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Gwynne K, Jiang S, Venema R, Christie V, Boughtwood T, Ritha M, Skinner J, Ali N, Rambaldini B, Calma T. Genomics and inclusion of Indigenous peoples in high income countries. Hum Genet 2023; 142:1407-1416. [PMID: 37479894 PMCID: PMC10449672 DOI: 10.1007/s00439-023-02587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
Genomics research related to Indigenous people has been at worst exploitative and at best, retrospectively on a journey to improve effective engagement of Indigenous individuals and communities. Genomics can positively impact all stages of clinical management, and to improve genomic effectiveness researchers aggregate genomic data from diverse global sub-populations, such as shared ancestry groupings, as people within these groupings will have a greater proportion of shared DNA traits. While genomics is already being used worldwide to improve lives, its utility and effectiveness has not been maximized for individuals with Indigenous ancestry. Several large datasets of human genetic variation have been made publicly available, of which the most widely used is the Genome Aggregation Database (gnomAD), but none of these databases currently contain any population-specific data for Indigenous populations. There are many reasons why Indigenous people have been largely left out of genomics research and, because of this, miss out on the benefits offered. It is also clear that if research is to be effective, it needs to be done 'with' and not 'on' Indigenous communities. This systematic review of the literature regarding Indigenous peoples (in high income countries) and genomics aims to review the existing literature and identify areas of strength and weakness in study design and conduct, focusing on the effectiveness of Indigenous community engagement.
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Affiliation(s)
- Kylie Gwynne
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Shirley Jiang
- University of Toronto, 27 King's College Circuit, Toronto, Canada
| | - Robertson Venema
- University of Toronto, 27 King's College Circuit, Toronto, Canada
| | - Vita Christie
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia.
| | - Tiffany Boughtwood
- Australian Genomics, 50 Flemington Rd, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Marida Ritha
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - John Skinner
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Nyesa Ali
- Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Boe Rambaldini
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Tom Calma
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
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2
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Soares GH, Hedges J, Sethi S, Poirier B, Jamieson L. From biocolonialism to emancipation: considerations on ethical and culturally respectful omics research with indigenous Australians. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2023; 26:487-496. [PMID: 37171744 PMCID: PMC10425494 DOI: 10.1007/s11019-023-10151-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
As part of a (bio)colonial project, the biological information of Indigenous Peoples has historically been under scientific scrutiny, with very limited benefits for communities and donors. Negative past experiences have contributed to further exclude Indigenous communities from novel developments in the field of omics research. Over the past decade, new guidelines, reflections, and projects of genetic research with Indigenous Peoples have flourished in Australia, providing opportunities to move the field into a place of respect and ethical relationships. This review explores the ethical and cultural implications of the use of biological samples from Indigenous communities in biomedical research. A structured framework outlining emerging topics of interest for the development of respectful omics research partnerships with Indigenous Australians is presented. This paper highlights aspects related to Indigenous governance, community and individual consent, respectful handling of biological samples, data management, and communication in order to protect Indigenous interests and rights and to promote communities' autonomy.
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Affiliation(s)
- Gustavo H Soares
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia.
| | - Joanne Hedges
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Sneha Sethi
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Brianna Poirier
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
| | - Lisa Jamieson
- Australian Research Centre for Population Oral Health, The University of Adelaide, Adelaide, SA, Australia
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3
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Kaladharan S, Vidgen ME, Pearson JV, Donoghue VK, Whiteman DC, Waddell N, Pratt G. Ask the people: developing guidelines for genomic research with Aboriginal and Torres Strait Islander peoples. BMJ Glob Health 2021; 6:bmjgh-2021-007259. [PMID: 34732514 PMCID: PMC8572381 DOI: 10.1136/bmjgh-2021-007259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/18/2021] [Indexed: 01/07/2023] Open
Abstract
In health and medical research, guidelines are a set of statements and recommendations, whereby experts or stakeholders assess published literature to generate practical advice for a specific audience. This emphasis on guidelines development with expert consultation and published literature is not practical or inclusive when working in disciplines with minimal data and addressing issues that concern under-represented communities. Here we describe the process used for developing guidelines for the conduct of genomic research projects in partnership with Aboriginal and Torres Strait Islander peoples. A new technology with individual and community level ethical and social implications, and First Nations peoples with cultural and community expectations for research. We developed the guidelines through a consultation process that used participatory action research to engage with various stakeholders during multiple rounds of tailored activities. The end product, ‘Genomic Partnerships: Guidelines for Genomics Research with Aboriginal and Torres Strait Islander peoples of Queensland’ reflects the needs of the end-users and perspectives of the Aboriginal and Torres Strait Islander peoples, communities and organisations that participated. Through this process, we have identified recommendations for developing guidelines with other under-represented communities.
