Amanda Y. Chong
A5072029606- vaccines and immunoinformatics approaches
- T-cell and B-cell Immunology
- IL-33, ST2, and ILC Pathways
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- SARS-CoV-2 and COVID-19 Research
- Polyomavirus and related diseases
- Genetic Associations and Epidemiology
- Immune Cell Function and Interaction
- Immunotherapy and Immune Responses
- Cytokine Signaling Pathways and Interactions
- COVID-19 Clinical Research Studies
- RNA regulation and disease
- Paleontology and Evolutionary Biology
- Respiratory viral infections research
- Parvovirus B19 Infection Studies
- Evolution and Paleontology Studies
- Microbial infections and disease research
- Inflammasome and immune disorders
- Genetic and phenotypic traits in livestock
- Tumors and Oncological Cases
- Immune responses and vaccinations
- NF-κB Signaling Pathways
- Genetic diversity and population structure
- Full-Duplex Wireless Communications
University of Oxford
2019-2025
Centre for Human Genetics
2019-2025
Ludwig Cancer Research
2024-2025
Oxford BioMedica (United Kingdom)
2022
The University of Sydney
2011-2017
Earlham Institute
2017
Fracture Analysis Consultants (United States)
2014
To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus saltwater crocodile), Gavialis gangeticus Indian gharial). We observed an exceptionally slow rate genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content movement, gene family evolution,...
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying severity in an integrated comparison influenza sepsis versus healthy volunteers. identify signatures correlates host response. Hallmarks disease involved cells, their inflammatory mediators networks, including progenitor cells myeloid lymphocyte subsets, features the repertoire,...
Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine immunogenicity varies between individuals, and immune responses correlate with efficacy. Using data from 1,076 participants enrolled in ChAdOx1 nCov-19 efficacy trials the United Kingdom, we found that inter-individual variation normalized antibody against SARS-CoV-2 spike its receptor-binding domain (RBD) at 28 days after first vaccination shows genome-wide significant association major histocompatibility complex...
Certain infectious agents are recognised causes of cancer and other chronic diseases. To understand the pathological mechanisms underlying such relationships, here we design a Multiplex Serology platform to measure quantitative antibody responses against 45 antigens from 20 including human herpes, hepatitis, polyoma, papilloma, retroviruses, as well Chlamydia trachomatis, Helicobacter pylori Toxoplasma gondii, then assayed random subset 9695 UK Biobank participants. We find seroprevalence...
Latin America continues to be severely underrepresented in genomics research, and fine-scale genetic histories complex trait architectures remain hidden owing insufficient data1. To fill this gap, the Mexican Biobank project genotyped 6,057 individuals from 898 rural urban localities across all 32 states Mexico at a resolution of 1.8 million genome-wide markers with linked disease information creating valuable nationwide genotype-phenotype database. Here, using ancestry deconvolution...
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) Indian gharial (Gavialis gangeticus) genomes. status of these projects our planned analyses are described.
The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. MHC generally divided into subregions (classes I, II and III) containing genes similar function across species, but different gene number organisation. Crocodylia (crocodilians) are widely distributed represent evolutionary distinct group among higher genomic organisation within this lineage has been largely unexplored. Here,...
Crocodilians are thought to be hosts a diverse and divergent complement of endogenous retroviruses (ERVs) but comprehensive investigation is yet performed. The recent sequencing three crocodilian genomes provides an opportunity for more detailed accurate representation the ERV diversity that present in these species. Here we investigate diversity, distribution evolution ERVs from key species, outline processes driving proliferation evolution.ERVs related sequences make up less than 2%...
How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships populations with African ancestries. We undertook analyses of antibody responses from Uganda (n = 1391), Burkina Faso 353) South Africa 755), identifying associations between leukocyte antigen (HLA) response for five eight tested antigens spanning pertussis, diphtheria hepatitis B vaccines. In addition, through HLA typing 1,702 individuals 11 ancestry derived...
