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Roman S, Campos-Medina L, Leal-Mercado L. Personalized nutrition: the end of the one-diet-fits-all era. Front Nutr 2024; 11:1370595. [PMID: 38854164 PMCID: PMC11157041 DOI: 10.3389/fnut.2024.1370595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
Personalized Nutrition emerged as a new trend for providing nutritional and food advice based on the individual's genetic composition, a field driven by the advancements in the multi-omic sciences throughout the last century. It intends not only to tailor the recommended daily allowances of nutrients and functional foods that a person may need but also to maintain the principles of sustainability and eco-friendliness. This principle implies the implementation of strategies within the healthcare system to advocate for the ending of the one-diet-fits-all paradigm by considering a personalized diet as an ally to prevent diet-related chronic diseases. In this Perspective, we highlight the potential benefits of such a paradigm within the region of Latin America, particularly Mexico, where the genetic admixture of the population, food biodiversity, and food culture provide unique opportunities to establish personalized nutrigenetic strategies. These strategies could play a crucial role in preventing chronic diseases and addressing the challenges confronted in the region.
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Affiliation(s)
- Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Liliana Campos-Medina
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
- Doctoral Program in Molecular Biology in Medicine, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Leonardo Leal-Mercado
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Fray Antonio Alcalde, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
- Doctoral Program in Molecular Biology in Medicine, Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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Althagafi A, Zhapa-Camacho F, Hoehndorf R. Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning. Bioinformatics 2024; 40:btae301. [PMID: 38696757 PMCID: PMC11132820 DOI: 10.1093/bioinformatics/btae301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/05/2024] [Accepted: 04/30/2024] [Indexed: 05/04/2024] Open
Abstract
MOTIVATION Whole-exome and genome sequencing have become common tools in diagnosing patients with rare diseases. Despite their success, this approach leaves many patients undiagnosed. A common argument is that more disease variants still await discovery, or the novelty of disease phenotypes results from a combination of variants in multiple disease-related genes. Interpreting the phenotypic consequences of genomic variants relies on information about gene functions, gene expression, physiology, and other genomic features. Phenotype-based methods to identify variants involved in genetic diseases combine molecular features with prior knowledge about the phenotypic consequences of altering gene functions. While phenotype-based methods have been successfully applied to prioritizing variants, such methods are based on known gene-disease or gene-phenotype associations as training data and are applicable to genes that have phenotypes associated, thereby limiting their scope. In addition, phenotypes are not assigned uniformly by different clinicians, and phenotype-based methods need to account for this variability. RESULTS We developed an Embedding-based Phenotype Variant Predictor (EmbedPVP), a computational method to prioritize variants involved in genetic diseases by combining genomic information and clinical phenotypes. EmbedPVP leverages a large amount of background knowledge from human and model organisms about molecular mechanisms through which abnormal phenotypes may arise. Specifically, EmbedPVP incorporates phenotypes linked to genes, functions of gene products, and the anatomical site of gene expression, and systematically relates them to their phenotypic effects through neuro-symbolic, knowledge-enhanced machine learning. We demonstrate EmbedPVP's efficacy on a large set of synthetic genomes and genomes matched with clinical information. AVAILABILITY AND IMPLEMENTATION EmbedPVP and all evaluation experiments are freely available at https://github.com/bio-ontology-research-group/EmbedPVP.
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Affiliation(s)
- Azza Althagafi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia
- Computer Science Department, College of Computers and Information Technology, Taif University, Taif 26571, Saudi Arabia
| | - Fernando Zhapa-Camacho
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia
| | - Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia
- Computer Science Program, Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia
- SDAIA-KAUST Center of Excellence in Data Science and Artificial Intelligence, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia
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Jayasinghe K, Chamika WAS, Jayaweera K, Abhayasinghe K, Dissanayake L, Sumathipala A, Ives J. All you Need is Trust? Public Perspectives on Consenting to Participate in Genomic Research in the Sri Lankan District of Colombo. Asian Bioeth Rev 2024; 16:281-302. [PMID: 38586568 PMCID: PMC10994890 DOI: 10.1007/s41649-023-00269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 04/09/2024] Open
Abstract
Engagement with genomic medicine and research has increased globally during the past few decades, including rapid developments in Sri Lanka. Genomic research is carried out in Sri Lanka on a variety of scales and with different aims and perspectives. However, there are concerns about participants' understanding of genomic research, including the validity of informed consent. This article reports a qualitative study aiming to explore the understanding, knowledge, and attitudes of the Sri Lankan public towards genomic medicine and to inform the development of an effective and appropriate process for informed consent in that setting. Purposive sampling was employed. Participants were recruited from a sub-group of the public in Colombo, Sri Lanka who had either consented or refused to donate genetic material for a biobank. Data were collected using face-to-face semi-structured interviews. Interview data were transcribed verbatim and translated into English. Conventional content analysis was used. The analysis developed three key themes: a) 'Scientific literacy' describes an apparent lack of scientific knowledge that seems to affect a participant's ability to understand the research, b) 'Motivation' describes narratives about why participants chose (not) to take part in the research, despite not understanding it, and c) 'Trust' describes how trust served to mitigate the apparent ethical deficit created by not being fully informed. In this article, we argue that informed trust is likely an acceptable basis for consent, particularly in settings where scientific literacy might be low. However, researchers must work to be worthy of that trust and ensure that misconceptions are actively addressed.
