EGAS00001001565-sc-2022-04-26T09:28:52Z - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001008736 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies:
1. 3781 British Pakistani/British Bangladeshi adults from East London Genes and Health
2. 2791 British South Asian mothers from Born in Bradford
3. 1428 British South Asian adults from Birmingham
4. 86 individuals (mixed ancestries) from families with rare diseases, from Queen Mary University London
All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866.
Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true:
SNPs: "QD < 2.0 || FS > 30 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0"
Indels: "QD < 2.0 || FS > 30 || ReadPosRankSum < -20.0"
| EGAD00001004581 | EGA
Project description:This includes variant calls (single nucleotide variants and small insertions/deletions) from 8086 (mostly British Pakistani/British Bangladeshi) individuals from the following studies:
1. 5236 British Pakistani/British Bangladeshi adults from East London Genes and Health (ELGH)
2. 2624 British South Asian mothers from Born in Bradford (mostly Pakistani) (BiB)
3. 1061 British South Asian adults from Birmingham (mostly Pakistani) (Birm)
All of the Birmingham and most of the Born in Bradford samples were previously sequenced as part of PMID: 26940866.
In the sample list file, the columns of interest to most people will be:
vcf.id - sample ID from the vcf
cohort - which cohort they're in
sex.assigned - sex inferred from coverage on the X and Y chromosomes. Individuals for whom this did not match their reported sex have been discarded
total, chrX and chrY - coverage within bait regions across all chromosomes, chrX and chrY respectively
Mapping was done with bwa-mem and variant calling was carried out with GATK HaplotypeCaller. We removed variant sites for which the following was true: SNPs: "QD < 2.0 || FS > 30 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0" Indels: "QD < 2.0 || FS > 30 || ReadPosRankSum < -20.0"
| EGAD00001005469 | EGA
Project description:Genes & Health is a cohort of British Bangladeshi and British Pakistani individuals. In the Feb2020 data freeze, 28,022 individuals were genotyped on the Illumina Infinium Global Screening Array v3 chip (with the additional Multi-Disease variants). Imputation was performed using the Michigan Imputation Server with the GenomeAsia pilot reference panel, which contains 1,739 genomes and 642 from them are from South Asian groups. This dataset contains imputed SNPs with imputation accuracy >0.3 and MAF >0.1%.
| EGAS00001005373 | EGA
Project description:Genotyped data for 28,022 British individuals with South Asian ancestry from the Genes and Health cohort (Feb2020), which were imputed with the GenomeAsia pilot reference panel.
| EGAD00001007815 | EGA
Project description:Background and study aims
Colorectal cancer is one of the most common cancers worldwide, and the risk of its development increases with age. It is therefore of great importance to undertake preventive measures against colorectal cancer in order to reduce its increasing prevalence. Undergoing cancer screening is one of the most effective ways of preventing the development of colorectal cancer through early detection, leading to increased chances of successful treatment and survival. Despite the proven benefits of cancer screening, studies showed that South Asian ethnic minorities, both in Hong Kong and worldwide, do not tend to use the publicly available cancer screening services, resulting in a higher chance of these individuals developing colorectal cancer, particularly among older adults. It was shown that their reduced tendency to undergo cancer screening is partly contributed by their low level of health knowledge and barriers to accessing health and cancer preventive services. In view of this, educational programmes are required to educate older South Asians ethnic minorities on the importance of cancer screening. With studies showing that younger family members educated on the importance of cancer screening are more able to recommend their older family members to undergo cancer screening, such an education programme should be targeted for families rather than older adults alone. This study aims to develop a multimedia health promotion programme for families of South Asian ethnic minorities in Hong Kong, to increase their awareness of the importance of undergoing cancer screening in colorectal cancer prevention.
Who can participate?
Pairs of healthy South Asian (Indian, Pakistani and Nepali) adults living in Hong Kong, comprising a younger family member aged between 18 and 61 and an older family member aged between 62 and 71
What does the study involve?
Each pair of participants is randomly allocated into either group A or group B. Participants in group A receive the educational programme. It is delivered in one session using multiple means including a health talk on colorectal cancer and cancer screening, presentation of a video clip depicting the benefits of family support in motivating an older family member to undergo cancer screening, and a health information booklet. Participants in group B receive this programme after those in group A have completed the programme. For participants in both groups, before and after group A participants have received the programme, the researchers assess the following: whether the younger family members of each participant pair are willing to encourage their older family members to consult a family doctor for undertaking colorectal cancer screening, and are prepared to assist older family members in collecting samples for colorectal cancer screening; whether the older family members of each participant pair have seen a family doctor for an appointment in colorectal cancer screening. The researchers also assess whether participants in both groups are satisfied with the programme after they have attended it.
| 2422724 | ecrin-mdr-crc
Project description:The Healthy Brain Initiative (HBI) is a longitudinal study focused on older adults in South Florida, with the goal of advancing dementia prevention and promoting brain health. We generated DNA methylation profiles for 88 HBI participants aged over 65. The Illumina MethylationEPIC v2.0 Beadchip was used to obtain DNA methylation profiles across approximately 935k CpGs from human blood samples.
2024-11-08 | GSE281429 | GEO
Project description:Previously developed gene expression signatures had high predictive accuracy at distinguishing viral and bacterial infection in a South Asian cohort with ARI caused by typical and atypical pathogens.
2020-07-06 | GSE149947 | GEO
Project description:Birth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights from population genetics to rare disease associations. Avon Longitudinal Study of Parents and Children (ALSPAC)recruited 14,775 babies of predominantly White ethnicity in the Avon county of south-west England between 1991 and 1992. Born in Bradford (BiB) is similarly focused on a particular local area, the city of Bradford in the north of England, and recruited 13,858 babies between 2007 and 2011, of whom ~41% self-report as white British and ~59% as other ethnicities, predominantly Pakistani. Millennium Cohort Study (MCS) is a national cohort that recruited 18,827 children born between 2000 and 2002, intentionally over-sampling areas with high child poverty, large ethnic minority populations, and smaller UK nations (Wales, Scotland and Northern Ireland) Available here is a subset of exome-sequenced parents and children from these studies (CRAMS and post-QC VCFs) as detailed in this data note. Phenotypic data is also available by submitting an application to the corresponding cohort: https://www.bristol.ac.uk/alspac/researchers/our-data/[bristol.ac.uk]
| EGAD00001015371 | EGA
Project description:AWI-Gen Phase 1 Population cross-sectional study of older adults (mostly between 40 and 60 years), men and women. Six study sites in four sub-Saharan African counties. Ghana, Burkina Faso, Kenya and South Africa. ~12,500 participants, some groups are missing data for specific variables. Questionnaire data (demography, health history, family health history, behaviour and infection data); anthropometry; laboratory assays on blood and urine.
| EGAD00001006425 | EGA
Project description:Japanese encephalitis virus (JEV) is a causative agent of encephalitis, mostly prevalent in Asia and South-Asian countries. Neuroinflammation is the hallmark of encephalitis, mediated in parts through the activation of brain-resident microglial cell, thus playing a critical role in determining pathogenesis. Deregulated activity of microglia can be lethal for the brain tissue. Interferon Regulatory Factor 8 (Irf8) mediates differentiation and transformation of microglia to reactive phenotypes and also regulates antiviral response through cross-talk with interferon pathway. In this study, we have conducted a comparative study between JEV infected C57BL/6 wild type and Irf8 Knockout (IRF8-/-) to identify the genes directly or indirectly regulated by IRF8.
2021-08-09 | GSE154002 | GEO