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GENOMIC AND ENVIRONMENTAL RISK FACTORS FOR CARDIOMETABOLIC DISEASE IN KENYA, AWI-Gen PHASE II

Kenya, 2020 - 2021
Health and Well-Being (HaW)
Catheine Kyobutungi, Michele Ramsay
Last modified December 04, 2024 Page views 58493 Documentation in PDF Metadata DDI/XML JSON

Identification

IDNO
DDI-KEN-APHRC-AWIGen2-2019-v1.0
Title
GENOMIC AND ENVIRONMENTAL RISK FACTORS FOR CARDIOMETABOLIC DISEASE IN KENYA, AWI-Gen PHASE II
Subtitle
AWI-Gen PHASE II
Country
Name Country code
Kenya KEN
Abstract
The Genomic and environmental risk factors for cardiometabolic disease in Africans (AWI-Gen) project was a collaborative study between the University of the Witwatersrand (Wits) and the INDEPTH Network funded under the Human Heredity and Health in Africa (H3Africa) initiative. The H3Africa was a ground-breaking initiative to build institutional and individual capacity to undertake genetic and genomic studies in the African region. This collaboration, involved five INDEPTH sites i.e. 1) Navrongo - Ghana; 2) Nanoro - Burkina Faso; 3&4) Agincourt and Digkale - South Africa; and 5) Nairobi - Kenya) plus the Soweto-based birth-to-twenty cohort. AWI-Gen phase I was a population based cross-sectional study with a research platform of over 12,045 participants aged 40-60 years from Burkina Faso, Ghana, Kenya and South Africa. It aimed to understand the interplay between genetic, epigenetic and environmental risk factors for obesity and related cardiometabolic diseases (CMD) in sub-Saharan Africa and it generated epi-demographic, environmental, health history, behavioral, anthropometric, physiological and genetic data across a range of rapidly transitioning African settings. This provided a unique resource to examine genetic associations and gene-environment interactions that will contribute to Afrocentric risk prediction models and African-appropriate Mendelian Randomization instruments, and exploit their potential to improve personal and population health - while strengthening regional research capacity. We plan to continue this work in AWIGEN-phase II among the same participants recruited in AWIGen-I offering an opportunity to examine data in a longitudinal manner.
The AWI-Gen phase II project aims to establish the genomic contribution to CMD and risk at a time when multiple interacting transitions, in the presence of high background HIV or malaria prevalence, are driving a rapid escalation in CMD across the African continent. The project capitalizes on the unique strengths of existing longitudinal cohorts and well-established health and demographic surveillance systems(HDSS) run by the partner institutions. The six study sites represent geographic and social variability of African populations which are also at different stages of the demographic and epidemiological transitions. The work in Kenya will be undertaken in the Nairobi Urban Health and Demographic Surveillance System (NUHDSS) run by African Population and Health Research Center (APHRC) following participants who were recruited in AWIGEN-Phase I.
AWI-Gen II consisted of five main aims: i) AIM-1 (Sub-study 1): Genetic associations studies to elucidate functional pathways involved in determining body composition and risk for CMD by detecting pivotal genomic and environmental contributors; ii) AIM 2 (Sub-study 2): Genomics and bioinformatics-impact of genomic diversity on disease risk and precision public health; iii) AIM 3 (Sub-study 3): Examine changes over the menopausal transition in body composition and CMD risk; iv) AIM 4 (Sub-study 4): Examine gut microbiome in older adults and its relationship to obesity, diabetes and glucose tolerance and ageing; and v) AIM 5 (Sub-study 5): Explore respiratory disease in context of multi-morbidity.
In this application, we sought ethical approval for the Kenya study only. The other partners sought approval from their appropriate ethics review authorities in their countries. The study budget was $248,613 and was funded by National Institute of Health (NIH)-USA under H3Africa. Data collection was undertaken for approximately 12 months but sample processing, data analysis, manuscript writing, capacity building and policy engagement was continued up to three years after field work (up to 2022).

