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Robertson CC, Elgamal RM, Henry-Kanarek BA, Arvan P, Chen S, Dhawan S, Eizirik DL, Kaddis JS, Vahedi G, Parker SCJ, Gaulton KJ, Soleimanpour SA. Untangling the genetics of beta cell dysfunction and death in type 1 diabetes. Mol Metab 2024; 86:101973. [PMID: 38914291 DOI: 10.1016/j.molmet.2024.101973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) is a complex multi-system disease which arises from both environmental and genetic factors, resulting in the destruction of insulin-producing pancreatic beta cells. Over the past two decades, human genetic studies have provided new insight into the etiology of T1D, including an appreciation for the role of beta cells in their own demise. SCOPE OF REVIEW Here, we outline models supported by human genetic data for the role of beta cell dysfunction and death in T1D. We highlight the importance of strong evidence linking T1D genetic associations to bona fide candidate genes for mechanistic and therapeutic consideration. To guide rigorous interpretation of genetic associations, we describe molecular profiling approaches, genomic resources, and disease models that may be used to construct variant-to-gene links and to investigate candidate genes and their role in T1D. MAJOR CONCLUSIONS We profile advances in understanding the genetic causes of beta cell dysfunction and death at individual T1D risk loci. We discuss how genetic risk prediction models can be used to address disease heterogeneity. Further, we present areas where investment will be critical for the future use of genetics to address open questions in the development of new treatment and prevention strategies for T1D.
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Affiliation(s)
- Catherine C Robertson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Center for Precision Health Research, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ruth M Elgamal
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Belle A Henry-Kanarek
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Peter Arvan
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA; Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephen C J Parker
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
| | - Kyle J Gaulton
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
| | - Scott A Soleimanpour
- Department of Internal Medicine and Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA.
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2
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Don J, Schork AJ, Glusman G, Rappaport N, Cummings SR, Duggan D, Raju A, Hellberg KLG, Gunn S, Monti S, Perls T, Lapidus J, Goetz LH, Sebastiani P, Schork NJ. The relationship between 11 different polygenic longevity scores, parental lifespan, and disease diagnosis in the UK Biobank. GeroScience 2024; 46:3911-3927. [PMID: 38451433 PMCID: PMC11226417 DOI: 10.1007/s11357-024-01107-1] [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: 10/30/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
Large-scale genome-wide association studies (GWAS) strongly suggest that most traits and diseases have a polygenic component. This observation has motivated the development of disease-specific "polygenic scores (PGS)" that are weighted sums of the effects of disease-associated variants identified from GWAS that correlate with an individual's likelihood of expressing a specific phenotype. Although most GWAS have been pursued on disease traits, leading to the creation of refined "Polygenic Risk Scores" (PRS) that quantify risk to diseases, many GWAS have also been pursued on extreme human longevity, general fitness, health span, and other health-positive traits. These GWAS have discovered many genetic variants seemingly protective from disease and are often different from disease-associated variants (i.e., they are not just alternative alleles at disease-associated loci) and suggest that many health-positive traits also have a polygenic basis. This observation has led to an interest in "polygenic longevity scores (PLS)" that quantify the "risk" or genetic predisposition of an individual towards health. We derived 11 different PLS from 4 different available GWAS on lifespan and then investigated the properties of these PLS using data from the UK Biobank (UKB). Tests of association between the PLS and population structure, parental lifespan, and several cancerous and non-cancerous diseases, including death from COVID-19, were performed. Based on the results of our analyses, we argue that PLS are made up of variants not only robustly associated with parental lifespan, but that also contribute to the genetic architecture of disease susceptibility, morbidity, and mortality.
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Affiliation(s)
- Janith Don
- Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Andrew J Schork
- The Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
- GLOBE Institute, Copenhagen University, Copenhagen, Denmark
| | | | | | - Steve R Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - David Duggan
- Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Anish Raju
- Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Kajsa-Lotta Georgii Hellberg
- The Institute of Biological Psychiatry, Copenhagen University Hospital, Copenhagen, Denmark
- GLOBE Institute, Copenhagen University, Copenhagen, Denmark
| | - Sophia Gunn
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Stefano Monti
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Thomas Perls
- Department of Medicine, Section of Geriatrics, Boston University, Boston, MA, USA
| | - Jodi Lapidus
- Department of Biostatistics, Oregon Health & Science University, Portland, OR, USA
| | - Laura H Goetz
- Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Veterans Affairs Loma Linda Health Care, Loma Linda, CA, USA
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA, USA
- Tufts University School of Medicine and Data Intensive Study Center, Boston, MA, USA
| | - Nicholas J Schork
- Translational Genomics Research Institute (TGen), Phoenix, AZ, USA.
- The City of Hope National Medical Center, Duarte, CA, USA.
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Joglekar MV, Kaur S, Pociot F, Hardikar AA. Prediction of progression to type 1 diabetes with dynamic biomarkers and risk scores. Lancet Diabetes Endocrinol 2024; 12:483-492. [PMID: 38797187 DOI: 10.1016/s2213-8587(24)00103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 05/29/2024]
Abstract
Identifying biomarkers of functional β-cell loss is an important step in the risk stratification of type 1 diabetes. Genetic risk scores (GRS), generated by profiling an array of single nucleotide polymorphisms, are a widely used type 1 diabetes risk-prediction tool. Type 1 diabetes screening studies have relied on a combination of biochemical (autoantibody) and GRS screening methodologies for identifying individuals at high-risk of type 1 diabetes. A limitation of these screening tools is that the presence of autoantibodies marks the initiation of β-cell loss, and is therefore not the best biomarker of progression to early-stage type 1 diabetes. GRS, on the other hand, represents a static biomarker offering a single risk score over an individual's lifetime. In this Personal View, we explore the challenges and opportunities of static and dynamic biomarkers in the prediction of progression to type 1 diabetes. We discuss future directions wherein newer dynamic risk scores could be used to predict type 1 diabetes risk, assess the efficacy of new and emerging drugs to retard, or prevent type 1 diabetes, and possibly replace or further enhance the predictive ability offered by static biomarkers, such as GRS.