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Affiliation(s)
- Sid Kaladharan
- Aboriginal and Torres Strait Islander Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Nambour General Hospital, Sunshine Coast Hospital and Health Service, Nambour, Queensland, Australia
| | - Miranda E Vidgen
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - John V Pearson
- Genome Informatics, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Victoria K Donoghue
- Aboriginal and Torres Strait Islander Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Queensland Aboriginal and Islander Health Council, Brisbane, Queensland, Australia
| | - David C Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Nicola Waddell
- Medical Genomics, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Gregory Pratt
- Aboriginal and Torres Strait Islander Health, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
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4
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Koenigstein F, Boekstegers F, Wilson JF, Fuentes-Guajardo M, Gonzalez-Jose R, Bedoya G, Bortolini MC, Acuña-Alonzo V, Gallo C, Linares AR, Rothhammer F, Bermejo JL. Inbreeding, native American ancestry and child mortality: Linking human selection and paediatric medicine. Hum Mol Genet 2021; 31:975-984. [PMID: 34673976 PMCID: PMC8947305 DOI: 10.1093/hmg/ddab302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 11/13/2022] Open
Abstract
The children of related parents show increased risk of early mortality. The Native American genome typically exhibits long stretches of homozygosity, and Latin Americans are highly heterogeneous regarding the individual burden of homozygosity, the proportion, and the type of Native American ancestry. We analysed nationwide mortality and genome-wide genotype data from admixed Chileans to investigate the relationship between common causes of child mortality, homozygosity and Native American ancestry. Results from two-stage linear-Poisson regression revealed a strong association between the sum length of runs of homozygosity (SROH) above 1.5 Megabases (Mb) in each genome and mortality due to intracranial non-traumatic haemorrhage of foetus and new-born (5% increased risk of death per Mb in SROH, P = 1 × 10-3) and disorders related to short gestation and low birth weight (P = 3 × 10-4). The major indigenous populations in Chile are Aymara-Quechua in the north of the country, and the Mapuche-Huilliche in the south. The individual proportion of Aymara-Quechua ancestry was associated with an increased risk of death due to anencephaly and similar malformations (P = 4 × 10-5), and the risk of death due to Edwards and Patau trisomy syndromes decreased 4% per 1% Aymara-Quechua ancestry proportion (P = 4 × 10-4) and 5% per 1% Mapuche-Huilliche ancestry proportion (P = 2 × 10-3). The present results suggest that short gestation, low birth weight and intracranial non-traumatic haemorrhage mediate the negative effect of inbreeding on human selection. Independent validation of the identified associations between common causes of child death, homozygosity and fine-scale ancestry proportions may inform paediatric medicine.
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Affiliation(s)
- Fabienne Koenigstein
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - Felix Boekstegers
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Tarapacá University, Arica, Chile
| | - Rolando Gonzalez-Jose
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina
| | - Gabriel Bedoya
- Instituto de Biología, Grupo Genmol, Universidad de Antioquía, Medellín, Colombia
| | - Maria Cátira Bortolini
- Instituto de Biociências, Universidad Federal do Rio Grande do Sul, Puerto Alegre, Brazil
| | | | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Andres Ruiz Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.,Aix-Marseille Université, CNRS, EFS, ADES, Marseille, France.,Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London, UK
| | | | - Justo Lorenzo Bermejo
- Statistical Genetics Research Group, Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany
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5
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Dalach P, Savarirayan R, Baynam G, McGaughran J, Kowal E, Massey L, Jenkins M, Paradies Y, Kelaher M. "This is my boy's health! Talk straight to me!" perspectives on accessible and culturally safe care among Aboriginal and Torres Strait Islander patients of clinical genetics services. Int J Equity Health 2021; 20:103. [PMID: 33865398 PMCID: PMC8052687 DOI: 10.1186/s12939-021-01443-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/05/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Aboriginal and Torres Strait Islander people do not enjoy equal access to specialist health services that adequately meet their needs. Clinical genetics services are at the vanguard of realising the health benefits of genomic medicine. As the field continues to expand in clinical utility and implementation, it is critical that Aboriginal and Torres Strait Islander people are able to participate and benefit equally to avoid further widening of the existing health gap. This is the first study to explore barriers to accessing clinical genetics services among Aboriginal and Torres Strait Islander people, which has been acknowledged as a key strategic priority in Australian genomic health policy. METHODS A participatory design process engaged a majority-Aboriginal Project Reference Group and Aboriginal End-User Group. 