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Affiliation(s)
- Krishani Jayasinghe
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - W. A. S. Chamika
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Kaushalya Jayaweera
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Kalpani Abhayasinghe
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Lasith Dissanayake
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Athula Sumathipala
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Jonathan Ives
- Centre for Ethics in Medicine, Bristol Medical School, University of Bristol, Bristol, UK
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Tokutomi T, Yoshida A, Fukushima A, Yamamoto K, Ishigaki Y, Kawame H, Fuse N, Nagami F, Suzuki Y, Sakurai-Yageta M, Uruno A, Suzuki K, Tanno K, Ohmomo H, Shimizu A, Yamamoto M, Sasaki M. The Health History of First-Degree Relatives' Dyslipidemia Can Affect Preferences and Intentions following the Return of Genomic Results for Monogenic Familial Hypercholesterolemia. Genes (Basel) 2024; 15:384. [PMID: 38540442 PMCID: PMC10970353 DOI: 10.3390/genes15030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 06/14/2024] Open
Abstract
Genetic testing is key in modern healthcare, particularly for monogenic disorders such as familial hypercholesterolemia. This Tohoku Medical Megabank Project study explored the impact of first-degree relatives' dyslipidemia history on individual responses to familial hypercholesterolemia genomic results. Involving 214 participants and using Japan's 3.5KJPN genome reference panel, the study assessed preferences and intentions regarding familial hypercholesterolemia genetic testing results. The data revealed a significant inclination among participants with a family history of dyslipidemia to share their genetic test results, with more than 80% of participants intending to share positive results with their partners and children and 98.1% acknowledging the usefulness of positive results for personal health management. The study underscores the importance of family health history in genetic-testing perceptions, highlighting the need for family-centered approaches in genetic counseling and healthcare. Notable study limitations include the regional scope and reliance on questionnaire data. The study results emphasize the association between family health history and genetic-testing attitudes and decisions.
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Affiliation(s)
- Tomoharu Tokutomi
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
- Department of Clinical Genetics, School of Medicine, Iwate Medical University, Morioka 020-8505, Japan
| | - Akiko Yoshida
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
- Department of Clinical Genetics, School of Medicine, Iwate Medical University, Morioka 020-8505, Japan
| | - Akimune Fukushima
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
- Department of Clinical Genetics, School of Medicine, Iwate Medical University, Morioka 020-8505, Japan
| | - Kayono Yamamoto
- Department of Clinical Genetics, School of Medicine, Iwate Medical University, Morioka 020-8505, Japan
| | - Yasushi Ishigaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Kozo Tanno
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
| | - Hideki Ohmomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa 020-3694, Japan; (A.Y.)
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Harris BHL, McCabe C, Shafique H, Lammy S, Tookman L, Flanagan J, Miron-Barroso S, Lythgoe M, Clark J, Walsh JL, Di Giovannantonio M, Krell J. Diversity of thought: public perceptions of genetic testing across ethnic groups in the UK. J Hum Genet 2024; 69:19-25. [PMID: 37907557 PMCID: PMC10774120 DOI: 10.1038/s10038-023-01199-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023]
Abstract
Genetic testing is becoming rapidly more accessible to the general populous either through or outside healthcare systems. Few large-scale studies have been carried out to gauge public opinion in this growing area. Here, we undertook the largest cross-sectional study on genetic testing in the UK. The primary purpose of this study is to identify the differences in attitudes toward genetic testing across ethnic groups. A cohort of 6500 individuals from a diverse population completed a 72-item survey in a cross-sectional study. Responses between ethnic minority and white individuals in the UK were compared using a wilcoxon rank-sum and chi-square tests. The white cohort was approximately twice as likely to have taken a genetic test and 13% more had heard about genetic testing before the survey. The ethnic minority cohort appeared more apprehensive about the impact of genetic testing on employability. This study highlights that in the UK, significant differences in opinions regarding genetic testing exist between white individuals and ethnic minority individuals. There is an urgent need to develop more inclusive strategies to equally inform individuals from all backgrounds to avoid disparities in the utilisation of genetic testing.