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Affiliation(s)
- Mugdha V Joglekar
- School of Medicine, Western Sydney University, Sydney, NSW, Australia
| | | | - Flemming Pociot
- Steno Diabetes Center Copenhagen, Herlev, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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4
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Lewis SJ, Williams CL, Mortimer GL, Oram RA, Hagopian WA, Gillespie KM, Long AE. Islet autoantibody frequency in relatives of children with type 1 diabetes who have a type 2 diabetes diagnosis. Diabet Med 2024:e15394. [PMID: 38937948 DOI: 10.1111/dme.15394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
AIM This study aimed to evaluate characteristics of autoimmunity in individuals who have a type 2 diagnosis and are relatives of children with type 1 diabetes. METHODS Pre-diagnosis samples (median 17 months before onset) from relatives who were later diagnosed with type 2 diabetes were measured for autoantibodies to glutamate decarboxylase 65 (GADA), islet antigen-2 (IA-2A), zinc transporter 8 (ZnT8A) and insulin (IAA) as well as the type 1 diabetes genetic risk score (GRS2). Associations between islet autoantibodies, insulin treatment and GRS2 were analysed using Fisher's exact and t-tests. RESULTS Among 226 relatives (64% men; mean age at sampling 41 years; mean age 54 years at diagnosis), 32 (14%) were islet autoantibody-positive for at least one autoantibody more than a decade before diagnosis. Approximately half of these (n = 15) were treated with insulin. GADA-positivity was higher in insulin-treated relatives than in non-insulin-treated relatives (12/18 [67%] vs. 6/18 [33%], p < 0.001). IAA-positivity was observed in 13/32 (41%) of relatives with autoantibodies. GRS2 scores were increased in autoantibody-positive relatives (p = 0.032), but there was no clear evidence for a difference according to treatment (p = 0.072). CONCLUSION This study highlights the importance of measuring islet autoantibodies, including IAA, in relatives of people with type 1 diabetes to avoid misdiagnosis.
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Affiliation(s)
- Shanice J Lewis
- Translational Health Sciences, Diabetes and Metabolism, Bristol Medical School, University of Bristol, Bristol, UK
| | - Claire L Williams
- Translational Health Sciences, Diabetes and Metabolism, Bristol Medical School, University of Bristol, Bristol, UK
| | - Georgina L Mortimer
- Translational Health Sciences, Diabetes and Metabolism, Bristol Medical School, University of Bristol, Bristol, UK
| | - Richard A Oram
- Institute of Biomedical and Clinical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - William A Hagopian
- Pacific Northwest Diabetes Research Institute, University of Washington, Seattle, Washington, USA
| | - Kathleen M Gillespie
- Translational Health Sciences, Diabetes and Metabolism, Bristol Medical School, University of Bristol, Bristol, UK
| | - Anna E Long
- Translational Health Sciences, Diabetes and Metabolism, Bristol Medical School, University of Bristol, Bristol, UK
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5
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Fuhri Snethlage CM, Balvers M, Ferwerda B, Rampanelli E, de Groen P, Roep BO, Herrema H, McDonald TJ, van Raalte DH, Weedon MN, Oram RA, Nieuwdorp M, Hanssen NMJ. Associations between diabetes-related genetic risk scores and residual beta cell function in type 1 diabetes: the GUTDM1 study. Diabetologia 2024:10.1007/s00125-024-06204-6. [PMID: 38922416 DOI: 10.1007/s00125-024-06204-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
AIMS/HYPOTHESIS Use of genetic risk scores (GRS) may help to distinguish between type 1 diabetes and type 2 diabetes, but less is known about whether GRS are associated with disease severity or progression after diagnosis. Therefore, we tested whether GRS are associated with residual beta cell function and glycaemic control in individuals with type 1 diabetes. METHODS Immunochip arrays and TOPMed were used to genotype a cross-sectional cohort (n=479, age 41.7 ± 14.9 years, duration of diabetes 16.0 years [IQR 6.0-29.0], HbA1c 55.6 ± 12.2 mmol/mol). Several GRS, which were originally developed to assess genetic risk of type 1 diabetes (GRS-1, GRS-2) and type 2 diabetes (GRS-T2D), were calculated. GRS-C1 and GRS-C2 were based on SNPs that have previously been shown to be associated with residual beta cell function. Regression models were used to investigate the association between GRS and residual beta cell function, assessed using the urinary C-peptide/creatinine ratio, and the association between GRS and continuous glucose monitor metrics. RESULTS Higher GRS-1 and higher GRS-2 both showed a significant association with undetectable UCPCR (OR 0.78; 95% CI 0.69, 0.89 and OR 0.84: 95% CI 0.75, 0.93, respectively), which were attenuated after correction for sex and age of onset (GRS-2) and disease duration (GRS-1). Higher GRS-C2 was associated with detectable urinary C-peptide/creatinine ratio (≥0.01 nmol/mmol) after correction for sex and age of onset (OR 6.95; 95% CI 1.19, 40.75). A higher GRS-T2D was associated with less time below range (TBR) (OR for TBR<4% 1.41; 95% CI 1.01 to 1.96) and lower glucose coefficient of variance (β -1.53; 95% CI -2.76, -0.29). CONCLUSIONS/INTERPRETATION Diabetes-related GRS are associated with residual beta cell function in individuals with type 1 diabetes. These findings suggest some genetic contribution to preservation of beta cell function.
