EGAGenomicsPopulation Genomicshttps://ega-archive.org/studies/EGAS00001000918EGAEGA study EGAS00001000918banfora_20150706_autosomesjohannesburg_20150706_autosomesHLA sequence data and final calls for VaccGene and 1000Gp3 African populationsbanfora_20150706_Xvaccgene_1000G_MKK_hlauganda_Xjohannesburg_20150706_Xuganda_autosomesEGArestrictedstudy, living, wide, African unspecified., whole genome, wide/broad, broad, Genomes, Vaccine, Infants, pre-mortem, AssociationsGenome-Wide Association, Hunter Carpenter Macdonald syndrome, Materials, Institutional Ethics, Vaccines, acetylglucosaminyltransferase-like protein, Hemophilus influenzae, A4, Pertusses, growth and development, Cost-Minimization, Relative, Personal, Bcg, BCG, SERA, neurodegeneration with brain iron accumulation caused by mutation in PLA2G6, atopy, INAD, Lyt-2, BSAC, responsivity, Birth Cohorts, Coccobacillus pfeifferi, Analysis, Cost Comparison, myd, Infectious Diseases, Republic of South Africa, mega, DmelCG15112, gamma sarcoglycan, Institutional Ethics Committee, GWA Study, thymus nucleic acid, 1.1.1.95, like-acetylglucosaminyltransferase, Analyses, Genomes, Chip, ChIP, Bsac, CHIP, serum hepatitis, Mbp-1, Comparison, 4930479N23, response to intravesical immunotherapy with live attenuated BCG, Shots, 3-((phenylacetyl)amino)-2, Social, Cost Analysis, chip, sample, malate anion, s, Social Power, Marsh, Itg, Power, Ethics Committee, Diagnostic Findings, PGAD, close to, response to Bacillus Calmette-Guerin strain of Mycobacterium bovis, Rubeola, Mal-D, l(2)k04405, Infectious Disease, cHILD, early onset of peripheral gangrene, pediatric interstitial lung disease, Corynebacterium diphtheriae Infection, Regional, Endowment, Ity, Lyt2, Pertussis, familial, Plasmodium, Genome-Wide, not genetically inherited, dMRTF, PGDH, Expanded, Malaria Vaccine, 6-dioxo-3-piperidinyl)benzeneacetamide, FCERI, Financial, Genome Wide Association Study, consent, mKIAA0609, 1270, Relative Risks, ity, malate dianion, atomo, 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genetic, plasmodiosis, atom, Marsh Fever, fees, Malarial, Corynebacterium diphtheriae Infections, Influenza-bacillus, Infants, 35 kDa dystrophin-associated glycoprotein, TALLA, Traits, DNAn+1, tm4sf2, CG4114, CG5203, Leu2, AI323365, Pneumococcal Vaccine, l(2)04405, CG14951, 3PGDH, response to Bacillus Calmette Guerin strain of Mycobacterium bovis, SGCG, near to, read, LFA-1, N-acetyl-D-glucosamine 2-epimerase, H15r, Pressure, chemical analysis, malate, CG9933, Relative Risk, Costs and Cost Analyses, CD231, Costs, DMDA1, Ldb, LDB, Committee, postnatal growth, Heterogeneities, Cost-Minimization Analysis, CG6634, Chromatin Immunoprecipitation, Childhood, ion(2-), extra, Ugt1a13, School Age Populations, Ugt1a12, included, Ugt1a10, Nramp, l(2)01270, Genogroups, like-glycosyltransferase, children's interstitial lung disease, vicinity of, Power (Psychology), CD11A, Remittent Fever, Desoxyribonukleinsaeure, Institutional Ethics Committees, Association Studies, Cost Measure, hereditary, Cd11a, 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Diastolic Pressure, TYPE, froggy, Symptoms and Signs, Deoxyribonucleic acids, Gyltl1a, DAGA4, Committees, corynebacterium infection, Homo sapiens, Cost Minimization Analysis, Clostridium tetani, T-cell surface glycoprotein Lyt-2, Genetic heterogeneity, CHILD, 35DAG, Studies, CD8A, A-10, Institutional, PE31, Finding, interstitial lung disease of childhood, SCG3, reactivity, study, Union of South Africa, Genetic, Galapagos Islands, response to Bacillus Calmette Guerin strain of Mycobacterium bovis solution, Infections, Whooping, Birth, Affordability, Haemophilus meningitidis, DmelCG32296, R74651, los, Measures, Hepatitis B Virus Infection, CD8a, DmelCG14779, infection due to Bordetella pertussis, LARGE, financing, paediatric interstitial lung disease, Genome Wide Association Scan, funding, BPFD#36, mrx58, Abstract, l(1)G0044, Pneumovax, Corynebacterium diphtheriae, great, Diastolic, heterogeneity, DmelCG3924, Republic of Uganda, elements, School Age Population, 0610033N24Rik, African unspecified, Vaccinations, PP1131, Paludism, BACTS1, CG12188, Disease, KARAK syndrome, Clostridium tetani Infections, RnBP, Pneumococcal, Polysaccharide Vaccine, GlcNAc 2-epimerase, Infectious, Rotaviruses, Regional Ethics, Cistrons, LGMD2C, chronic hepatitis B, Lsh, development, count in organism, Signs and Symptoms, EG:80H7.2, Pnu-Imune Vaccine, Regional Ethics Committee, Genogroup, cd231, Infection, Active, atomus, 3-PGDH, Professional, ds-DNA, MS4A1, CG15112, Atopic allergy, Systolic Pressure, neuroaxonal dystrophy presenting with neonatal dysmorphic features, nmr2, Cost, Risks, chILD syndrome, Pricing, TBX20, CG3924, Active Immunizations, TRAITS, sample population, Genome Wide Association Studies, cost, Personal Power, dLDB/Chip, Pulse, Pressures, Vaccine, approaches, Management, Modern