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Affiliation(s)
- Benjamin H L Harris
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- St Anne's College, 56 Woodstock Rd, Oxford, OX2 6HS, UK
| | | | - Hana Shafique
- Duke University School of Medicine, Durham, NC, 27710, USA
| | - Simon Lammy
- Department of Neurosurgery, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Laura Tookman
- Hammersmith Hospital, Imperial College Healthcare NHS trust, London, W12 0HS, UK
| | - James Flanagan
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0HS, UK
| | - Sofia Miron-Barroso
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0HS, UK
| | - Mark Lythgoe
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0HS, UK
| | - James Clark
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0HS, UK
| | - Jason L Walsh
- Hammersmith Hospital, Imperial College Healthcare NHS trust, London, W12 0HS, UK
| | | | - Jonathan Krell
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0HS, UK.
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Basumatary B, Maurya PK, Verma MK. Mapping the Landscape of Indian Genomics Research: A Scientometric Analysis. Rejuvenation Res 2023. [PMID: 36943297 DOI: 10.1089/rej.2023.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
This Scientometric study aimed to provide state-of-the-art information on research growth and trends, areas of potential growth and development in genomics in India, and identify the key players (organizations or institutions, and funding agencies). It was found that the number of publications and citations related to genomics research has been steadily increasing over the years, indicating a growing interest and investment in the field as the Indian Council of Agricultural Research was the leading contributor to the field. Among the 159 contributing countries from 2012 to 2021, India contributed 4.46 percent of publications. The Department of Biotechnology (Ministry of Science and Technology, India) provided the most funds for genomics research. In the last decade, research was primarily focused on "Genetic Diversity", "Polymorphism", "Comparative Genomics", "Phylogeny", " Random amplification of polymorphic DNA (RAPD)", "Single-nucleotide polymorphism (SNP)", "Polymerase chain reaction (PCR)", "Gene Expression", etc. The study's findings may shed light on the strengths and weaknesses of the country's research infrastructure, as well as the effectiveness of government policies and funding mechanisms.
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Affiliation(s)
- Bwsrang Basumatary
- Mizoram University, 29670, Library and Information Science, Aizawl, Mizoram, India;
| | - Pawan Kumar Maurya
- Central University of Haryana, 242287, Biochemistry, R No. 302, Department Of Biochemistry, Central University Of Haryana, Mahendergargh, Mahendergarh, Mahendragarh, Haryana, India, 123031;
| | - Manoj Kumar Verma
- Mizoram University, 29670, Library and Information Science, Tanhril, Aizawl, India, 796004;
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Sunita, Singh Y, Beamer G, Sun X, Shukla P. Recent developments in systems biology and genetic engineering toward design of vaccines for TB. Crit Rev Biotechnol 2022; 42:532-547. [PMID: 34641752 PMCID: PMC11208086 DOI: 10.1080/07388551.2021.1951649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Tuberculosis (TB) is one of the most prevalent diseases worldwide. The currently available Bacillus Calmette-Guérin vaccine is not sufficient in protecting against pulmonary TB. Although many vaccines have been evaluated in clinical trials, but none of them yet has proven to be more successful. Thus, new strategies are urgently needed to design more effective TB vaccines. The emergence of new technologies will undoubtedly accelerate the process of vaccine development. This review summarizes the potential and validated applications of emerging technologies, including: systems biology (genomics, proteomics, and transcriptomics), genetic engineering, and other computational tools to discover and develop novel vaccines against TB. It also discussed that the significant implementation of these approaches will play crucial roles in the development of novel vaccines to cure and control TB.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Gillian Beamer
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, MA, USA
| | - Xingmin Sun
- Department of Molecular Medicine, College of Medicine (COM), University of South Florida, Tampa, FL, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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Mereness JA, Mariani TJ. The critical role of collagen VI in lung development and chronic lung disease. Matrix Biol Plus 2021; 10:100058. [PMID: 34195595 PMCID: PMC8233475 DOI: 10.1016/j.mbplus.2021.100058] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 01/20/2023] Open
Abstract
Type VI collagen (collagen VI) is an obligate extracellular matrix component found mainly in the basement membrane region of many mammalian tissues and organs, including skeletal muscle and throughout the respiratory system. Collagen VI is probably most recognized in medicine as the genetic cause of a spectrum of muscular dystrophies, including Ullrich Congenital Myopathy and Bethlem Myopathy. Collagen VI is thought to contribute to myopathy, at least in part, by mediating muscle fiber integrity by anchoring myoblasts to the muscle basement membrane. Interestingly, collagen VI myopathies present with restrictive respiratory insufficiency, thought to be due primarily to thoracic muscular weakening. Although it was recently recognized as one of the (if not the) most abundant collagens in the mammalian lung, there is a substantive knowledge gap concerning its role in respiratory system development and function. A few studies have suggested that collagen VI insufficiency is associated with airway epithelial cell survival and altered lung function. Our recent work suggested collagen VI may be a genomic risk factor for chronic lung disease in premature infants. Using this as motivation, we thoroughly assessed the role of collagen VI in lung development and in lung epithelial cell biology. Here, we describe the state-of-the-art for collagen VI cell and developmental biology within the respiratory system, and reveal its essential roles in normal developmental processes and airway epithelial cell phenotype and intracellular signaling.