63 semi-structured interviews were conducted with Aboriginal and/or Torres Strait Islander people who had accessed the government-funded clinical genetics service in Western Australia, Queensland or the Northern Territory between 2014 and 2018. The sample included patients, parents and carers. Participants were asked to recount their 'patient journey', from referral through to post-appointment and reflect on their perceptions of genetics and its implications for the health of themselves and their families. Analysis tracked chronological service engagement, followed by an inductive thematic approach. RESULTS Barriers to access and engagement were present at each stage of the patient journey. These included challenges in obtaining a referral, long waiting periods, limited genetic literacy, absence of Aboriginal support services, communication challenges and lack of adequate psychosocial support and follow-up after attendance. Participants' overall experiences of attending a genetic health service were varied, with positive perceptions tied closely to a diagnosis being achieved. The experience of (and expectation for) recognition of cultural identity and provision of culturally safe care was low among participants. Unaddressed concerns continued to cause significant distress in some people years after their appointment took place. CONCLUSIONS There is significant scope for improving the care provided to Aboriginal and Torres Strait Islander people at clinical genetics services. Immediate attention to minimising logistical barriers, developing relationships with Aboriginal Community Controlled Health Services and providing practical and specific cultural safety training for practitioners is required at the service-level. Our findings strongly support the development of guidelines or policies recognising the collective cultural needs of Aboriginal and Torres Strait Islander people in relation to genomic health care.
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Affiliation(s)
- Philippa Dalach
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia.
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute and University of Melbourne, Parkville, Victoria, Australia
| | - Gareth Baynam
- Western Australian Department of Health, Genetic Services of Western Australia, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, Western Australian Department of Health, Perth, Australia
- Telethon Kids Institute and Division of Paediatrics, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, St Lucia, Queensland, Australia
| | - Emma Kowal
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong, Victoria, Australia
| | - Libby Massey
- Machado Joseph Disease Foundation, Alyangula, Northern Territory, Australia
- James Cook University, Townsville, Queensland, Australia
| | - Misty Jenkins
- Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Yin Paradies
- Alfred Deakin Institute for Citizenship and Globalisation, Deakin University, Geelong, Victoria, Australia
| | - Margaret Kelaher
- Centre for Health Policy, School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
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6
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Tong SY, D'Antoine H, McKinnon M, Turner K, Hudson M, Brown N, Carapetis JR, Bessarab DC. Lessons learned in genetic research with Indigenous Australian participants. Med J Aust 2020; 212:200-202.e1. [PMID: 32017112 DOI: 10.5694/mja2.50499] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Steven Yc Tong
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and Peter Doherty Institute for Infection and Immunity, Melbourne, VIC.,Menzies School of Health Research, Darwin, NT
| | | | | | - Kyle Turner
- Victorian Infectious Disease Service, Royal Melbourne Hospital, and Peter Doherty Institute for Infection and Immunity, Melbourne, VIC
| | - Maui Hudson
- University of Waikato, Hamilton, Waikato, New Zealand
| | - Ngiare Brown
- South Australian Health and Medical Research Institute, Adelaide, SA
| | | | - Dawn C Bessarab
- Centre for Aboriginal Medical and Dental Health, University of Western Australia, Perth, WA
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7
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McWhirter RE, Otahal P, Taylor-Thomson D, Maypilama EL, Rumbold AR, Dickinson JL, Thorn JC, Boyle JA, Condon JR. Recurrence patterns identify aggressive form of human papillomavirus-dependent vulvar cancer. Aust N Z J Obstet Gynaecol 2019; 60:231-237. [PMID: 31603537 DOI: 10.1111/ajo.13075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/26/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND Vulvar cancer is rare and, as a result, is understudied. Treatment is predominantly surgery, irrespective of the type of vulvar cancer, and is associated with physical, emotional and sexual complications. A cluster of human papillomavirus (HPV)-dependent vulvar cancer patients was identified in Arnhem Land Northern Territory (NT), Australia, in which young Indigenous women were diagnosed at 70 times the national incidence rate. AIMS To assess whether women from the Arnhem Land cluster differ from women with vulvar squamous cell carcinoma (VSCC) and vulvar intraepithelial neoplasia (VIN) resident elsewhere in the NT in recurrence after treatment, disease progression and mortality. MATERIALS AND METHODS A retrospective cohort study of NT-resident women diagnosed with VIN or invasive vulvar cancer (VSCC) between 1 January 1993 and 30 June 2015 was undertaken. Time to recurrence was assessed using cumulative incidence plots and Fine and Gray competing risk regression models. Mean cumulative count was used to estimate the burden of recurrent events. RESULTS Indigenous women from Arnhem Land experienced more recurrences after treatment than non-Indigenous women, the cancers recurred faster, and Indigenous women have worse survival at five years. CONCLUSIONS In characterising the epidemiological features of this cluster, we have identified a particularly aggressive form of vulvar cancer. This provides a unique opportunity for elucidating the aetiopathological pathways driving vulvar cancer development that may ultimately lead to preventive and therapeutic targets for this neglected malignancy. Further, these findings have important implications for clinical practice and HPV vaccination policy in the affected population.