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Affiliation(s)
- Coco M Fuhri Snethlage
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Manon Balvers
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam UMC, Amsterdam, the Netherlands
| | - Elena Rampanelli
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Pleun de Groen
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Bart O Roep
- Leids Universitair Medisch Centrum, Internal Medicine, Leiden, the Netherlands
| | - Hilde Herrema
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Timothy J McDonald
- Peninsula College of Medicine and Dentistry, Peninsula NIHR Clinical Research Facility, Exeter, Devon, UK
| | - Daniël H van Raalte
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Endocrinology and Metabolism, Amsterdam UMC, Amsterdam, the Netherlands
- Diabeter Center Amsterdam, Amsterdam, the Netherlands
| | - Michael N Weedon
- Peninsula College of Medicine and Dentistry, Peninsula NIHR Clinical Research Facility, Exeter, Devon, UK
| | - Richard A Oram
- Peninsula College of Medicine and Dentistry, Peninsula NIHR Clinical Research Facility, Exeter, Devon, UK
| | - Max Nieuwdorp
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Diabeter Center Amsterdam, Amsterdam, the Netherlands
| | - Nordin M J Hanssen
- Department of (Experimental) Vascular and Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Diabeter Center Amsterdam, Amsterdam, the Netherlands
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6
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Phillip M, Achenbach P, Addala A, Albanese-O'Neill A, Battelino T, Bell KJ, Besser REJ, Bonifacio E, Colhoun HM, Couper JJ, Craig ME, Danne T, de Beaufort C, Dovc K, Driscoll KA, Dutta S, Ebekozien O, Larsson HE, Feiten DJ, Frohnert BI, Gabbay RA, Gallagher MP, Greenbaum CJ, Griffin KJ, Hagopian W, Haller MJ, Hendrieckx C, Hendriks E, Holt RIG, Hughes L, Ismail HM, Jacobsen LM, Johnson SB, Kolb LE, Kordonouri O, Lange K, Lash RW, Lernmark Å, Libman I, Lundgren M, Maahs DM, Marcovecchio ML, Mathieu C, Miller KM, O'Donnell HK, Oron T, Patil SP, Pop-Busui R, Rewers MJ, Rich SS, Schatz DA, Schulman-Rosenbaum R, Simmons KM, Sims EK, Skyler JS, Smith LB, Speake C, Steck AK, Thomas NPB, Tonyushkina KN, Veijola R, Wentworth JM, Wherrett DK, Wood JR, Ziegler AG, DiMeglio LA. Consensus guidance for monitoring individuals with islet autoantibody-positive pre-stage 3 type 1 diabetes. Diabetologia 2024:10.1007/s00125-024-06205-5. [PMID: 38910151 DOI: 10.1007/s00125-024-06205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Given the proven benefits of screening to reduce diabetic ketoacidosis (DKA) likelihood at the time of stage 3 type 1 diabetes diagnosis, and emerging availability of therapy to delay disease progression, type 1 diabetes screening programmes are being increasingly emphasised. Once broadly implemented, screening initiatives will identify significant numbers of islet autoantibody-positive (IAb+) children and adults who are at risk of (confirmed single IAb+) or living with (multiple IAb+) early-stage (stage 1 and stage 2) type 1 diabetes. These individuals will need monitoring for disease progression; much of this care will happen in non-specialised settings. To inform this monitoring, JDRF in conjunction with international experts and societies developed consensus guidance. Broad advice from this guidance includes the following: (1) partnerships should be fostered between endocrinologists and primary-care providers to care for people who are IAb+; (2) when people who are IAb+ are initially identified there is a need for confirmation using a second sample; (3) single IAb+ individuals are at lower risk of progression than multiple IAb+ individuals; (4) individuals with early-stage type 1 diabetes should have periodic medical monitoring, including regular assessments of glucose levels, regular education about symptoms of diabetes and DKA, and psychosocial support; (5) interested people with stage 2 type 1 diabetes should be offered trial participation or approved therapies; and (6) all health professionals involved in monitoring and care of individuals with type 1 diabetes have a responsibility to provide education. The guidance also emphasises significant unmet needs for further research on early-stage type 1 diabetes to increase the rigour of future recommendations and inform clinical care.
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Affiliation(s)
- Moshe Phillip
- Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Peter Achenbach
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum Rechts Der Isar, Munich, Germany
| | - Ananta Addala
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tadej Battelino
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolism, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Kirstine J Bell
- Charles Perkins Centre and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Rachel E J Besser
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre Human Genetics, Nuffield Department of Medicine Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Ezio Bonifacio
- Center for Regenerative Therapies Dresden, Faculty of Medicine, Technical University of Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Centre Munich at the University Clinic Carl Gustav Carus of TU Dresden and Faculty of Medicine, Dresden, Germany
| | - Helen M Colhoun
- The Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Public Health, NHS Fife, Kirkcaldy, UK
| | - Jennifer J Couper
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Division of Paediatrics, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Maria E Craig
- Charles Perkins Centre and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Discipline of Paediatrics & Child Health, School of Clinical Medicine, UNSW Medicine & Health, Sydney, NSW, Australia
| | | | - Carine de Beaufort
- International Society for Pediatric and Adolescent Diabetes (ISPAD), Berlin, Germany
- Diabetes & Endocrine Care Clinique Pédiatrique (DECCP), Clinique Pédiatrique/Centre Hospitalier (CH) de Luxembourg, Luxembourg City, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-Belval, Luxembourg
| | - Klemen Dovc
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Endocrinology, Diabetes and Metabolism, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Kimberly A Driscoll
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Clinical and Health Psychology, University of Florida, Gainesville, FL, USA
- Department of Pediatrics, University of Florida Diabetes Institute, Gainesville, FL, USA
| | | | | | - Helena Elding Larsson
- Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
- Department of Pediatrics, Skåne University Hospital, Malmö and Lund, Sweden
| | | | - Brigitte I Frohnert
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Carla J Greenbaum
- Center for Interventional Immunology and Diabetes Program, Benaroya Research Institute, Seattle, WA, USA
| | - Kurt J Griffin
- Sanford Research, Sioux Falls, SD, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - William Hagopian
- Pacific Northwest Diabetes Research Institute, University of Washington, Seattle, WA, USA
| | - Michael J Haller
- Department of Pediatrics, University of Florida Diabetes Institute, Gainesville, FL, USA
- Division of Endocrinology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Christel Hendrieckx
- School of Psychology, Deakin University, Geelong, VIC, Australia
- The Australian Centre for Behavioural Research in Diabetes, Diabetes Victoria, Carlton, VIC, Australia
- Institute for Health Transformation, Deakin University, Geelong, VIC, Australia
| | - Emile Hendriks
- Department of Paediatrics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Richard I G Holt