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Affiliation(s)
- Jared A. Mereness
- Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, Department of Pediatrics, University of Rochester, Rochester, NY, USA
- Department of Biomedical Genetics, University of Rochester, Rochester, NY, USA
| | - Thomas J. Mariani
- Corresponding author. Division of Neonatology and Pediatric Molecular and Personalized Medicine Program, University of Rochester Medical Center, 601 Elmwood Ave, Box 850, Rochester, NY 14642, USA.
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Bourdon JL, Dorsey A, Zalik M, Pietka A, Salyer P, Bray MJ, Bierut LJ, Ramsey AT. In-vivo design feedback and perceived utility of a genetically-informed smoking risk tool among current smokers in the community. BMC Med Genomics 2021; 14:139. [PMID: 34039360 PMCID: PMC8152342 DOI: 10.1186/s12920-021-00976-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 05/05/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The use of genetically-informed personalized risk information for behavioral disorders, namely smoking and smoking-related behaviors, is a promising yet understudied area. The Genetics and Smoking Risk Profile, or RiskProfile, leverages genetic and environmental information to communicate one's risk for smoking-related diseases. Although prior studies have examined attitudes toward genetic results, little research has investigated these perceptions through a lens of in-vivo testing; that is, user-centered design feedback in response to personalized genetic results being returned contemporaneously. This qualitative study engaged current smokers in usability testing of the RiskProfile within the context of concurrently receiving this personalized, genetically-informed smoking cessation intervention. METHODS Eighty-nine participants who were current smokers responded to open-ended interview questions on perceptions of smoking-related genetic information and the content and format of the RiskProfile intervention that they had received moments before. Data were analyzed via the conventional content analysis approach in which themes were allowed to emerge throughout the analysis. RESULTS Participants were able to reference and offer design input on specific elements of the RiskProfile. Overall, current smokers perceived the RiskProfile to have high potential utility. Constructive feedback that current smokers offered about the tool centered around suggested improvements to optimize its usability and technical content. CONCLUSIONS The detailed and constructive feedback from participants highlights that in-vivo feedback offers a useful design approach that addresses concerns of rigor and relevance when returning genetic results. This unique method demonstrated perceived utility and constructive design feedback for the RiskProfile among current smokers and can play an important role in optimizing the design and implementation of personalized genetic risk interventions moving forward.
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Affiliation(s)
- Jessica L Bourdon
- Wellbridge Center for Addiction Treatment and Research, Center for Addiction Science, 525 Jan Way, Room 1523, Calverton, NY, 11922, USA.
