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Reference genotype and exome data from an Australian Aboriginal population for health-based research.

ABSTRACT: Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no 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 72 Aboriginal individuals to a depth of 20X coverage in ?80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.

SUBMITTER: Tang D

PROVIDER: S-EPMC4828942 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Reference genotype and exome data from an Australian Aboriginal population for health-based research.

Tang Dave D Anderson Denise D Francis Richard W RW Syn Genevieve G Jamieson Sarra E SE Lassmann Timo T Blackwell Jenefer M JM

Scientific data 20160412

Genetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no 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 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucle ...[more]

PMID: 27070114

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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:INTRODUCTION:In Australia, suicide is the leading cause of death for people aged 15-44 years. Health professionals deliver most of our key suicide prevention strategies via health services, but other efficacious population-level strategies include means restriction and public awareness campaigns. Currently, we have no population-level data allowing us to determine which individuals, in what parts of Australia, are likely to use our most promising interventions delivered by health services. The aims of this study are to describe: (1) health service utilisation rates in the year prior to death by suicide, and how this varies by individual case characteristics; (2) prescribed medicines use in the year prior to death by suicide, medicines used in suicide by poisoning and how this varies by individual case characteristics. METHODS AND ANALYSIS:This is a population-based case series study of all suicide cases in Australia identified through the National Coronial Information System (NCIS) from 2013 to 2019. Cases will be linked to administrative claims data detailing health service use and medicines dispensed in the year before death. We will also obtain findings from the coronial enquiry, including toxicology. Descriptive statistics will be produced to characterise health service and prescribed medicine use and how utilisation varies by age, sex, method of death and socioeconomic status. We will explore the geographical variability of health service and medicine use, highlighting regions in Australia associated with more limited access. ETHICS AND DISSEMINATION:This project involves the use of sensitive and confidential data. Data will be linked using a third-party privacy-preserving protocol meaning that investigators will not have access to identifiable information once the data have been linked. Statistical analyses will be carried out in a secure environment. This study has been approved by the following ethics committees: (1) the Justice Department Human Research Ethics Committee (REF: CF/17/23250), (2) the Western Australian Coroners Court (REF: EC 14/18?M0400), (3) the Australian Institute of Health and Welfare (REF: EO2017/4/366) and (4) NSW Population & Health Services Research Ethics Committee (REF: 2017/HRE1204). Findings will be published in peer-reviewed journals, presented at conferences and communicated to regulatory authorities, clinicians and policy-makers.

Project description:IntroductionOtitis media (OM) is one of the most common infectious diseases affecting children globally and the most common reason for antibiotic prescription and paediatric surgery. Australian Aboriginal children have higher rates of OM than non-Aboriginal children; however, there are no data comparing OM hospitalization rates between them at the population level. We report temporal trends for OM hospitalizations and in-hospital tympanostomy tube insertion (TTI) in a cohort of 469,589 Western Australian children born between 1996 and 2012.Materials and methodsWe used the International Classification of Diseases codes version 10 to identify hospitalizations for OM or TTI recorded as a surgical procedure. Using age-specific population denominators, we calculated hospitalization rates per 1,000 child-years by age, year and level of socio-economic deprivation.ResultsThere were 534,674 hospitalizations among 221,588 children hospitalized at least once before age 15 years. Aboriginal children had higher hospitalization rates for OM than non-Aboriginal children (23.3/1,000 [95% Confidence Interval (CI) 22.8,24.0] vs 2.4/1,000 [95% CI 2.3,2.4] child-years) with no change in disparity over time. Conversely non-Aboriginal children had higher rates of TTI than Aboriginal children (13.5 [95% CI 13.2,13.8] vs 10.1 [95% CI 8.9,11.4]). Children from lower socio-economic backgrounds had higher OM hospitalization rates than those from higher socio-economic backgrounds, although for Aboriginal children hospitalization rates were not statistically different across all levels of socio-economic disadvantage. Hospitalizations for TTI among non-Aboriginal children were more common among those from higher socio-economic backgrounds. This was also true for Aboriginal children; however, the difference was not statistically significant. There was a decline in OM hospitalization rates between 1998 and 2005 and remained stable thereafter.ConclusionAboriginal children and children from lower socio-economic backgrounds were over-represented with OM-related hospitalizations but had fewer TTIs. Despite a decrease in OM and TTI hospitalization rates during the first half of the study for all groups, the disparity between Aboriginal and non-Aboriginal children and between those of differing socioeconomic deprivation remained.

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Reference genotype and exome data from an Australian Aboriginal population for health-based research.

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Reference genotype and exome data from an Australian Aboriginal population for health-based research.

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