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Affiliation(s)
- Rebekah E McWhirter
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,Centre for Law and Genetics, Faculty of Law, University of Tasmania, Hobart, Tasmania, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Petr Otahal
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Debbie Taylor-Thomson
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | - Alice R Rumbold
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Jane C Thorn
- Department of Obstetrics and Gynaecology, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Jacqueline A Boyle
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.,Monash Centre for Health Research and Implementation, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - John R Condon
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
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8
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Castles S, Wainer Z, Jayasekara H. Risk factors for cancer in the Australian Aboriginal and Torres Strait Islander population: a systematic review. Aust J Prim Health 2016; 22:190-197. [PMID: 27118100 DOI: 10.1071/py15048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 10/07/2015] [Indexed: 11/23/2022]
Abstract
Cancer incidence in the Australian Aboriginal and Torres Strait Islander population is higher and survival lower compared with non-Indigenous Australians. A proportion of these cancers are potentially preventable if factors associated with carcinogenesis are known and successfully avoided. We conducted a systematic review of the published literature to examine risk factors for cancer in the Australian Aboriginal and Torres Strait Islander population. Electronic databases Medline, Web of Science and the Australian Aboriginal and Torres Strait Islander Health Bibliographic Index were searched through August 2014 using broad search terms. Studies reporting a measure of association between a risk factor and any cancer site in the Australian Aboriginal and Torres Strait Islander population were eligible for inclusion. Ten studies (1991-2014) were identified, mostly with small sample sizes, showing marked heterogeneity in terms of methods used to assess exposure and capture outcomes, and often using descriptive comparative analyses. Relatively young (as opposed to elderly) and geographically remote Aboriginal and Torres Strait Islanders were found to be at increased risk for selected cancers while most modifiable lifestyle and behavioural risk factors were rarely assessed. Further studies examining associations between potential risk factors and cancer will help define public health policy for cancer prevention in the Australian Aboriginal and Torres Strait Islander population.
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Affiliation(s)
- Simon Castles
- Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett Street, East Melbourne, Vic. 8006, Australia
| | - Zoe Wainer
- Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett Street, East Melbourne, Vic. 8006, Australia
| | - Harindra Jayasekara
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Carlton, Vic. 3010, Australia
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9
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McWhirter R, Nicol D, Savulescu J. Genomics in research and health care with Aboriginal and Torres Strait Islander peoples. Monash Bioeth Rev 2016; 33:203-9. [PMID: 26507135 DOI: 10.1007/s40592-015-0037-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Genomics is increasingly becoming an integral component of health research and clinical care. The perceived difficulties associated with genetic research involving Aboriginal and Torres Strait Islander people mean that they have largely been excluded as research participants. This limits the applicability of research findings for Aboriginal and Torres Strait Islander patients. Emergent use of genomic technologies and personalised medicine therefore risk contributing to an increase in existing health disparities unless urgent action is taken. To allow the potential benefits of genomics to be more equitably distributed, and minimise potential harms, we recommend five actions: (1) ensure diversity of participants by implementing appropriate protocols at the study design stage; (2) target diseases that disproportionately affect disadvantaged groups; (3) prioritise capacity building to promote Indigenous leadership across research professions; (4) develop resources for consenting patients or participants from different cultural and linguistic backgrounds; and (5) integrate awareness of issues relating to Indigenous people into the governance structures, formal reviews, data collection protocols and analytical pipelines of health services and research projects.