| | - Amelia Dorsey
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Maia Zalik
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Amanda Pietka
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Patricia Salyer
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael J Bray
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Laura J Bierut
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
| | - Alex T Ramsey
- Department of Psychiatry, Washington University in St. Louis, St. Louis, MO, USA
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10
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Computational discovery and assessment of non-synonymous single nucleotide polymorphisms from target gene pool associated with Parkinson's disease. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bourdon JL, Davies RA, Long EC. Four Actionable Bottlenecks and Potential Solutions to Translating Psychiatric Genetics Research: An Expert Review. Public Health Genomics 2020; 23:171-183. [PMID: 33147585 PMCID: PMC7854816 DOI: 10.1159/000510832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/27/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Psychiatric genetics has had limited success in translational efforts. A thorough understanding of the present state of translation in this field will be useful in the facilitation and assessment of future translational progress. PURPOSE A narrative literature review was conducted. Combinations of 3 groups of terms were searched in EBSCOhost, Google Scholar, and PubMed. The review occurred in multiple steps, including abstract collection, inclusion/exclusion criteria review, coding, and analysis of included papers. RESULTS One hundred and fourteen articles were analyzed for the narrative review. Across those, 4 bottlenecks were noted that, if addressed, may provide insights and help improve and increase translation in the field of psychiatric genetics. These 4 bottlenecks are emphasizing linear translational frameworks, relying on molecular genomic findings, prioritizing certain psychiatric disorders, and publishing more reviews than experiments. CONCLUSIONS These entwined bottlenecks are examined with one another. Awareness of these bottlenecks can inform stakeholders who work to translate and/or utilize psychiatric genetic information. Potential solutions include utilizing nonlinear translational frameworks as well as a wider array of psychiatric genetic information (e.g., family history and gene-environment interplay) in this area of research, expanding which psychiatric disorders are considered for translation, and when possible, conducting original research. Researchers are urged to consider how their research is translational in the context of the frameworks, genetic information, and psychiatric disorders discussed in this review. At a broader level, these efforts should be supported with translational efforts in funding and policy shifts.
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Affiliation(s)
- Jessica L Bourdon
- Department of Psychiatry, Brown School of Social Work, Washington University in St. Louis, St. Louis, Missouri, USA,
| | - Rachel A Davies
- Yerkes National Primate Research Center, Division of Behavioral Neuroscience and Psychiatric Disorders, Emory University, Atlanta, Georgia, USA
| | - Elizabeth C Long
- Edna Bennett Pierce Prevention Research Center, Pennsylvania State University, University Park, Pennsylvania, USA
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Fatumo S, Ebenezer TE, Ekenna C, Isewon I, Ahmad U, Adetunji C, Oladipo EK, Adebiyi M, Adebiyi E, Nashiru O. The Nigerian Bioinformatics and Genomics Network (NBGN): a collaborative platform to advance bioinformatics and genomics in Nigeria. Glob Health Epidemiol Genom 2020; 5:e3. [PMID: 32742665 PMCID: PMC7372179 DOI: 10.1017/gheg.2020.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/24/2020] [Accepted: 04/20/2020] [Indexed: 12/29/2022] Open
Abstract
Africa plays a central importance role in the human origins, and disease susceptibility, agriculture and biodiversity conservation. Nigeria as the most populous and most diverse country in Africa, owing to its 250 ethnic groups and over 500 different native languages is imperative to any global genomic initiative. The newly inaugurated Nigerian Bioinformatics and Genomics Network (NBGN) becomes necessary to facilitate research collaborative activities and foster opportunities for skills' development amongst Nigerian bioinformatics and genomics investigators. NBGN aims to advance and sustain the fields of genomics and bioinformatics in Nigeria by serving as a vehicle to foster collaboration, provision of new opportunities for interactions between various interdisciplinary subfields of genomics, computational biology and bioinformatics as this will provide opportunities for early career researchers. To provide the foundation for sustainable collaborations, the network organises conferences, workshops, trainings and create opportunities for collaborative research studies and internships, recognise excellence, openly share information and create opportunities for more Nigerians to develop the necessary skills to exceed in genomics and bioinformatics. NBGN currently has attracted more than 650 members around the world. Research collaborations between Nigeria, Africa and the West will grow and all stakeholders, including funding partners, African scientists, researchers across the globe, physicians and patients will be the eventual winners. The exponential membership growth and diversity of research interests of NBGN just within weeks of its establishment and the unanticipated attendance of its activities suggest the significant importance of the network to bioinformatics and genomics research in Nigeria.
