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Reference exome data for Australian Aboriginal populations to support health-based research.

ABSTRACT: Whole exome sequencing (WES) is a popular and successful technology which is widely used in both research and clinical settings. However, there is a paucity of reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an 'intersect-then-combine' (ITC) approach, using GATK and SAMtools to call variants. A total of 289,829 variants were identified in at least one individual in the NT cohort and 248,374 variants in at least one individual in the WA cohort. Of these, 166,719 variants were present in both cohorts, whilst 123,110 variants were private to the NT cohort and 81,655 were private to the WA cohort. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.

SUBMITTER: Weeks AL

PROVIDER: S-EPMC7190730 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Reference exome data for Australian Aboriginal populations to support health-based research.

Weeks Alexia L AL D'Antoine Heather A HA McKinnon Melita M Syn Genevieve G Bessarab Dawn D Brown Ngiare N Tong Steven Y C SYC Reményi Bo B Steer Andrew A Gray Lesley-Ann LA Inouye Michael M Carapetis Jonathan R JR Blackwell Jenefer M JM Lassmann Timo T

Scientific data 20200429 1

Whole exome sequencing (WES) is a popular and successful technology which is widely used in both research and clinical settings. However, there is a paucity of reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) pop ...[more]

PMID: 32350262

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Project description:BackgroundCommunity engagement or community involvement in Aboriginal health research is a process that involves partnering, collaborating and involving Aboriginal and Torres Strait Islander people or potential research participants to empower them to have a say in how research with Aboriginal communities is conducted. In the context of Aboriginal health, this is particularly important so that researchers can respond to the priorities of the community under study and conduct research in a way that is respectful of Aboriginal cultural values and beliefs. One approach to incorporating the principals of community engagement and to ensure cultural oversight and guidance to projects is to engage a community reference group. The aim of this study was to describe the process of establishing an Aboriginal community reference group and terms of reference. The community reference group was established to guide the research activities of a newly formed research collaboration aiming to to develop osteoarthritis care that meets the needs of Aboriginal and Torres Strait Islander people in Australia.MethodsAdopting a Participatory Action Research approach, this two-phase study was conducted in Victoria, Australia. In phase one, semi-structured research yarns (a cultural form of conversation used as a data gathering tool) were conducted collaboratively by Aboriginal and non-Aboriginal co-investigators to explore Aboriginal health stakeholder perspectives on establishing a community reference group and terms of reference. In phase two, recommendations in phase one were identified to invite members to participate in the community reference group and to ratify the terms of reference through a focus group. Data were analyzed using a framework analysis approach.ResultsThirteen people (eight female, four male) participated in phase one. Participants represented diverse professional backgrounds including physiotherapy, nursing, general practice, health services management, hospital liaison, cultural safety education, health research and the arts. Three themes were identified in phase one; Recruitment and Representation (trust and relationships, in-house call-outs, broad-spectrum expertise and Aboriginal majority); Purpose (community engagement, research steering, knowledge dissemination and advocacy) and; Function and Logistics (frequency and format of meetings, size of group, roles and responsibilities, authority, communication and dissemination). In phase two, six Aboriginal people were invited to become members of the community reference group who recommended changes which were incorporated into the seven domains of the terms of reference.ConclusionThe findings of this study are captured in a 10-step framework which describes practical strategies for establishing a community reference group and terms of reference in Aboriginal health research.

Project description:IntroductionResearch with Indigenous populations is not always designed with cultural sensitivity. Few publications evaluate or describe in detail seeking consent for research with Indigenous participants. When potential participants are not engaged in a culturally respectful manner, participation rates and research quality can be adversely affected. It is unethical to proceed with research without truly informed consent.Methods and analysisWe describe a culturally appropriate research protocol that is invited by Aboriginal communities of the Fitzroy Valley in Western Australia. The Picture Talk Project is a research partnership with local Aboriginal leaders who are also chief investigators. We will interview Aboriginal leaders about research, community engagement and the consent process and hold focus groups with Aboriginal community members about individual consent. Cultural protocols will be applied to recruit and conduct research with participants. Transcripts will be analysed using NVivo10 qualitative software and themes synthesised to highlight the key issues raised by the community about the research process. This protocol will guide future research with the Aboriginal communities of the Fitzroy Valley and may inform the approach to research with other Indigenous communities of Australia or the world. It must be noted that no community is the same and all research requires local consultation and input. To conduct culturally sensitive research, respected local people from the community who have knowledge of cultural protocol and language are engaged to guide each step of the research process from the project design to the delivery of results.Ethics and disseminationEthics approval was granted by the University of Sydney Human Research Ethics Committee (No. 2012/348, reference:14760), the Western Australia Country Health Service Ethics Committee (No. 2012:15), the Western Australian Aboriginal Health Ethics Committee and reviewed by the Kimberley Aboriginal Health Planning Forum Research Sub-Committee (No. 2012-008). Results will be disseminated through peer review articles, a local Fitzroy Valley report and conference presentations.

Dataset Information

Reference exome data for Australian Aboriginal populations to support health-based research.

Publications

Reference exome data for Australian Aboriginal populations to support health-based research.

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