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- National Institute for Health and Care Research Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Heba M Ismail
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Laura M Jacobsen
- Division of Endocrinology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Suzanne B Johnson
- Department of Behavioral Sciences and Social Medicine, Florida State University College of Medicine, Tallahassee, FL, USA
| | - Leslie E Kolb
- Association of Diabetes Care & Education Specialists, Chicago, IL, USA
| | | | - Karin Lange
- Medical Psychology, Hannover Medical School, Hannover, Germany
| | | | - Åke Lernmark
- Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
| | - Ingrid Libman
- Division of Pediatric Endocrinology and Diabetes, University of Pittsburgh, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Markus Lundgren
- Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
- Department of Pediatrics, Kristianstad Hospital, Kristianstad, Sweden
| | - David M Maahs
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Loredana Marcovecchio
- Department of Pediatrics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Chantal Mathieu
- Department of Endocrinology, UZ Gasthuisberg, KU Leuven, Leuven, Belgium
| | | | - Holly K O'Donnell
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Tal Oron
- Institute for Endocrinology and Diabetes, National Center for Childhood Diabetes, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
- Faculty of Medical and Health Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shivajirao P Patil
- Department of Family Medicine, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Rodica Pop-Busui
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Marian J Rewers
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Desmond A Schatz
- Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Rifka Schulman-Rosenbaum
- Division of Endocrinology, Long Island Jewish Medical Center, Northwell Health, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY, USA
| | - Kimber M Simmons
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emily K Sims
- Division of Pediatric Endocrinology and Diabetology, Herman B Wells Center for Pediatric Research, Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jay S Skyler
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Laura B Smith
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Cate Speake
- Center for Interventional Immunology and Diabetes Program, Benaroya Research Institute, Seattle, WA, USA
| | - Andrea K Steck
- Department of Pediatrics, Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Ksenia N Tonyushkina
- Division of Endocrinology and Diabetes, Baystate Children's Hospital and University of Massachusetts Chan Medical School - Baystate, Springfield, MA, USA
| | - Riitta Veijola
- Research Unit of Clinical Medicine, Department of Pediatrics, Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - John M Wentworth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Diabetes and Endocrinology, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Diane K Wherrett
- Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Jamie R Wood
- Department of Pediatric Endocrinology, Rainbow Babies and Children's Hospital, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Anette-Gabriele Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum Rechts Der Isar, Munich, Germany
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7
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Teixeira PF, Battelino T, Carlsson A, Gudbjörnsdottir S, Hannelius U, von Herrath M, Knip M, Korsgren O, Elding Larsson H, Lindqvist A, Ludvigsson J, Lundgren M, Nowak C, Pettersson P, Pociot F, Sundberg F, Åkesson K, Lernmark Å, Forsander G. Assisting the implementation of screening for type 1 diabetes by using artificial intelligence on publicly available data. Diabetologia 2024; 67:985-994. [PMID: 38353727 PMCID: PMC11058797 DOI: 10.1007/s00125-024-06089-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/06/2023] [Indexed: 04/30/2024]
Abstract
The type 1 diabetes community is coalescing around the benefits and advantages of early screening for disease risk. To be accepted by healthcare providers, regulatory authorities and payers, screening programmes need to show that the testing variables allow accurate risk prediction and that individualised risk-informed monitoring plans are established, as well as operational feasibility, cost-effectiveness and acceptance at population level. Artificial intelligence (AI) has the potential to contribute to solving these issues, starting with the identification and stratification of at-risk individuals. ASSET (AI for Sustainable Prevention of Autoimmunity in the Society; www.asset.healthcare ) is a public/private consortium that was established to contribute to research around screening for type 1 diabetes and particularly to how AI can drive the implementation of a precision medicine approach to disease prevention. ASSET will additionally focus on issues pertaining to operational implementation of screening. The authors of this article, researchers and clinicians active in the field of type 1 diabetes, met in an open forum to independently debate key issues around screening for type 1 diabetes and to advise ASSET. The potential use of AI in the analysis of longitudinal data from observational cohort studies to inform the design of improved, more individualised screening programmes was also discussed. A key issue was whether AI would allow the research community and industry to capitalise on large publicly available data repositories to design screening programmes that allow the early detection of individuals at high risk and enable clinical evaluation of preventive therapies. Overall, AI has the potential to revolutionise type 1 diabetes screening, in particular to help identify individuals who are at increased risk of disease and aid in the design of appropriate follow-up plans. We hope that this initiative will stimulate further research on this very timely topic.
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Affiliation(s)
| | - Tadej Battelino
- University Medical Center Ljubljana, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Anneli Carlsson
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Soffia Gudbjörnsdottir
- Swedish National Diabetes Register, Centre of Registers, Gothenburg, Sweden
- Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Matthias von Herrath
- Global Chief Medical Office, Novo Nordisk, A/S, Søborg, Denmark
- Diabetes Research Institute, University of Miami, Miami, FL, USA
| | - Mikael Knip
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Olle Korsgren
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
- Department of Pediatrics, Skåne University Hospital, Malmö, Sweden
| | | | - Johnny Ludvigsson
- Crown Princess Victoria Children's Hospital and Division of Pediatrics, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Markus Lundgren
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Paediatrics, Kristianstad Hospital, Kristianstad, Sweden
| | | | - Paul Pettersson
- Division of Networked and Embedded Systems, Mälardalen University, Västerås, Sweden
- MainlyAI AB, Stockholm, Sweden
| | - Flemming Pociot
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frida Sundberg
- Department of Paediatrics, Institute for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Karin Åkesson
- Department of Clinical and Experimental Medicine, Division of Pediatrics and Diabetes Research Center, Linköping University, Linköping, Sweden
- Department of Pediatrics, Ryhov County Hospital, Jönköping, Sweden
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden.
| | - Gun Forsander
- Department of Paediatrics, Institute for Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden.