Abstract Iron is an essential trace element for both humans and pathogens, but its genetic determinants are understudied in Africa where iron deficiency infectious diseases highly prevalent. We conducted genome-wide association studies six iron-related biomarkers 3928 children from five sites across with replication 2868 African American adults. identify a previously unreported loci transferrin GTF3C5, gene regulating cellular iron-uptake, soluble receptor FREM3 , the Dantu locus, hepcidin...
Abstract Cytomegalovirus (CMV) is a globally endemic latent herpes virus that profoundly impacts T cell immunity. We investigated the oncological consequences of CMV infection across 341 prospectively recruited patients receiving immune checkpoint blockade (ICB) for melanoma. + with metastatic melanoma (MM) have higher lymphocyte counts, reduced neutrophil to ratio and divergent CD8 gene expression. Combination anti-CTLA-4/anti-PD-1 ICB, but not single-agent anti-PD-1 induces cytotoxicity...
<title>Abstract</title> Sepsis is a heterogeneous clinical syndrome with high mortality rate and personalised stratification strategies are proposed as essential to successful targeted therapeutics. Here, we characterise genetic variation that modulates <italic>MTOR</italic>, critical regulator of metabolism immune responses in sepsis. The effects highly context specific, involving regulatory element affects <italic>MTOR</italic> expression activated T cells opposite direction effect...
Abstract The platypus O rnithorhynchus anatinus is an endemic monotreme species with a wide latitudinal distribution in eastern A ustralia, including T asmania. Understanding of the phylogeography within this very limited at present and represents gap documentation ustralia's unique biodiversity. We analysed mitochondrial DNA sequences (partial control region complete cytochrome b , portions flanking tRNAs ) 74 individuals from across species. Phylogenetic analysis concatenated corroborated...
Abstract Background Certain infectious agents are recognised causes of cancer and potentially other chronic diseases. Identifying associations understanding pathological mechanisms involving subsequent disease risk will be possible through measuring exposure to multiple in large-scale prospective cohorts such as UK Biobank. Methods Following expert consensus we designed a Multiplex Serology platform capable simultaneously quantitative antibody responses against 45 antigens from 20 implicated...
Current Genome-Wide Association Studies (GWAS) rely on genotype imputation to increase statistical power, improve fine-mapping of association signals, and facilitate meta-analyses. Due the complex demographic history Latin America lack balanced representation Native American genomes in current panels, discovery locally relevant disease variants is likely be missed, limiting scope impact biomedical research these populations. Therefore, necessity better diversity genomic databases a...
Abstract Human polyomaviruses are widespread in humans and can cause severe disease immunocompromised individuals. To identify human genetic determinants of the humoral immune response against polyomaviruses, we performed genome-wide association studies meta-analyses qualitative quantitative immunoglobulin G responses BK polyomavirus (BKPyV), JC (JCPyV), Merkel cellpolyomavirus (MCPyV), WU (WUPyV), 6 (HPyV6) 15,660 individuals European ancestry from three independent studies. We observed...
The number of gluten-free diet followers without celiac disease (CD) is increasing. However, little known about the characteristics these individuals.
Summary Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete understanding potentially druggable immune mediators disease. To advance this, we present a comprehensive multi-omic blood atlas in patients with varying severity compare influenza, sepsis healthy volunteers. We identify signatures correlates host response. Hallmarks disease revealed cells, their inflammatory networks as potential therapeutic targets, including progenitor cells specific myeloid...
Abstract Genetic colocalization analyses are frequently conducted to determine if causal signals at a genetic locus shared between two phenotypes. However, is rarely undertaken the HLA locus, due its complex linkage disequilibrium (LD) and high polymorphism density. This lack of inference method limits our ability translate associations into therapeutic targets. Here we present that uses alleles, instead nucleotide variants, perform traits genes. The method, which call HLA-colocalization,...