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1
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Buonaiuto S, Marsico F, Mohammed A, Chinthala LK, Amos-Abanyie EK, Prins P, Mozhui K, Rooney RJ, Williams RW, Davis RL, Finkel TH, Brown CW, Colonna V. The Biorepository and Integrative Genomics resource for inclusive genomics: insights from a diverse pediatric and admixed cohort. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2025.01.03.25319944. [PMID: 39802793 PMCID: PMC11722445 DOI: 10.1101/2025.01.03.25319944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2025]
Abstract
The Biorepository and Integrative Genomics (BIG) Initiative in Tennessee has developed a pioneering resource to address gaps in genomic research by linking genomic, phenotypic, and environmental data from a diverse Mid-South population, including underrepresented groups. We analyzed 13,152 exomes from BIG and found significant genetic diversity, with 50% of participants inferred to have non-European or several types of admixed ancestry. Ancestry within the BIG cohort is stratified, with distinct geographic and demographic patterns, as African ancestry is more common in urban areas, while European ancestry is more common in suburban regions. We observe ancestry-specific rates of novel genetic variants, which are enriched for functional or clinical relevance. Disease prevalence analysis linked ancestry and environmental factors, showing higher odds ratios for asthma and obesity in minority groups, particularly in the urban area. Finally, we observe discrepancies between self-reported race and genetic ancestry, with related individuals self-identifying in differing racial categories. These findings underscore the limitations of race as a biomedical variable. BIG has proven to be an effective model for community-centered precision medicine. We integrated genomics education, and fostered great trust among the contributing communities. Future goals include cohort expansion, and enhanced genomic analysis, to ensure equitable healthcare outcomes.
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Affiliation(s)
| | | | | | | | | | - Pjotr Prins
- Dept of Genetics, Genomics and Informatics, UTHSC, USA
| | - Kyobeni Mozhui
- Dept of Genetics, Genomics and Informatics, UTHSC, USA
- Department of Preventive Medicine, Division of Preventive Medicine, UTHSC, USA
| | | | - Robert W Williams
- Department of Preventive Medicine, Division of Preventive Medicine, UTHSC, USA
| | | | - Terri H Finkel
- Regeneron Genetics Center, Tarrytown, NY, USA, Dept of Pediatrics, Division of Genetics, UTHSC, USA
- Dept of Pediatrics, Division of Rheumatology, UTHSC, USA
| | - Chester W Brown
- Dept of Genetics, Genomics and Informatics, UTHSC, USA
- Regeneron Genetics Center, Tarrytown, NY, USA, Dept of Pediatrics, Division of Genetics, UTHSC, USA
| | - Vincenza Colonna
- Dept of Genetics, Genomics and Informatics, UTHSC, USA
- Dept of Pediatrics, Division of Rheumatology, UTHSC, USA
- Institute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy
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Voorhies K, Mohammed A, Chinthala L, Kong SW, Lee IH, Kho AT, McGeachie M, Mandl KD, Raby B, Hayes M, Davis RL, Wu AC, Lutz SM. GSDMB/ORMDL3 Rare/Common Variants Are Associated with Inhaled Corticosteroid Response among Children with Asthma. Genes (Basel) 2024; 15:420. [PMID: 38674355 PMCID: PMC11049905 DOI: 10.3390/genes15040420] [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: 02/23/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Inhaled corticosteroids (ICS) are efficacious in the treatment of asthma, which affects more than 300 million people in the world. While genome-wide association studies have identified genes involved in differential treatment responses to ICS in asthma, few studies have evaluated the effects of combined rare and common variants on ICS response among children with asthma. Among children with asthma treated with ICS with whole exome sequencing (WES) data in the PrecisionLink Biobank (91 White and 20 Black children), we examined the effect and contribution of rare and common variants with hospitalizations or emergency department visits. For 12 regions previously associated with asthma and ICS response (DPP10, FBXL7, NDFIP1, TBXT, GLCCI1, HDAC9, TBXAS1, STAT6, GSDMB/ORMDL3, CRHR1, GNGT2, FCER2), we used the combined sum test for the sequence kernel association test (SKAT) adjusting for age, sex, and BMI and stratified by race. Validation was conducted in the Biorepository and Integrative Genomics (BIG) Initiative (83 White and 134 Black children). Using a Bonferroni threshold for the 12 regions tested (i.e., 0.05/12 = 0.004), GSDMB/ORMDL3 was significantly associated with ICS response for the combined effect of rare and common variants (p-value = 0.003) among White children in the PrecisionLink Biobank and replicated in the BIG Initiative (p-value = 0.02). Using WES data, the combined effect of rare and common variants for GSDMB/ORMDL3 was associated with ICS response among asthmatic children in the PrecisionLink Biobank and replicated in the BIG Initiative. This proof-of-concept study demonstrates the power of biobanks of pediatric real-life populations in asthma genomic investigations.