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Affiliation(s)
- Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK
- Uganda Medical Informatics Centre, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- H3 Africa Bioinformatics Network (H3 ABioNet) Node, CGRI/NABDA, Abuja, Nigeria
| | - ThankGod E. Ebenezer
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park Innovation Centre, NorwichNR4 7UZ, UK
| | | | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Umar Ahmad
- Medical Genetics Laboratory, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra, Selangor, Malaysia
- Department of Anatomy, Faculty of Medicine, Bauchi State University, Gadau, Nigeria
| | | | - Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Marion Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Department of Computer Science, Landmark University, Omu-Aran, Nigeria
| | - Ezekiel Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Oyekanmi Nashiru
- H3 Africa Bioinformatics Network (H3 ABioNet) Node, CGRI/NABDA, Abuja, Nigeria
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Whitley KV, Tueller JA, Weber KS. Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations. Int J Mol Sci 2020; 21:ijms21030768. [PMID: 31991576 PMCID: PMC7037382 DOI: 10.3390/ijms21030768] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/18/2020] [Accepted: 01/22/2020] [Indexed: 12/23/2022] Open
Abstract
Since the completion of the Human Genome Project in 2003, genomic sequencing has become a prominent tool used by diverse disciplines in modern science. In the past 20 years, the cost of genomic sequencing has decreased exponentially, making it affordable and accessible. Bioinformatic and biological studies have produced significant scientific breakthroughs using the wealth of genomic information now available. Alongside the scientific benefit of genomics, companies offer direct-to-consumer genetic testing which provide health, trait, and ancestry information to the public. A key area that must be addressed is education about what conclusions can be made from this genomic information and integrating genomic education with foundational genetic principles already taught in academic settings. The promise of personal genomics providing disease treatment is exciting, but many challenges remain to validate genomic predictions and diagnostic correlations. Ethical and societal concerns must also be addressed regarding how personal genomic information is used. This genomics revolution provides a powerful opportunity to educate students, clinicians, and the public on scientific and ethical issues in a personal way to increase learning. In this review, we discuss the influence of personal genomics in society and focus on the importance and benefits of genomics education in the classroom, clinics, and the public and explore the potential consequences of personal genomic education.
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Genomics of Particulate Matter Exposure Associated Cardiopulmonary Disease: A Narrative Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16224335. [PMID: 31703266 PMCID: PMC6887978 DOI: 10.3390/ijerph16224335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 12/25/2022]
Abstract
Particulate matter (PM) exposure is associated with the development of cardiopulmonary disease. Our group has studied the adverse health effects of World Trade Center particulate matter (WTC-PM) exposure on firefighters. To fully understand the complex interplay between exposure, organism, and resultant disease phenotype, it is vital to analyze the underlying role of genomics in mediating this relationship. A PubMed search was performed focused on environmental exposure, genomics, and cardiopulmonary disease. We included original research published within 10 years, on epigenetic modifications and specific genetic or allelic variants. The initial search resulted in 95 studies. We excluded manuscripts that focused on work-related chemicals, heavy metals and tobacco smoke as primary sources of exposure, as well as reviews, prenatal research, and secondary research studies. Seven full-text articles met pre-determined inclusion criteria, and were reviewed. The effects of air pollution were evaluated in terms of methylation (n = 3), oxidative stress (n = 2), and genetic variants (n = 2). There is evidence to suggest that genomics plays a meditating role in the formation of adverse cardiopulmonary symptoms and diseases that surface after exposure events. Genomic modifications and variations affect the association between environmental exposure and cardiopulmonary disease, but additional research is needed to further define this relationship.
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15
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In silico Identification of potential Drug Target and Analysis of Effective Single Nucleotide Polymorphisms for autism spectrum Disorder. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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The importance of gene-environment interactions in human obesity. Clin Sci (Lond) 2017; 130:1571-97. [PMID: 27503943 DOI: 10.1042/cs20160221] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
The worldwide obesity epidemic has been mainly attributed to lifestyle changes. However, who becomes obese in an obesity-prone environment is largely determined by genetic factors. In the last 20 years, important progress has been made in the elucidation of the genetic architecture of obesity. In parallel with successful gene identifications, the number of gene-environment interaction (GEI) studies has grown rapidly. This paper reviews the growing body of evidence supporting gene-environment interactions in the field of obesity. Heritability, monogenic and polygenic obesity studies provide converging evidence that obesity-predisposing genes interact with a variety of environmental, lifestyle and treatment exposures. However, some skepticism remains regarding the validity of these studies based on several issues, which include statistical modelling, confounding, low replication rate, underpowered analyses, biological assumptions and measurement precision. What follows in this review includes (1) an introduction to the study of GEI, (2) the evidence of GEI in the field of obesity, (3) an outline of the biological mechanisms that may explain these interaction effects, (4) methodological challenges associated with GEI studies and potential solutions, and (5) future directions of GEI research. Thus far, this growing body of evidence has provided a deeper understanding of GEI influencing obesity and may have tremendous applications in the emerging field of personalized medicine and individualized lifestyle recommendations.
