{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Population Genomics"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000918"],"host":["EGA"],"description":["EGA study EGAS00001000918"],"dataset_title":["banfora_20150706_autosomes","johannesburg_20150706_autosomes","HLA sequence data and final calls for VaccGene and 1000Gp3 African populations","banfora_20150706_X","vaccgene_1000G_MKK_hla","uganda_X","johannesburg_20150706_X","uganda_autosomes"],"repository":["EGA"],"category":["restricted"],"additional_accession":[]},"is_claimable":false,"name":"Genome wide association study of vaccine responses in infants living in the Developing World  VaccGene   Phase II African Cohorts","description":"Human genetic heterogeneity accounts for approximately 70% of the observed variability in\nresponse to common childhood vaccinations. Identifying the elements of this heterogeneity\nwill enable the development of vaccines which have improved clinical and cost effectiveness\nthrough rational adjuventation approaches, or by targeting particular at-risk or responsive\nsubgroups. The studies published to date have been limited in terms of the number of vaccine\nsubtypes analysed, diversity of the populations included, sample sizes and breadth of other\nenvironmental and lifestyle variables which may explain some of the remainder of variation in\nthe response to each vaccine. Nevertheless, these studies have proposed that the genes\nwhich harbour the variants associated with vaccine responsiveness reside within regions of\nthe genome associated with immune function such as the HLA locus and FOXP1and ITGAL.\nWe are proposing one of the largest genome-wide association studies of vaccine response\never undertaken, which will provide unparalleled power to identify the genetic factors\nassociated with the response to all of the most commonly used childhood vaccines\nworldwide. For the first phase of the project (Prelim I0308) we genotyped ca. 1,400 children\nfrom the Entebbe Mother and Baby (EMaB) study, an ongoing birth cohort in southern\nUganda, using the Illumina HumanOmni2.5-8 chip. Analyses for response to vaccination\nagainst diphtheria, tetanus, pertussis, Haemophilus influenzae, measles, hepatitis B and BCG\nare now underway. Working alongside other ongoing studies, we plan for the second phase\nof the project to expand sample sizes to up to 7,000 individuals in total. This large cohort will\ninclude 1,500 South African infants, 500 Burkina Faso infants, 1,800 children from Ecuador\nand up to 1,800 from a variety of countries (MAL-ED Consortium). The principal measured\nphenotypes will be the serological responses at 6 or 12 months of age to the vaccines\nadministered to all enrolled children as part of expanded programme of immunisation in all\ncountries. As for the primary Ugandan study the responses will be analysed as quantitative\ntraits using mixed model (GEMMA) analyses following imputation using a combined 1000\nGenome and African Genome Variation Project reference panel. The data will be analysed as\none large discovery mega-analysis to maximise the power of finding the relevant associated\nvariants. Interim GWAS analyses will be performed on each population to test for population\nspecific signals. Other phenotypes that will be assessed in the new studies include\nquantitative response to BCG, rotavirus and pneumococcal vaccines (South Africa, Ecuador\nand Uganda), clinical and immunological response to malaria vaccines (Burkina),\nimmunological correlates of atopy (Ecuador and Uganda) and malaria infection (Burkina,\nEcuador and Uganda) in addition to non-communicable disease traits such as blood pressure\npage 1\n[A8] If applicable, provide text (abstract) which will accompany data for this study in the ENA/EGA.\n[A9] Does this project use samples?\n[A10] Please choose which types of sample you will be using\n[A12] Please state the anticipated date (month/year) samples will be available in-house (if known). If samples are\nalready in-house, type 'in-house' here. Please note that for sequencing, genotyping and microarrays this is essential\nfor scheduling the work.\n[A13] Please state the anticipated project start date (month/year).\n[A14] Please state the project duration (months).\n[A15] Please read WTSI's Data Sharing Policy and Guidelines, then explain your data sharing plans for the project\n[A16] Are the data sharing plans of this project compliant with the Institute's Guidelines?\n[A17] Are there any conflicts of interest related to this proposal?\n(Uganda).\nWe are requesting funds to genotype on the Illumina HumanOmni2.5-8 platform 2,000 African\ninfants recruited through ongoing maternal and child vaccine clinical trials (against\npneumococcus in Soweto, South Africa, and malaria in Banfora, Burkina Faso). The DNA\nfrom the Burkina cohort is at the University of Oxford and ready to be shipped, while the DNA\nfrom the South African cohort will be available by mid-2014. Appropriate consent for genetic\nanalyses has been acquired for the proposed study cohorts from both local ethics committees\nand UK-based Committees.","dates":{"updated":"2023-09-27 13:06:45"},"accession":"EGAS00001000918","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00010002581","EGAD00010002580","EGAD00010002578","EGAD00010002582","EGAD00001011379","EGAD00010002577","EGAD00010002579","EGAD00010002583","EGAC00001000205"]}}