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8
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Peña E, Mas-Bermejo P, Lecube A, Ciudin A, Arenas C, Simó R, Rigla M, Caixàs A, Rosa A. Use of polygenic risk scores to assess weight loss after bariatric surgery: a 5-year follow-up study. J Gastrointest Surg 2024:S1091-255X(24)00485-2. [PMID: 38821212 DOI: 10.1016/j.gassur.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/19/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
BACKGROUND Bariatric surgery (BS) is currently the most effective long-term treatment of severe obesity. However, the interindividual variability observed in surgical outcomes suggests a moderating effect of several factors, including individual genetic background. This study aimed to investigate the contribution of the genetic architecture of body mass index (BMI) to the variability in weight loss outcomes after BS. METHODS A total of 106 patients with severe obesity who underwent Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy were followed up for 5 years. Changes in BMI (BMIchange) and percentage of total weight loss (%TWL) were evaluated during the postoperative period. Polygenic risk scores (PRSs), including 50 genetic variants, were calculated for each participant to determine their genetic risk of high BMI based on a previous genome-wide association study. Generalized estimating equation models were used to study the role of the individual's polygenic score and other factors on BMIchange and %TWL in the long term after surgery. RESULTS This study found an effect of the polygenic score on %TWL and BMIchange, in which patients with lower scores had better outcomes after surgery than those with higher scores. Furthermore, when analyzing only patients who underwent RYGB, the results were replicated, showing greater weight loss after surgery for patients with lower polygenic scores. DISCUSSION Our results indicate that genetic background assessed with PRSs, along with other individual factors, such as biological sex, age, and preoperative BMI, has an effect on BS outcomes and could represent a useful tool for estimating surgical outcomes in advance.
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Affiliation(s)
- Elionora Peña
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Patricia Mas-Bermejo
- Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
| | - Albert Lecube
- Department of Endocrinology and Nutrition, Arnau de Vilanova University Hospital, Institut de Recerca Biomèdica de Lleida, Universitat de Lleida, Lleida, Spain
| | - Andreea Ciudin
- Diabetes and Metabolism Research Unit, Department of Endocrinology and Nutrition, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción Arenas
- Statistics Section of the Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Rafael Simó
- Diabetes and Metabolism Research Unit, Department of Endocrinology and Nutrition, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Rigla
- Department of Endocrinology and Nutrition, Institut d'Investigació i Innovació, Parc Taulí Hospital Universitari, Sabadell, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Assumpta Caixàs
- Department of Endocrinology and Nutrition, Institut d'Investigació i Innovació, Parc Taulí Hospital Universitari, Sabadell, Spain; Departament de Medicina, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Araceli Rosa
- Secció de Zoologia i Antropologia Biòlogica, Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica En Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain.
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9
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Triolo TM, Parikh HM, Tosur M, Ferrat L, You L, Gottlieb PA, Oram RA, Onengut-Gumuscu S, Krischer JP, Rich SS, Steck AK, Redondo MJ. Genetic Associations with C-peptide Levels before Type 1 Diabetes Diagnosis in At-Risk Relatives. J Clin Endocrinol Metab 2024:dgae349. [PMID: 38767115 DOI: 10.1210/clinem/dgae349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
OBJECTIVE We sought to determine whether the type 1 diabetes genetic risk score-2 (T1D-GRS2) and single nucleotide polymorphisms (SNPs) are associated with C-peptide preservation before type 1 diabetes diagnosis. METHODS We conducted a retrospective analysis of 713 autoantibody-positive participants who developed type 1 diabetes in the TrialNet Pathway to Prevention Study who had T1DExomeChip data. We evaluated the relationships of 16 known SNPs and T1D-GRS2 with area under the curve (AUC) C-peptide levels during oral glucose tolerance tests conducted in the 9 months before diagnosis. RESULTS Higher T1D-GRS2 was associated with lower C-peptide AUC in the 9 months before diagnosis in univariate (β=-0.06, P<0.0001) and multivariate (β=-0.03, P=0.005) analyses. Participants with the JAZF1 rs864745 T allele had lower C-peptide AUC in both univariate (β=-0.11, P=0.002) and multivariate (β=-0.06, P=0.018) analyses. CONCLUSIONS The type 2 diabetes-associated JAZF1 rs864745 T allele and higher T1D-GRS2 are associated with lower C-peptide AUC prior to diagnosis of type 1 diabetes, with implications for the design of prevention trials.
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Affiliation(s)
- Taylor M Triolo
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus
| | - Hemang M Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Mustafa Tosur
- Department of Pediatrics, Division of Diabetes and Endocrinology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
- USDA/ARS Children's Nutrition Research Center, Houston, TX, USA
| | | | - Lu You
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Peter A Gottlieb
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus
| | | | | | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Andrea K Steck
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus
| | - Maria J Redondo
- Department of Pediatrics, Division of Diabetes and Endocrinology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
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10
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Zheng Z, Liu S, Sidorenko J, Wang Y, Lin T, Yengo L, Turley P, Ani A, Wang R, Nolte IM, Snieder H, Yang J, Wray NR, Goddard ME, Visscher PM, Zeng J. Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries. Nat Genet 2024; 56:767-777. [PMID: 38689000 PMCID: PMC11096109 DOI: 10.1038/s41588-024-01704-y] [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: 10/01/2022] [Accepted: 03/05/2024] [Indexed: 05/02/2024]
Abstract
We develop a method, SBayesRC, that integrates genome-wide association study (GWAS) summary statistics with functional genomic annotations to improve polygenic prediction of complex traits. Our method is scalable to whole-genome variant analysis and refines signals from functional annotations by allowing them to affect both causal variant probability and causal effect distribution. We analyze 50 complex traits and diseases using ∼7 million common single-nucleotide polymorphisms (SNPs) and 96 annotations. SBayesRC improves prediction accuracy by 14% in European ancestry and up to 34% in cross-ancestry prediction compared to the baseline method SBayesR, which does not use annotations, and outperforms other methods, including LDpred2, LDpred-funct, MegaPRS, PolyPred-S and PRS-CSx. Investigation of factors affecting prediction accuracy identifies a significant interaction between SNP density and annotation information, suggesting whole-genome sequence variants with annotations may further improve prediction. Functional partitioning analysis highlights a major contribution of evolutionary constrained regions to prediction accuracy and the largest per-SNP contribution from nonsynonymous SNPs.
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Affiliation(s)
- Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Shouye Liu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Julia Sidorenko
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Ying Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Loic Yengo
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Patrick Turley
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
- Department of Economics, University of Southern California, Los Angeles, CA, USA
| | - Alireza Ani
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rujia Wang
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Michael E Goddard
- Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Victoria, Australia
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, Bundoora, Victoria, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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11
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Liu Y, Ritchie SC, Teo SM, Ruuskanen MO, Kambur O, Zhu Q, Sanders J, Vázquez-Baeza Y, Verspoor K, Jousilahti P, Lahti L, Niiranen T, Salomaa V, Havulinna AS, Knight R, Méric G, Inouye M. Integration of polygenic and gut metagenomic risk prediction for common diseases. NATURE AGING 2024; 4:584-594. [PMID: 38528230 PMCID: PMC11031402 DOI: 10.1038/s43587-024-00590-7] [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] [Received: 08/11/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024]
Abstract
Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.
