciparum-Infected Erythrocytes

(2011) M. Cyrklaff et al.   SCIENCE

Human leukocyte antigen associations with humoral and cellular immunity following a second dose of measles-containing vaccine: Persistence, dampening, and extinction of associations found after a first dose

(2011) Robert M. Jacobson et al.   VACCINE

Association between Single‐Nucleotide Polymorphisms inMal/TIRAPandInterleukin‐10Genes and Susceptibility to InvasiveHaemophilus influenzaeSerotype b Infection in Immunized Children

(2010) Shamez N. Ladhani et al.   CLINICAL INFECTIOUS DISEASES

Infections of People with Complement Deficiencies and Patients Who Have Undergone Splenectomy

(2010) S. Ram et al.   CLINICAL MICROBIOLOGY REVIEWS

Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease

(2010) Sonia Davila et al.   NATURE GENETICS

Genetics and Beyond – The Transcriptome of Human Monocytes and Disease Susceptibility

(2010) Tanja Zeller et al.   PLoS One

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

(2010)   SCIENCE

Leprosy and the Adaptation of Human Toll-Like Receptor 1

(2010) Sunny H. Wong et al.   PLoS Pathogens

Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance

(2009) Dongliang Ge et al.   NATURE

Genetic variation in IL28B and spontaneous clearance of hepatitis C virus

(2009) David L. Thomas et al.   NATURE

Common Genetic Variation and the Control of HIV-1 in Humans

(2009) Jacques Fellay et al.   PLoS Genetics

Pyogenic Bacterial Infections in Humans with MyD88 Deficiency

(2008) H. von Bernuth et al.   SCIENCE