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View article: Identity by descent and local ancestry mapping of HCV spontaneous clearance in populations of diverse ancestries
Identity by descent and local ancestry mapping of HCV spontaneous clearance in populations of diverse ancestries Open
Background Acute infection with hepatitis C virus (HCV) affects millions of individuals worldwide. Host genetics plays a role in spontaneous clearance of the acute infection which occurs in approximately 30% of the individuals. Common vari…
View article: Cohort profile: the Johns Hopkins COVID Long Study (JHCLS)—a US nationwide prospective cohort study
Cohort profile: the Johns Hopkins COVID Long Study (JHCLS)—a US nationwide prospective cohort study Open
Purpose COVID-19 continues to affect millions of individuals worldwide, both in the short and long term. The post-acute complications of SARS-CoV-2 infection, referred to as long COVID, result in diverse symptoms affecting multiple organ s…
View article: A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction
A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction Open
Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved metho…
View article: Cohort profile: the Johns Hopkins COVID Long Study (JHCLS), a United States Nationwide Prospective Cohort Study
Cohort profile: the Johns Hopkins COVID Long Study (JHCLS), a United States Nationwide Prospective Cohort Study Open
Purpose COVID-19 disease continues to affect millions of individuals worldwide, both in the short and long term. The post-acute complications of SARS-CoV-2 infection, referred to as long COVID, result in diverse symptoms affecting multiple…
View article: Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH
Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH Open
Biological sex and host genetics influence HIV pathogenesis. Females have a higher likelihood of spontaneous viral control and lower set point viral load (spVL). No prior studies have assessed sex-specific genetics of HIV. To address this,…
View article: Mosaic chromosomal alterations detected in men living with HIV and the relationship to non-Hodgkin lymphoma
Mosaic chromosomal alterations detected in men living with HIV and the relationship to non-Hodgkin lymphoma Open
Objectives: People with HIV (PWH) have an elevated risk of non-Hodgkin lymphoma (NHL) and other diseases. Studying clonal hematopoiesis (CH), the clonal expansion of mutated hematopoietic stem cells, could provide insights regarding elevat…
View article: Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common control subjects
Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common control subjects Open
View article: A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV
A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV Open
Hepatitis B virus (HBV) remains a global public health concern, with over 250 million individuals living with chronic HBV infection (CHB) and no curative therapy currently available. Viral diversity is associated with CHB pathogenesis and …
View article: Identity by descent mapping of HCV spontaneous clearance in populations of diverse ancestry
Identity by descent mapping of HCV spontaneous clearance in populations of diverse ancestry Open
View article: Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction
Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction Open
Background Control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission requires understanding SARS-CoV-2 replication dynamics. Methods We developed a multiplexed droplet digital polymerase chain reaction (ddPCR) as…
View article: Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common controls
Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common controls Open
Genome-wide association studies (GWAS) have been performed to identify host genetic factors for a range of phenotypes, including for infectious diseases. The use of population-based common controls from biobanks and extensive consortiums i…
View article: Benchmarking statistical methods for analyzing parent–child dyads in genetic association studies
Benchmarking statistical methods for analyzing parent–child dyads in genetic association studies Open
Genetic association studies of child health outcomes often employ family‐based study designs. One of the most popular family‐based designs is the case–parent trio design that considers the smallest possible nuclear family consisting of two…
View article: Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1
Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1 Open
View article: Decreased Activated CD4<sup>+</sup>T Cell Repertoire Diversity After Antiretroviral Therapy in HIV-1/HCV Coinfection Correlates with CD4<sup>+</sup>T Cell Recovery
Decreased Activated CD4<sup>+</sup>T Cell Repertoire Diversity After Antiretroviral Therapy in HIV-1/HCV Coinfection Correlates with CD4<sup>+</sup>T Cell Recovery Open
Dysfunctional immune activation accumulates during chronic viral infection and contributes to disease pathogenesis. In HIV-1, immune activation is exacerbated by concurrent infection with hepatitis C virus (HCV), accelerating depletion of …
View article: Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies
Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies Open
Genetic association studies of child health outcomes often employ family-based designs. One of the most popular family-based designs is the case-parent trio design that considers the smallest possible nuclear family consisting of two paren…
View article: Whole genome sequencing identifies novel genetic mutations in patients with eczema herpeticum
Whole genome sequencing identifies novel genetic mutations in patients with eczema herpeticum Open
Background Eczema herpeticum (EH) is a rare complication of atopic dermatitis (AD) caused by disseminated herpes simplex virus (HSV) infection. The role of rare and/or deleterious genetic variants in disease etiology is largely unknown. Th…
View article: Correction: Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection
Correction: Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection Open
View article: Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection
Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection Open
View article: A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus
A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus Open
Background Spontaneous clearance of acute hepatitis C virus (HCV) infection is more common in women than in men, independent of known risk factors. Methods To identify sex-specific genetic loci, we studied 4423 HCV-infected individuals (29…
View article: A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome
A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome Open
The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of …
View article: Association of HLA-DRB1∗09:01 with tIgE levels among African-ancestry individuals with asthma
Association of HLA-DRB1∗09:01 with tIgE levels among African-ancestry individuals with asthma Open
View article: Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations
Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations Open
View article: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations (vol 10, 880, 2019)
Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations (vol 10, 880, 2019) Open
View article: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations
Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations Open
Asthma is a complex disease with striking disparities across racial and ethnic groups. Despite its relatively high burden, representation of individuals of African ancestry in asthma genome-wide association studies (GWAS) has been inadequa…
View article: Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent
Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent Open
View article: Assembly of a pan-genome from deep sequencing of 910 humans of African descent
Assembly of a pan-genome from deep sequencing of 910 humans of African descent Open
View article: Genotype imputation performance of three reference panels using African ancestry individuals
Genotype imputation performance of three reference panels using African ancestry individuals Open
View article: Genotype Imputation Performance of Three Reference Panels Using African Ancestry Individuals
Genotype Imputation Performance of Three Reference Panels Using African Ancestry Individuals Open
Genotype imputation is used to estimate unobserved genotypes from genome-wide maker data, to increase genome coverage and power for genome-wide association studies. Imputation has been most successful for European ancestry populations in w…
View article: Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome Open
View article: Effect of polymorphisms on TGFB1 on allergic asthma and helminth infection in an African admixed population
Effect of polymorphisms on TGFB1 on allergic asthma and helminth infection in an African admixed population Open