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Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Shu Mei Teo
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Centre for Youth Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Matti O Ruuskanen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Computing, University of Turku, Turku, Finland
| | - Oleg Kambur
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Jon Sanders
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
| | - Karin Verspoor
- School of Computing Technologies, RMIT University, Melbourne, Victoria, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - Pekka Jousilahti
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Teemu Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Division of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aki S Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, FIMM-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Clinical Pathology, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia.
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
- The Alan Turing Institute, London, UK.
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12
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Kim NY, Lee H, Kim S, Kim YJ, Lee H, Lee J, Kwak SH, Lee S. The clinical relevance of a polygenic risk score for type 2 diabetes mellitus in the Korean population. Sci Rep 2024; 14:5749. [PMID: 38459065 PMCID: PMC10923897 DOI: 10.1038/s41598-024-55313-0] [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: 05/30/2023] [Accepted: 02/22/2024] [Indexed: 03/10/2024] Open
Abstract
The clinical utility of a type 2 diabetes mellitus (T2DM) polygenic risk score (PRS) in the East Asian population remains underexplored. We aimed to examine the potential prognostic value of a T2DM PRS and assess its viability as a clinical instrument. We first established a T2DM PRS for 5490 Korean individuals using East Asian Biobank data (269,487 samples). Subsequently, we assessed the predictive capability of this T2DM PRS in a prospective longitudinal study with baseline data and data from seven additional follow-ups. Our analysis showed that the T2DM PRS could predict the transition of glucose tolerance stages from normal glucose tolerance to prediabetes and from prediabetes to T2DM. Moreover, T2DM patients in the top-decile PRS group were more likely to be treated with insulin (hazard ratio = 1.69, p value = 2.31E-02) than were those in the remaining PRS groups. T2DM PRS values were significantly high in the severe diabetes subgroup, characterized by insulin resistance and β -cell dysfunction (p value = 0.0012). The prediction models with the T2DM PRS had significantly greater Harrel's C-indices than did corresponding models without it. By utilizing prospective longitudinal study data and extensive clinical risk factor information, our analysis provides valuable insights into the multifaceted clinical utility of the T2DM PRS.
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Affiliation(s)
- Na Yeon Kim
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Haekyung Lee
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, South Korea
| | - Sehee Kim
- Department of Clinical Epidemiology and Biostatistics, Asan Medical Center, Seoul, South Korea
| | - Ye-Jee Kim
- Department of Clinical Epidemiology and Biostatistics, Asan Medical Center, Seoul, South Korea
| | - Hyunsuk Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Junhyeong Lee
- Graduate School of Data Science, Seoul National University, Seoul, South Korea
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, South Korea.
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13
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Loginovic P, Wang F, Li J, Ferrat L, Mirshahi UL, Rao HS, Petzold A, Tyrrell J, Green HD, Weedon MN, Ganna A, Tuomi T, Carey DJ, Oram RA, Braithwaite T. Applying a genetic risk score model to enhance prediction of future multiple sclerosis diagnosis at first presentation with optic neuritis. Nat Commun 2024; 15:1415. [PMID: 38418465 PMCID: PMC10902342 DOI: 10.1038/s41467-024-44917-9] [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: 10/16/2023] [Accepted: 01/09/2024] [Indexed: 03/01/2024] Open
Abstract
Optic neuritis (ON) is associated with numerous immune-mediated inflammatory diseases, but 50% patients are ultimately diagnosed with multiple sclerosis (MS). Differentiating MS-ON from non-MS-ON acutely is challenging but important; non-MS ON often requires urgent immunosuppression to preserve vision. Using data from the United Kingdom Biobank we showed that combining an MS-genetic risk score (GRS) with demographic risk factors (age, sex) significantly improved MS prediction in undifferentiated ON; one standard deviation of MS-GRS increased the Hazard of MS 1.3-fold (95% confidence interval 1.07-1.55, P < 0.01). Participants stratified into quartiles of predicted risk developed incident MS at rates varying from 4% (95%CI 0.5-7%, lowest risk quartile) to 41% (95%CI 33-49%, highest risk quartile). The model replicated across two cohorts (Geisinger, USA, and FinnGen, Finland). This study indicates that a combined model might enhance individual MS risk stratification, paving the way for precision-based ON treatment and earlier MS disease-modifying therapy.
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Affiliation(s)
- Pavel Loginovic
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Heavitree Road, Exeter, EX1 2HZ, UK
| | - Feiyi Wang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jiang Li
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Lauric Ferrat
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | | | - H Shanker Rao
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Axel Petzold
- Neuro-ophthalmology Expert Center, Amsterdam UMC, Amsterdam, The Netherlands
- Department of Neuro-ophthalmology, The National Hospital for Neurology and Neurosurgery, Queen Square, UCL Institute of Neurology, London, UK
- Neuro-ophthalmology service, Moorfields Eye Hospital, London, UK
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Harry D Green
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Abdominal Center, Endocrinology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - David J Carey
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Richard A Oram
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK.