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Affiliation(s)
- Rebekah McWhirter
- Menzies Institute for Medical Research, University of Tasmania, Private Bag 23, Hobart, TAS, 7000, Australia. .,Faculty of Law, Centre for Law and Genetics, University of Tasmania, Hobart, Australia.
| | - Dianne Nicol
- Faculty of Law, Centre for Law and Genetics, University of Tasmania, Hobart, Australia
| | - Julian Savulescu
- Faculty of Philosophy, Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford, UK
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10
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Yang TL, Guo Y, Zhang JG, Xu C, Tian Q, Deng HW. Genome-wide Survey of Runs of Homozygosity Identifies Recessive Loci for Bone Mineral Density in Caucasian and Chinese Populations. J Bone Miner Res 2015; 30:2119-26. [PMID: 25983029 PMCID: PMC4615523 DOI: 10.1002/jbmr.2558] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 04/28/2015] [Accepted: 05/13/2015] [Indexed: 02/01/2023]
Abstract
Runs of homozygosity (ROHs), in which both parental alleles are identical, have been proposed to have recessive effects on multiple human complex diseases. Osteoporosis is a common complex disease characterized by low bone mineral density (BMD), which is highly heritable. And recessive loci that contribute to BMD variations have been identified. In this study, we performed a genome-wide ROHs association study using our SNP array data from three GWAS samples including 4,900 subjects from Caucasian and Chinese populations. Significant results were further subjected to replication in 3,747 additional subjects. ROHs associated with BMD were also tested for associations with osteoporotic fractures in a GWAS fracture sample. Combining results from all the samples, we identified 697 autosomal regions with ROHs. Among these, we detected genome-wide significant associations between BMD and 6 ROHs, including ROH1q31.3, 1p31.1, 3q26.1, 11q12.1, 21q22.1 and 15q22.3 (combined P = 6.29 × 10(-5)-3.17 × 10(-8)). Especially, ROH1p31.1 was found to be associated with increased risk of osteoporotic hip fractures (odds ratio [OR] = 3.71, P = 0.032). To investigate the functional relevance of the identified ROHs, we performed cis-expression quantitative trait locus (eQTL) analysis in lymphoblast cell lines. Three ROHs, including ROH1p31.1, 11q12.1, and 15q22.3, were found to be significantly associated with mRNA expression levels of their nearby genes (PeQTL < 0.05). In summary, our findings reveal that ROHs could play as recessive-acting determinants contributing to the pathogenesis of osteoporosis. Further molecular and functional studies are needed to explore and clarify the potential mechanism.
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Affiliation(s)
- Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P. R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P. R. China
| | - Ji-Gang Zhang
- School of Public Health and Tropical Medicine, Tulane University New Orleans, LA 70112, USA
| | - Chao Xu
- School of Public Health and Tropical Medicine, Tulane University New Orleans, LA 70112, USA
| | - Qing Tian
- School of Public Health and Tropical Medicine, Tulane University New Orleans, LA 70112, USA
| | - Hong-Wen Deng
- School of Public Health and Tropical Medicine, Tulane University New Orleans, LA 70112, USA
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11
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Christofidou P, Nelson CP, Nikpay M, Qu L, Li M, Loley C, Debiec R, Braund PS, Denniff M, Charchar FJ, Arjo AR, Trégouët DA, Goodall AH, Cambien F, Ouwehand WH, Roberts R, Schunkert H, Hengstenberg C, Reilly MP, Erdmann J, McPherson R, König IR, Thompson JR, Samani NJ, Tomaszewski M. Runs of Homozygosity: Association with Coronary Artery Disease and Gene Expression in Monocytes and Macrophages. Am J Hum Genet 2015; 97:228-37. [PMID: 26166477 PMCID: PMC4573243 DOI: 10.1016/j.ajhg.2015.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/04/2015] [Indexed: 02/07/2023] Open
Abstract
Runs of homozygosity (ROHs) are recognized signature of recessive inheritance. Contributions of ROHs to the genetic architecture of coronary artery disease and regulation of gene expression in cells relevant to atherosclerosis are not known. Our combined analysis of 24,320 individuals from 11 populations of white European ethnicity showed an association between coronary artery disease and both the count and the size of ROHs. Individuals with coronary artery disease had approximately 0.63 (95% CI: 0.4-0.8) excess of ROHs when compared to coronary-artery-disease-free control subjects (p = 1.49 × 10(-9)). The average total length of ROHs was approximately 1,046.92 (95% CI: 634.4-1,459.5) kb greater in individuals with coronary artery disease than control subjects (p = 6.61 × 10(-7)). None of the identified individual ROHs was associated with coronary artery disease after correction for multiple testing. However, in aggregate burden analysis, ROHs favoring increased risk of coronary artery disease were much more common than those showing the opposite direction of association with coronary artery disease (p = 2.69 × 10(-33)). Individual ROHs showed significant associations with monocyte and macrophage expression of genes in their close proximity-subjects with several individual ROHs showed significant differences in the expression of 44 mRNAs in monocytes and 17 mRNAs in macrophages when compared to subjects without those ROHs. This study provides evidence for an excess of homozygosity in coronary artery disease in outbred populations and suggest the potential biological relevance of ROHs in cells of importance to the pathogenesis of atherosclerosis.