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Cameron LD, Biesecker BB, Peters E, Taber JM, Klein WMP. Self-Regulation Principles Underlying Risk Perception and Decision Making within the Context of Genomic Testing. SOCIAL AND PERSONALITY PSYCHOLOGY COMPASS 2017; 11. [PMID: 29225669 DOI: 10.1111/spc3.12315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Advances in theory and research on self-regulation and decision-making processes have yielded important insights into how cognitive, emotional, and social processes shape risk perceptions and risk-related decisions. We examine how self-regulation theory can be applied to inform our understanding of decision-making processes within the context of genomic testing, a clinical arena in which individuals face complex risk information and potentially life-altering decisions. After presenting key principles of self-regulation, we present a genomic testing case example to illustrate how principles related to risk representations, approach and avoidance motivations, emotion regulation, defensive responses, temporal construals, and capacities such as numeric abilities can shape decisions and psychological responses during the genomic testing process. We conclude with implications for using self-regulation theory to advance science within genomic testing and opportunities for how this research can inform further developments in self-regulation theory.
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Christensen KD, Dukhovny D, Siebert U, Green RC. Assessing the Costs and Cost-Effectiveness of Genomic Sequencing. J Pers Med 2015; 5:470-86. [PMID: 26690481 PMCID: PMC4695866 DOI: 10.3390/jpm5040470] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Accepted: 12/04/2015] [Indexed: 11/17/2022] Open
Abstract
Despite dramatic drops in DNA sequencing costs, concerns are great that the integration of genomic sequencing into clinical settings will drastically increase health care expenditures. This commentary presents an overview of what is known about the costs and cost-effectiveness of genomic sequencing. We discuss the cost of germline genomic sequencing, addressing factors that have facilitated the decrease in sequencing costs to date and anticipating the factors that will drive sequencing costs in the future. We then address the cost-effectiveness of diagnostic and pharmacogenomic applications of genomic sequencing, with an emphasis on the implications for secondary findings disclosure and the integration of genomic sequencing into general patient care. Throughout, we ground the discussion by describing efforts in the MedSeq Project, an ongoing randomized controlled clinical trial, to understand the costs and cost-effectiveness of integrating whole genome sequencing into cardiology and primary care settings.
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Affiliation(s)
- Kurt D Christensen
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Dmitry Dukhovny
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA.
| | - Uwe Siebert
- Department of Public Health, Medical Decision Making and Health Technology Assessment, University for Health Sciences, Medical Informatics and Technology, Hall in Tirol 6060, Austria.
- Department of Health Policy and Management, Harvard School of Public Health, Boston, MA 02115, USA.
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Partners Personalized Medicine, Boston, MA 02115, USA.
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Patrick-Miller LJ, Egleston BL, Fetzer D, Forman A, Bealin L, Rybak C, Peterson C, Corbman M, Albarracin J, Stevens E, Daly MB, Bradbury AR. Development of a communication protocol for telephone disclosure of genetic test results for cancer predisposition. JMIR Res Protoc 2014; 3:e49. [PMID: 25355401 PMCID: PMC4259920 DOI: 10.2196/resprot.3337] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/12/2014] [Accepted: 07/18/2014] [Indexed: 12/26/2022] Open
Abstract
Background Dissemination of genetic testing for disease susceptibility, one application of “personalized medicine”, holds the potential to empower patients and providers through informed risk reduction and prevention recommendations. Genetic testing has become a standard practice in cancer prevention for high-risk populations. Heightened consumer awareness of “cancer genes” and genes for other diseases (eg, cardiovascular and Alzheimer’s disease), as well as the burgeoning availability of increasingly complex genomic tests (ie, multi-gene, whole-exome and -genome sequencing), has escalated interest in and demand for genetic risk assessment and the specialists who provide it. Increasing demand is expected to surpass access to genetic specialists. Thus, there is urgent need to develop effective and efficient models of delivery of genetic information that comparably balance the risks and benefits to the current standard of in-person communication. Objective The aim of this pilot study was to develop and evaluate a theoretically grounded and rigorously developed protocol for telephone communication of BRCA1/2 (breast cancer) test results that might be generalizable to genetic testing for other hereditary cancer and noncancer syndromes. Methods Stakeholder data, health communication literature, and our theoretical model grounded in Self-Regulation Theory of Health Behavior were used to develop a telephone communication protocol for the communication of BRCA1/2 genetic test results. Framework analysis of selected audiotapes of disclosure sessions and stakeholders’ feedback were utilized to evaluate the efficacy and inform refinements to this protocol. Results Stakeholder feedback (n=86) and audiotapes (38%, 33/86) of telephone disclosures revealed perceived disadvantages and challenges including environmental factors (eg, non-private environment), patient-related factors (eg, low health literacy), testing-related factors (eg, additional testing needed), and communication factors (eg, no visual cues). Resulting modifications to the communication protocol for BRCA1/2 test results included clarified patient instructions, scheduled appointments, refined visual aids, expanded disclosure checklist items, and enhanced provider training. Conclusions Analyses of stakeholders’ experiences and audiotapes of telephone disclosure of BRCA1/2 test results informed revisions to communication strategies and a protocol to enhance patient outcomes when utilizing telephone to disclose genetic test results.