- Academic Kidney Unit, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK.
| | - Tasanee Braithwaite
- King's College London, School of Immunology & Microbial Sciences and School of Life Course and Population Sciences, London, UK
- Medical Eye Unit, St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, Westminster Bridge Road, London, UK
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14
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Guertin KA, Repaske DR, Taylor JF, Williams ES, Onengut-Gumuscu S, Chen WM, Boggs SR, Yu L, Allen L, Botteon L, Daniel L, Keating KG, Labergerie MK, Lienhart TS, Gonzalez-Mejia JA, Starnowski MJ, Rich SS. Implementation of type 1 diabetes genetic risk screening in children in diverse communities: the Virginia PrIMeD project. Genome Med 2024; 16:31. [PMID: 38355597 PMCID: PMC10865687 DOI: 10.1186/s13073-024-01305-8] [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: 06/14/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Population screening for risk of type 1 diabetes (T1D) has been proposed to identify those with islet autoimmunity (presence of islet autoantibodies). As islet autoantibodies can be transient, screening with a genetic risk score has been proposed as an entry into autoantibody testing. METHODS Children were recruited from eight general pediatric and specialty clinics across Virginia with diverse community settings. Recruiters in each clinic obtained informed consent/assent, a medical history, and a saliva sample for DNA extraction in children with and without a history of T1D. A custom genotyping panel was used to define T1D genetic risk based upon associated SNPs in European- and African-genetic ancestry. Subjects at "high genetic risk" were offered a separate blood collection for screening four islet autoantibodies. A follow-up contact (email, mail, and telephone) in one half of the participants determined interest and occurrence of subsequent T1D. RESULTS A total of 3818 children aged 2-16 years were recruited, with 14.2% (n = 542) having a "high genetic risk." Of children with "high genetic risk" and without pre-existing T1D (n = 494), 7.0% (34/494) consented for autoantibody screening; 82.4% (28/34) who consented also completed the blood collection, and 7.1% (2/28) of them tested positive for multiple autoantibodies. Among children with pre-existing T1D (n = 91), 52% (n = 48) had a "high genetic risk." In the sample of children with existing T1D, there was no relationship between genetic risk and age at T1D onset. A major factor in obtaining islet autoantibody testing was concern over SARS-CoV-2 exposure. CONCLUSIONS Minimally invasive saliva sampling implemented using a genetic risk score can identify children at genetic risk of T1D. Consent for autoantibody screening, however, was limited largely due to the SARS-CoV-2 pandemic and need for blood collection.
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Affiliation(s)
- Kristin A Guertin
- Department of Public Health Sciences, University of Virginia, 1300 Jefferson Park Avenue, 3182 West Complex, Charlottesville, VA, 22903, USA
- Department of Public Health Sciences, UConn School of Medicine, UConn Health, 263 Farmington Avenue, MC 6325, Farmington, CT, 06030, USA
| | - David R Repaske
- Department of Pediatrics, Division of Pediatric Diabetes & Endocrinology, University of Virginia, UVAHealth, 1204 W Main Street, 6th Floor, Charlottesville, VA, 22903, USA
| | - Julia F Taylor
- Department of Pediatrics, Division of Pediatric Diabetes & Endocrinology, University of Virginia, UVAHealth, 1204 W Main Street, 6th Floor, Charlottesville, VA, 22903, USA
| | - Eli S Williams
- Department of Pathology, Division of Medical Genetics, UVAHealth, University of Virginia, 21 Hospital Drive, Charlottesville, VA, 22903, USA
| | - Suna Onengut-Gumuscu
- Department of Public Health Sciences, University of Virginia, 1300 Jefferson Park Avenue, 3182 West Complex, Charlottesville, VA, 22903, USA
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Wei-Min Chen
- Department of Public Health Sciences, University of Virginia, 1300 Jefferson Park Avenue, 3182 West Complex, Charlottesville, VA, 22903, USA
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Sarah R Boggs
- Department of Pediatrics, Division of Pediatric Diabetes & Endocrinology, University of Virginia, UVAHealth, 1204 W Main Street, 6th Floor, Charlottesville, VA, 22903, USA
| | - Liping Yu
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, 1774 Aurora Court, Suite A140, Aurora, CO, 80045, USA
| | - Luke Allen
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Lacey Botteon
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Louis Daniel
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Katherine G Keating
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Mika K Labergerie
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Tyler S Lienhart
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Jorge A Gonzalez-Mejia
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Matt J Starnowski
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA
| | - Stephen S Rich
- Department of Public Health Sciences, University of Virginia, 1300 Jefferson Park Avenue, 3182 West Complex, Charlottesville, VA, 22903, USA.
- Center for Public Health Genomics, University of Virginia, 1335 Lee Street, 3235 West Complex, Charlottesville, VA, 22903, USA.
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15
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Fanaropoulou NM, Tsatsani GC, Koufakis T, Kotsa K. Teplizumab: promises and challenges of a recently approved monoclonal antibody for the prevention of type 1 diabetes or preservation of residual beta cell function. Expert Rev Clin Immunol 2024; 20:185-196. [PMID: 37937833 DOI: 10.1080/1744666x.2023.2281990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/07/2023] [Indexed: 11/09/2023]
Abstract
INTRODUCTION Type 1 diabetes (T1D) is a chronic autoimmune endocrinopathy with increasing incidence that results in the depletion of pancreatic beta cells and exogenous insulin dependence. Despite technological advances in insulin delivery, disease control remains suboptimal, while previous immunotherapy options have failed to prevent T1D. Recently, teplizumab, an immunomodulating monoclonal antibody, was approved to delay or prevent T1D. AREAS COVERED Five randomized controlled trials have tested different regimens of administration, mostly 14-day schemes with dose escalation. In participants with new-onset T1D, teplizumab delayed C-peptide decline, improved glycemic control, and reduced insulin demand for a median of 1 or 2 years. Studies in at-risk relatives of patients showed a decrease in T1D incidence during 2 years of follow-up. Subgroups of responders with unique metabolic and immunological characteristics were identified. Mild to moderate adverse effects were reported, including transient rash, cytopenia, nausea, vomiting, and infections. EXPERT OPINION Teplizumab marks a turning point in T1D therapy. Areas of future research include the ideal population for screening, cost-effectiveness, and challenges in treatment accessibility. More studies are essential to evaluate the ideal duration of the regimen, the potential benefit of combinations with other drugs, and to identify endophenotypes with a high probability of response.