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Affiliation(s)
- Kirsten Voorhies
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Akram Mohammed
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Lokesh Chinthala
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - In-Hee Lee
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alvin T. Kho
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Michael McGeachie
- Channing Division for Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Benjamin Raby
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Melanie Hayes
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Robert L. Davis
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ann Chen Wu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Sharon M. Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Subasri M, Cressman C, Arje D, Schreyer L, Cooper E, Patel K, Ungar WJ, Barwick M, Denburg A, Hayeems RZ. Translating Precision Health for Pediatrics: A Scoping Review. CHILDREN (BASEL, SWITZERLAND) 2023; 10:897. [PMID: 37238445 PMCID: PMC10217253 DOI: 10.3390/children10050897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
Precision health aims to personalize treatment and prevention strategies based on individual genetic differences. While it has significantly improved healthcare for specific patient groups, broader translation faces challenges with evidence development, evidence appraisal, and implementation. These challenges are compounded in child health as existing methods fail to incorporate the physiology and socio-biology unique to childhood. This scoping review synthesizes the existing literature on evidence development, appraisal, prioritization, and implementation of precision child health. PubMed, Scopus, Web of Science, and Embase were searched. The included articles were related to pediatrics, precision health, and the translational pathway. Articles were excluded if they were too narrow in scope. In total, 74 articles identified challenges and solutions for putting pediatric precision health interventions into practice. The literature reinforced the unique attributes of children and their implications for study design and identified major themes for the value assessment of precision health interventions for children, including clinical benefit, cost-effectiveness, stakeholder values and preferences, and ethics and equity. Tackling these identified challenges will require developing international data networks and guidelines, re-thinking methods for value assessment, and broadening stakeholder support for the effective implementation of precision health within healthcare organizations. This research was funded by the SickKids Precision Child Health Catalyst Grant.
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Affiliation(s)
- Mathushan Subasri
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
| | - Celine Cressman
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
| | - Danielle Arje
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Leighton Schreyer
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
| | - Erin Cooper
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
| | - Komal Patel
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
| | - Wendy J. Ungar
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
- Institute for Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
| | - Melanie Barwick
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
- Institute for Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
| | - Avram Denburg
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
- Institute for Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
- Division of Haematology/Oncology, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Robin Z. Hayeems
- Child Health Evaluative Sciences Program, The Hospital for Sick Children Research Institute, Toronto, ON M5G 1X8, Canada; (M.S.); (C.C.); (D.A.); (L.S.); (E.C.); (K.P.); (W.J.U.); (M.B.); (A.D.)
- Institute for Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
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Bonizzi G, Zattoni L, Capra M, Cassi C, Taliento G, Ivanova M, Guerini-Rocco E, Fumagalli M, Monturano M, Albini A, Viale G, Orecchia R, Fusco N. Standard operating procedures for biobank in oncology. Front Mol Biosci 2022; 9:967310. [PMID: 36090048 PMCID: PMC9459387 DOI: 10.3389/fmolb.2022.967310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Biobanks are biorepositories that collect, process, store, catalog, and distribute human biological samples, and record the associated data. The role and action field of these strategic infrastructures for implementing precision medicine in translational research is continuously evolving. To ensure the optimal quality at all stages of biobanking, specific protocols are required and should be elaborated according to updated guidelines, recommendations, laws, and rules. This article illustrates the standard operating procedures, including protocols, troubleshooting, and quality controls, of a fully certified biobank in a referral Cancer Center. This model involves all clinical departments and research groups to support the dual mission of academic cancer centers, i.e. to provide high-quality care and high-quality research. All biobanking activities based on the type of biological specimens are detailed and the most tricky methodological aspects are discussed, from patients’ informed consent to specimen management.
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Affiliation(s)
- Giuseppina Bonizzi
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lorenzo Zattoni
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Maria Capra
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Cristina Cassi
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulio Taliento
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elena Guerini-Rocco
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marzia Fumagalli
- Technology Transfer Office, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Massimo Monturano
- Patient Safety and Risk Management Service, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Adriana Albini
- Scientific Directorate, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giuseppe Viale
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Roberto Orecchia
- Scientific Directorate, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Nicola Fusco
- Biobank for Translational and Digital Medicine, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- *Correspondence: Nicola Fusco,
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Kinkorová J, Topolčan O. Biobanks in the era of big data: objectives, challenges, perspectives, and innovations for predictive, preventive, and personalised medicine. EPMA J 2020; 11:333-341. [PMID: 32849924 PMCID: PMC7429593 DOI: 10.1007/s13167-020-00213-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/29/2020] [Indexed: 01/18/2023]
Abstract
Biobanking is entering the new era-era of big data. New technologies, techniques, and knowledge opened the potential of the whole domain of biobanking. Biobanks collect, analyse, store, and share the samples and associated data. Both samples and especially associated data are growing enormously, and new innovative approaches are required to handle samples and to utilize the potential of biobanking data. The data reached the quantity and quality of big data, and the scientists are facing the questions how to use them more efficiently, both retrospectively and prospectively with the aim to discover new preventive methods, optimize treatment, and follow up and to optimize healthcare processes. Biobanking in the era of big data contribute to the development of predictive, preventive, and personalised medicine, for every patient providing the right treatment at the right time. Biobanking in the era of big data contributes to the paradigm shift towards personalising of healthcare.
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Affiliation(s)
- Judita Kinkorová
- Laboratory of Immunoanalysis, University Hospital in Pilsen, Edvarda Beneše 1128/13, 30599 Pilsen, Czech Republic
- Faculty of Medicine in Pilsen, Charles University, Husova 3, 30100 Pilsen, Czech Republic
| | - Ondřej Topolčan
- Laboratory of Immunoanalysis, University Hospital in Pilsen, Edvarda Beneše 1128/13, 30599 Pilsen, Czech Republic
- Faculty of Medicine in Pilsen, Charles University, Husova 3, 30100 Pilsen, Czech Republic
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