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Affiliation(s)
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Biomedical Research Unit in Cardiovascular Disease, Leicester LE3 9QP, UK
| | - Majid Nikpay
- Ruddy Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON K1Y 4W7, Canada; Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON K1Y 3V5, Canada
| | - Liming Qu
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina Loley
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck 23562, Germany
| | - Radoslaw Debiec
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
| | - Peter S Braund
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
| | - Fadi J Charchar
- Faculty of Science and Technology, School of Applied and Biomedical Sciences, Federation University Australia, Ballarat, VIC 3350, Australia
| | - Ares Rocanin Arjo
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France; INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France; Sorbonne Universités, UPMC University, Paris 06, UMR_S 1166, Paris 75013, France
| | - David-Alexandre Trégouët
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France; INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France; Sorbonne Universités, UPMC University, Paris 06, UMR_S 1166, Paris 75013, France
| | - Alison H Goodall
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Biomedical Research Unit in Cardiovascular Disease, Leicester LE3 9QP, UK
| | - Francois Cambien
- ICAN Institute for Cardiometabolism and Nutrition, Paris 75013, France; INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris 75013, France; Sorbonne Universités, UPMC University, Paris 06, UMR_S 1166, Paris 75013, France
| | - Willem H Ouwehand
- Department of Haematology, Cambridge Biomedical Campus, University of Cambridge and NHS Blood and Transplant, Cambridge CB2 0PT, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Robert Roberts
- Ruddy Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON K1Y 4W7, Canada; Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON K1Y 3V5, Canada
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, Munich 80636, Germany; Deutsches Zentrum für Herz- und Kreislauf-Forschung (DZHK), Munich 80636, Germany
| | - Christian Hengstenberg
- Deutsches Herzzentrum München, Technische Universität München, Munich 80636, Germany; Deutsches Zentrum für Herz- und Kreislauf-Forschung (DZHK), Munich 80636, Germany
| | - Muredach P Reilly
- Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA 19148, USA
| | - Jeanette Erdmann
- Institute for Integrative and Experimental Genomics, University of Lübeck, Lübeck 23562, Germany
| | - Ruth McPherson
- Ruddy Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, ON K1Y 4W7, Canada; Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, ON K1Y 3V5, Canada
| | - Inke R König
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck 23562, Germany
| | - John R Thompson
- Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Biomedical Research Unit in Cardiovascular Disease, Leicester LE3 9QP, UK
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Biomedical Research Unit in Cardiovascular Disease, Leicester LE3 9QP, UK.
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12
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McWhirter RE, Marthick JR, Boyle JA, Dickinson JL. Genetic and epigenetic variation in vulvar cancer: Current research and future clinical practice. Aust N Z J Obstet Gynaecol 2014; 54:406-11. [DOI: 10.1111/ajo.12241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/22/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Rebekah E. McWhirter
- Menzies Research Institute Tasmania; University of Tasmania; Hobart Tasmania Australia
- Menzies School of Health Research; Charles Darwin University; Darwin Northern Territory Australia
| | - James R. Marthick
- Menzies Research Institute Tasmania; University of Tasmania; Hobart Tasmania Australia
| | - Jacqueline A. Boyle
- Monash Centre for Health Research and Implementation; School of Public Health and Preventive Medicine; Monash University; Clayton Victoria Australia
| | - Joanne L. Dickinson
- Menzies Research Institute Tasmania; University of Tasmania; Hobart Tasmania Australia
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