Ena-DATASET-H3AFRICA-05-09-2019-13:13:49:342-235 - samples
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ABSTRACT:
PROVIDER: EGAD00001005310 | EGA |
REPOSITORIES: EGA
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Project description:The Sahel/Savannah belt harbours diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated dense genome-wide genotype data of 327 individuals—comprising 14 ethnolinguistic groups, including ten previously unsampled populations. DNA samples were genotyped on the Illumina H3Africa Consortium Array (BeadChip type: H3Africa_2017_20021485_A2; designed for SNP-genotyping of 2,267,346 SNPs) at the SNP&SEQ Technology Platform, NGI/SciLifeLab Genomics (Sweden). Reference: Demographic and Selection Histories of Populations Across the Sahel/Savannah Belt. Fortes-Lima C, Tříska P, Čížková M, Podgorná E, Diallo MY, Schlebusch CM, Černý V. Molecular Biology and Evolution 2022 39(10):msac209. doi: 10.1093/molbev/msac209. PMID: 36173804 .
2022-10-31 | E-MTAB-12243 | biostudies-arrayexpress
Project description:SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina H3Africa array version 1
| EGAD00010002510 | EGA
Project description:The 6431 samples were genotyped on the H3Africa array.
| EGAD00010002365 | EGA
Project description:Since it is recognized that currently available chips may not be ideally suited to studying African populations, the H3Africa Genome Analysis working group undertook the task of designing a cost-effective GWAS chip with content appropriate for use in genomics research studies of individuals from the African continent. To address gaps in sequence data for some of the African populations being studied in H3Africa projects, a high coverage whole genome sequence dataset was generated at the Baylor College of Medicine with samples provided by H3Africa PIs and collaborators, funded by the National Institutes of Health. This dataset includes 350 high coverage and 160 medium coverage whole genome sequences from 348 populations. The data is accompanied by minimal metadata, including country, ethnic group and sex. This dataset was used in the design of the new genotyping chip for better coverage of variants in African populations.
| EGAS00001002976 | EGA
Project description:Precision medicine is being enabled in high-income countries by the growing availability of health data, increasing knowledge of the genetic determinants of disease and variation in response to treatment (pharmacogenomics), and the decreasing costs of data generation, which promote routine application of genomic technologies in the health sector. However, there is uncertainty about the feasibility of applying precision medicine approaches in low- and middle-income countries, due to the lack of population-specific knowledge, skills, and resources. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive new research into the genetic and environmental basis for human diseases of relevance to Africans as well as to build capacity for genomic research on the continent. Precision medicine requires this capacity, in addition to reference data on local populations, and skills to analyze and interpret genomic data from the bedside. The H3Africa consortium is collectively processing samples and data for over 70,000 participants across the continent, accompanied in most cases by rich clinical information on a variety of non-communicable and infectious diseases. These projects are increasingly providing novel insights into the genetic basis of diseases in indigenous populations, insights that have the potential to drive the development of new diagnostics and treatments. The consortium has also invested significant resources into establishing high-quality biorepositories in Africa, a bioinformatic network, and a strong training program that has developed skills in genomic data analysis and interpretation among bioinformaticians, wet-lab researchers, and health-care professionals. Here, we describe the current perspectives of the H3Africa consortium and how it can contribute to making precision medicine in Africa a reality.
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Project description:BackgroundFollowing the introduction of meningococcal serogroup C conjugate vaccine in Italy in 2005, changes in the epidemiology of Invasive Meningococcal Disease (IMD) were expected. The study aims were to describe the epidemiological trend and to characterize the isolates collected during the period 2008/09-2012/13 by multilocus sequence typing (MLST). Data on laboratory confirmed meningococcal diseases from National Surveillance System of IMD were reported.MethodsPoisson regression models were used to estimate the incidence rate over time. Serogrouping and MLST were performed following published methods.ResultsThe incidence rate of laboratory confirmed meningococcal disease decreased from 0.33 per 100,000 population in 2008/09 to 0.25 per 100,000 population in 2012/13. The serogroup B incidence rate was significantly higher (p<0.01) than that of other serogroups, among all age groups. The significant decrease of the IMD incidence rate (p = 0.01) reflects the decrease of serogroup B and C, in particular among individuals aged 15-24 years old (p<0.01). On the other hand, serogroup Y incidence increased during the period (from 0.01/100,000 in 2008/09 to 0.02/100,000 in 2012/13, p = 0.05). Molecular characterizations revealed that ST-41/44 cc and ST-11 cc were the main clonal complexes identified among serogroup B and C isolates, respectively. In particular, ST-41/44 cc was predominant in all age groups, whereas ST-11 cc was not identified in infants less than 1 year of age.ConclusionsIMD incidence declined in Italy and serogroup B caused most of the IMD cases, with infants having the highest risk of disease. Continued surveillance is needed to provide information concerning further changes in circulating meningococci with special regard to serogroup distribution. Moreover, knowledge of meningococcal genotypes is essential to detect hyper-invasive strains.
| S-EPMC4596568 | biostudies-literature
Project description:Although the adrenal glands are not common sites of metastasis from hepatocellular carcinoma (HCC), this metastasis can be met in patients with advanced HCC in some clinical settings. However, the effectiveness of radiotherapy against such metastases is unclear. Therefore, we performed the present multi-institutional study to investigate tumor response, overall survival (OS), treatment-related toxicity, and prognostic factors after radiotherapy. We retrospectively reviewed 134 patients who completed a planned radiotherapy for their adrenal metastases. Complete response was noted in 6 (4.3%), partial response in 48 (34.0%), and stable disease in 78 patients (55.3%). The median OS was 12.8 months, and the 1-, 2-, and 5-year OS rates were 53.1%, 23.9%, and 9.3%, respectively. Grade 3 anorexia occurred in 2 patients, grade 3 diarrhea in 1, and grade 3 fatigue in 1. Multivariate analyses revealed that the following factors had significant effects on OS: controlled intrahepatic tumor; controlled extrahepatic metastasis; and Child-Pugh class A. Although patients with adrenal metastasis from HCC had poor OS, radiotherapy provided an objective response rate of 38.3% and disease stability of 93.6%, with minimal adverse events. Therefore, radiotherapy for these patients could represent a good treatment modality, especially for patients with controlled intrahepatic tumors, controlled extrahepatic metastasis, and good hepatic function.
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Project description:GCMS single quad data including fecal samples, dietary samples, and quality control samples.
2019-05-26 | MSV000083859 | MassIVE
Project description:Samples from Zambia generated for the H3Africa Chip Design Study
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Project description:Samples from Benin generated for the H3Africa Chip Design Study
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