Man, AA407980, cardinality, Cough, SCARMD2, renin-binding protein, assay, response, CD8, responsive, Pneumococcal Polysaccharide Vaccine, growth, glycosyltransferase-like protein LARGE1falseGenome wide association study of vaccine responses in infants living in the Developing World VaccGene Phase II African CohortsHuman genetic heterogeneity accounts for approximately 70% of the observed variability in response to common childhood vaccinations. Identifying the elements of this heterogeneity will enable the development of vaccines which have improved clinical and cost effectiveness through rational adjuventation approaches, or by targeting particular at-risk or responsive subgroups. The studies published to date have been limited in terms of the number of vaccine subtypes analysed, diversity of the populations included, sample sizes and breadth of other environmental and lifestyle variables which may explain some of the remainder of variation in the response to each vaccine. Nevertheless, these studies have proposed that the genes which harbour the variants associated with vaccine responsiveness reside within regions of the genome associated with immune function such as the HLA locus and FOXP1and ITGAL. We are proposing one of the largest genome-wide association studies of vaccine response ever undertaken, which will provide unparalleled power to identify the genetic factors associated with the response to all of the most commonly used childhood vaccines worldwide. For the first phase of the project (Prelim I0308) we genotyped ca. 1,400 children from the Entebbe Mother and Baby (EMaB) study, an ongoing birth cohort in southern Uganda, using the Illumina HumanOmni2.5-8 chip. Analyses for response to vaccination against diphtheria, tetanus, pertussis, Haemophilus influenzae, measles, hepatitis B and BCG are now underway. Working alongside other ongoing studies, we plan for the second phase of the project to expand sample sizes to up to 7,000 individuals in total. This large cohort will include 1,500 South African infants, 500 Burkina Faso infants, 1,800 children from Ecuador and up to 1,800 from a variety of countries (MAL-ED Consortium). The principal measured phenotypes will be the serological responses at 6 or 12 months of age to the vaccines administered to all enrolled children as part of expanded programme of immunisation in all countries. As for the primary Ugandan study the responses will be analysed as quantitative traits using mixed model (GEMMA) analyses following imputation using a combined 1000 Genome and African Genome Variation Project reference panel. The data will be analysed as one large discovery mega-analysis to maximise the power of finding the relevant associated variants. Interim GWAS analyses will be performed on each population to test for population specific signals. Other phenotypes that will be assessed in the new studies include quantitative response to BCG, rotavirus and pneumococcal vaccines (South Africa, Ecuador and Uganda), clinical and immunological response to malaria vaccines (Burkina), immunological correlates of atopy (Ecuador and Uganda) and malaria infection (Burkina, Ecuador and Uganda) in addition to non-communicable disease traits such as blood pressure page 1 [A8] If applicable, provide text (abstract) which will accompany data for this study in the ENA/EGA. [A9] Does this project use samples? [A10] Please choose which types of sample you will be using [A12] Please state the anticipated date (month/year) samples will be available in-house (if known). If samples are already in-house, type 'in-house' here. Please note that for sequencing, genotyping and microarrays this is essential for scheduling the work. [A13] Please state the anticipated project start date (month/year). [A14] Please state the project duration (months). [A15] Please read WTSI's Data Sharing Policy and Guidelines, then explain your data sharing plans for the project [A16] Are the data sharing plans of this project compliant with the Institute's Guidelines? [A17] Are there any conflicts of interest related to this proposal? (Uganda). We are requesting funds to genotype on the Illumina HumanOmni2.5-8 platform 2,000 African infants recruited through ongoing maternal and child vaccine clinical trials (against pneumococcus in Soweto, South Africa, and malaria in Banfora, Burkina Faso). The DNA from the Burkina cohort is at the University of Oxford and ready to be shipped, while the DNA from the South African cohort will be available by mid-2014. Appropriate consent for genetic analyses has been acquired for the proposed study cohorts from both local ethics committees and UK-based Committees.2023-09-27 13:06:45EGAS000010009189606EGAD00010002581EGAD00010002580EGAD00010002578EGAD00010002582EGAD00001011379EGAD00010002577EGAD00010002579EGAD00010002583EGAC00001000205