Version

Version Date
2024-09-19
Version Notes
N/A

Scope

Keywords
Keyword
N/A

Coverage

Geographic Coverage
County coverage (Informal settlements of Korogocho and Viwandani in Nairobi)
Unit of Analysis
Individual
Household
Universe
The survey covered individual participants aged 45-65 years.

Producers and sponsors

Authoring entity/Primary investigators
Agency Name Affiliation
Catheine Kyobutungi African Population and Health Research Center
Michele Ramsay University of the Witwatersrand (Wits)
Producers
Name Affiliation Role
Shukri Mohamed African Population and Health Research Center Co-Investigator
Gershim Asiki African Population and Health Research Center Co-Investigator
Isaac Kisiangani African Population and Health Research Center Co-Investigator
Michèle Ramsay University of the Witwatersrand Co-Investigator
Furahini Tluway University of the Witwatersrand Co-Investigator
James Kavai African Population and Health Research Center Data Documentation Specialist
Bonface Ingumba African Population and Health Research Center Data Governance Officer
Funding Agency/Sponsor
Name Abbreviation Role
Amsterdam Insitute of Global Health and Development (AIGHD) through the Dutch lottery. AIGHD Funder
Other Identifications/Acknowledgments
Name
N/A

Sampling

Sampling Procedure
a) Study design: A prospective cohort study to examine genetic associations and gene-environment interactions with measures of change in CMD and risk derived over 5 years (AWI-Gen I survey was in 2014/2015, and survey for phenotypic characteristics (under AWI-Gen II) among the same individuals will was repeated in 2019/2020). This was an extend baseline (AWI-Gen I) to provide longitudinal data (AWI-Gen II).
b) Study site (geographical)
The study in Kenya was conducted in Nairobi, specifically in Korogocho and Viwandani urban informal settlements which are covered by the NUHDSS.
c) Study populations
Sub-study 1 & 5: Adult (40-60 years at baseline) residents of Korogocho and Viwandani informal settlements registered in the NUHDSS.
Sample size
A sample size of 2000 per site (12000 in total) was used in AWIGEN-I based on power calculations and effect sizes. The power calculations show that we have power to detect realistic effect sizes, based on studies in other populations. Figure 2 illustrates the relationship between power and effect size for two different phenotypes, illustrating that the detectable effect size is realistic.
Power analysis for a sample size of 12000 individuals based on proposed candidate gene study for BMI (shown on the left) and for DXA (total body fat) (shown on the right). Given a sample size of 12000 in the AWI-Gen study, this graph shows effect size (x) which could be detected at a given power (y) for different minor allele frequencies (ranging from 0.05-045). For example, with a minor allele frequency of 0.25, we will have 80% power to detect an effect size (Beta) of 0.20 per allele change in BMI, and an effect size of 0.25 per allele change in body fat percentage.
For AWIGEN 2, we will follow the same participants. We anticipate a retention of 70% from the 2000 participants recruited in phase 1. Thus, our sample size for AWIGEN-11 was approximately 1400 participants for the Kenyan site to for sub-studies 1 and 2.
For Sub-studies 3 & 4 we will randomly sample 250 individuals for each sub-study which is a large sample by most microbiome project standards.
For Sub-study 5 we will include all participants selected in Sub-study 1
Deviations from the Sample Design
N/A
Response Rate
59%
Weighting
N/A

Data Collection

Dates of Data Collection (YYYY/MM/DD)
Start date End date
2020-08-31 2021-07-28
Mode of data collection
Other [oth]
Supervision
Field visits, weekly meetings and running weekly quality controls such as spotchecks, sit inn interviews, mirrow interview and observation interviews
Type of Research Instrument
The questionnaire for AWIGen 2 was a structured questionnaire developed by the University of Witwatersrand. The questionnaire was translated from English to Swahili. The individual questionnaire was administered to an adult (40-60 years old), which collected various information of the individual including, age, gender, BMI, Visceral fat levels, T2 diabetes status, blood pressure, socio-economic status, lifestyle (diet, tobacco, alcohol, exercise etc.) and HIV infection status. In addition, for participants in microbiome study we will ask information on antibiotics use. We will repeat the anthropometric measurements including height, weight, waist and hip circumference and ultrasound measurements of visceral and subcutaneous fat, and cIMT.