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Affiliation(s)
- Linda J Patrick-Miller
- Department of Medicine, Division of Hematology-Oncology, Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, IL, United States.
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Collins J, Ryan L, Truby H. A systematic review of the factors associated with interest in predictive genetic testing for obesity, type II diabetes and heart disease. J Hum Nutr Diet 2013; 27:479-88. [DOI: 10.1111/jhn.12179] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- J. Collins
- Department of Nutrition and Dietetics; Monash University; Notting Hill VIC Australia
| | - L. Ryan
- Department of Nutrition and Dietetics; Monash University; Notting Hill VIC Australia
| | - H. Truby
- Department of Nutrition and Dietetics; Monash University; Notting Hill VIC Australia
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Haga SB, Barry WT, Mills R, Ginsburg GS, Svetkey L, Sullivan J, Willard HF. Public knowledge of and attitudes toward genetics and genetic testing. Genet Test Mol Biomarkers 2013; 17:327-35. [PMID: 23406207 PMCID: PMC3609633 DOI: 10.1089/gtmb.2012.0350] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Variable health literacy and genetic knowledge may pose significant challenges to engaging the general public in personal genomics, specifically with respect to promoting risk comprehension and healthy behaviors. METHODS We are conducting a multistage study of individual responses to genomic risk information for Type 2 diabetes mellitus. A total of 300 individuals were recruited from the general public in Durham, North Carolina: 60% self-identified as White; 70% female; and 65% have a college degree. As part of the baseline survey, we assessed genetic knowledge and attitudes toward genetic testing. RESULTS Scores of factual knowledge of genetics ranged from 50% to 100% (average=84%), with significant differences in relation to racial groups, the education level, and age. Scores were significantly higher on questions pertaining to the inheritance and causes of disease (mean score 90%) compared to scientific questions (mean score 77.4%). Scores on the knowledge survey were significantly higher than scores from European populations. Participants' perceived knowledge of the social consequences of genetic testing was significantly lower than their perceived knowledge of the medical uses of testing. More than half agreed with the statement that testing may affect a person's ability to obtain health insurance (51.3%) and 16% were worried about the consequences of testing for chances of finding a job. CONCLUSIONS Despite the relatively high educational status and genetic knowledge of the study population, we find an imbalance of knowledge between scientific and medical concepts related to genetics as well as between the medical applications and societal consequences of testing, suggesting that more effort is needed to present the benefits, risks, and limitations of genetic testing, particularly, at the social and personal levels, to ensure informed decision making.
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Affiliation(s)
- Susanne B Haga
- Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.
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Bloss CS, Darst BF, Topol EJ, Schork NJ. Direct-to-consumer personalized genomic testing. Hum Mol Genet 2011; 20:R132-41. [PMID: 21828075 DOI: 10.1093/hmg/ddr349] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Over the past 18 months, there have been notable developments in the direct-to-consumer (DTC) genomic testing arena, in particular with regard to issues surrounding governmental regulation in the USA. While commentaries continue to proliferate on this topic, actual empirical research remains relatively scant. In terms of DTC genomic testing for disease susceptibility, most of the research has centered on uptake, perceptions and attitudes toward testing among health care professionals and consumers. Only a few available studies have examined actual behavioral response among consumers, and we are not aware of any studies that have examined response to DTC genetic testing for ancestry or for drug response. We propose that further research in this area is desperately needed, despite challenges in designing appropriate studies given the rapid pace at which the field is evolving. Ultimately, DTC genomic testing for common markers and conditions is only a precursor to the eventual cost-effectiveness and wide availability of whole genome sequencing of individuals, although it remains unclear whether DTC genomic information will still be attainable. Either way, however, current knowledge needs to be extended and enhanced with respect to the delivery, impact and use of increasingly accurate and comprehensive individualized genomic data.
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Affiliation(s)
- Cinnamon S Bloss
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, 3344 N. Torrey Pines Court, La Jolla, CA 92037, USA
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