Data Processing

Cleaning Operations
Data was edited on REDCap during data entry and also secondary editing was performed once the files were submitted to the server.
Other Processing
N/A

Data Appraisal

Estimates of Sampling Error
N/A

Data access

Contact
Name Email URI
African Population and Health Researrch Center datarequests@aphrc.org aphrc.org
Conditions
APHRC data access condition

All non-APHRC staff seeking to use data generated at the Center must obtain written approval to use the data from the Director of Research.
This form is developed to assess applications for data use and facilitate responsible sharing of data with external partners/collaborators/researchers. By entering into this agreement, the undersigned agrees to use these data only for the purpose for which they were obtained and to abide by the conditions outlined below:

1.Data Ownership:
The data remain the property of APHRC; any unauthorized reproduction and sharing of the data is strictly prohibited. The user will, therefore, not release nor permit others to use or release the data to any other person without the written authorization from the Center.

2.Purpose:
The provided data must be used for the purpose specified in the Data Request Form; any other use not specified in the form must receive additional or separate authorization.

3.Respondent Identifiers:
The Center is committed to protecting the identity of the respondents who provide information in its research. All analytical data sets (both qualitative and quantitative) released by the Data Unit MUST are stripped of respondent identifiers to protect the identity of the respondents. By accepting to use APHRC data, the user is pledging that he/she will not, under any circumstance, regenerate the identifiers or permit others to use the data to learn the identity of any individual, household or community included in any data set.

4.Confidentiality pledge:
The user will not use nor permit others to use the data to report any information in the data sets that could identify, directly or by inference, individuals or households.

5.Reporting of errors or inconsistencies:
The user will promptly notify the Head of the Statistics and Survey Unit any errors discovered in the data as soon as the errors are discovered.

6.Publications resulting from APHRC data:
The Center requires external collaborators to work with APHRC staff on all publications resulting from its data. In order to facilitate this, lead authors should send a detailed concept note of the paper (including the background, rationale, data, analytical methods, and preliminary findings) to the Principle Investigator (or Theme Leader) for the project (with a copy to the Director of Research), who will circulate the abstract to concerned researchers for possible expression of interest in participating in the publication as co-authors. Any exception to the involvement of APHRC staff should be approved by the Director of Research, APHRC.

7.Security:
The user will take responsibility for the security of the data by ensuring that the data are used and stored in a secure environment where access is password protected. This will ensure that non-authorized people should not have access to the data.

8.Loss of privilege to use data:
In the event that APHRC determines that the data user is in violation of the conditions for using the data, or if the user wishes to cancel this agreement, the user will destroy the data files provided to him/her. APHRC retains the right to revoke this agreement or informs publishers to withhold publication of any work based wholly or in part on its data if the conditions for using the data are violated.

9.Acknowledgement:
Any work/reports from this data must acknowledge APHRC as the source of these data. For example, the suggested acknowledgement for NUHDSS data is:
"This research uses livelihoods data collected under the longitudinal Nairobi Urban Health and Demographic Surveillance System (NUHDSS) since 2006. The NUHDSS is carried out by the African Population and Health Research Center in two slums settlements (Korogocho and Viwandani) in Nairobi City."Additionally all funders, the study communities that provided the data, and staff who collected and analyzed or processed the data should be acknowledged.

10.Deposit of Reports/Papers:
The user should submit electronic and paper copies of all publications generated using APHRC data to the Policy Engagement and Communications Department, with copies to the Director of Research.

11.Change of contact details:
Citation requirement
Use of the dataset must be acknowledged using a citation which would include:
- the Identification of the Primary Investigator
- the title of the survey (including country, acronym and year of implementation)
- the survey reference number
- the source and date of download

Metadata production

Document ID
DDI-KEN-APHRC-AWIGen2-2019-v1.0
Producers
Name Abbreviation Role
African Population and Health Reseach Center APHRC Documentation of the DDI
Date of Production
2024-09-19
Document version
Version 1.0 (September 2024)