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Affiliation(s)
- Nina Maria Fanaropoulou
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgia C Tsatsani
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Theocharis Koufakis
- Second Propaedeutic Department of Internal Medicine, Hippokration General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kalliopi Kotsa
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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16
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Subramanian S, Khan F, Hirsch IB. New advances in type 1 diabetes. BMJ 2024; 384:e075681. [PMID: 38278529 DOI: 10.1136/bmj-2023-075681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
Type 1 diabetes is an autoimmune condition resulting in insulin deficiency and eventual loss of pancreatic β cell function requiring lifelong insulin therapy. Since the discovery of insulin more than 100 years ago, vast advances in treatments have improved care for many people with type 1 diabetes. Ongoing research on the genetics and immunology of type 1 diabetes and on interventions to modify disease course and preserve β cell function have expanded our broad understanding of this condition. Biomarkers of type 1 diabetes are detectable months to years before development of overt disease, and three stages of diabetes are now recognized. The advent of continuous glucose monitoring and the newer automated insulin delivery systems have changed the landscape of type 1 diabetes management and are associated with improved glycated hemoglobin and decreased hypoglycemia. Adjunctive therapies such as sodium glucose cotransporter-1 inhibitors and glucagon-like peptide 1 receptor agonists may find use in management in the future. Despite these rapid advances in the field, people living in under-resourced parts of the world struggle to obtain necessities such as insulin, syringes, and blood glucose monitoring essential for managing this condition. This review covers recent developments in diagnosis and treatment and future directions in the broad field of type 1 diabetes.
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Affiliation(s)
- Savitha Subramanian
- University of Washington Diabetes Institute, Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, WA, USA
| | - Farah Khan
- University of Washington Diabetes Institute, Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, WA, USA
| | - Irl B Hirsch
- University of Washington Diabetes Institute, Division of Metabolism, Endocrinology and Nutrition, University of Washington, Seattle, WA, USA
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17
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Billings LK, Shi Z, Wei J, Rifkin AS, Zheng SL, Helfand BT, Ilbawi N, Dunnenberger HM, Hulick PJ, Qamar A, Xu J. Utility of Polygenic Scores for Differentiating Diabetes Diagnosis Among Patients With Atypical Phenotypes of Diabetes. J Clin Endocrinol Metab 2023; 109:107-113. [PMID: 37560999 DOI: 10.1210/clinem/dgad456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023]
Abstract
CONTEXT Misclassification of diabetes type occurs in people with atypical presentations of type 1 diabetes (T1D) or type 2 diabetes (T2D). Although current clinical guidelines suggest clinical variables and treatment response as ways to help differentiate diabetes type, they remain insufficient for people with atypical presentations. OBJECTIVE This work aimed to assess the clinical utility of 2 polygenic scores (PGSs) in differentiating between T1D and T2D. METHODS Patients diagnosed with diabetes in the UK Biobank were studied (N = 41 787), including 464 (1%) and 15 923 (38%) who met the criteria for classic T1D and T2D, respectively, and 25 400 (61%) atypical diabetes. The validity of 2 published PGSs for T1D (PGST1D) and T2D (PGST2D) in differentiating classic T1D or T2D was assessed using C statistic. The utility of genetic probability for T1D based on PGSs (GenProb-T1D) was evaluated in atypical diabetes patients. RESULTS The joint performance of PGST1D and PGST2D for differentiating classic T1D or T2D was outstanding (C statistic = 0.91), significantly higher than that of PGST1D alone (0.88) and PGST2D alone (0.70), both P less than .001. Using an optimal cutoff of GenProb-T1D, 23% of patients with atypical diabetes had a higher probability of T1D and its validity was independently supported by clinical presentations that are characteristic of T1D. CONCLUSION PGST1D and PGST2D can be used to discriminate classic T1D and T2D and have potential clinical utility for differentiating these 2 types of diseases among patients with atypical diabetes.
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Affiliation(s)
- Liana K Billings
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA
| | - Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Andrew S Rifkin
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Brian T Helfand
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Nadim Ilbawi
- Department of Family Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Henry M Dunnenberger
- Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Peter J Hulick
- Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Arman Qamar
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Jianfeng Xu
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL 60637, USA
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL 60201, USA
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18
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Squires S, Weedon MN, Oram RA. Exploring the application of deep learning methods for polygenic risk score estimation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.14.23299972. [PMID: 38168416 PMCID: PMC10760287 DOI: 10.1101/2023.12.14.23299972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Polygenic risk scores (PRS) summarise genetic information into a single number with multiple clinical and research uses. Machine learning (ML) has revolutionised a diverse set of fields, however, the impact of ML on genomics in general, and PRSs in particular, has been less significant. We explore how ML can improve the generation of PRSs. Methods We train ML models on known PRSs using UK Biobank data. We explore whether the models can recreate human programmed PRSs, including using a single model to generate multiple PRSs, and the difficulty in using ML for PRS generation. We also investigate how ML can compensate for missing data and the constraints on performance. Results We demonstrate almost perfect generation of PRSs, including when using one model to predict multiple scores, and with little loss of performance with reduced quantity of training data. For an example set of missing SNPs the MLP produces predictions that enable separation of cases from population samples with an area under the receiver operating characteristic curve of 0.847 (95% CI: 0.828-0.864) compared to 0.798 (95% CI: 0.779-0.818) for the PRS. We provide evidence that input information is the limiting factor of further improvement. Conclusions ML can accurately generate PRSs, including with one model for multiple PRSs. The models are transferable and have high longevity. With certain missing SNPs the ML models can statistically significantly improve on normal PRS generation. Models trained are probably at the edge of performance and further improvements likely require use of additional input data.
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19
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McGrail C, Chiou J, Elgamal R, Luckett AM, Oram RA, Benaglio P, Gaulton KJ. Genetic discovery and risk prediction for type 1 diabetes in individuals without high-risk HLA-DR3/DR4 haplotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.11.23298405. [PMID: 37986756 PMCID: PMC10659516 DOI: 10.1101/2023.11.11.23298405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Over 10% of type 1 diabetes (T1D) cases do not have high-risk HLA-DR3 or DR4 haplotypes with distinct clinical features such as later onset and reduced insulin dependence. To identify genetic drivers of T1D in the absence of DR3/DR4, we performed association and fine-mapping analyses in 12,316 non-DR3/DR4 samples. Risk variants at the MHC and other loci genome-wide had heterogeneity in effects on T1D dependent on DR3/DR4, and non-DR3/DR4 T1D had evidence for a greater polygenic burden. T1D-assocated variants in non-DR3/DR4 were more enriched for loci, regulatory elements, and pathways for antigen presentation, innate immunity, and beta cells, and depleted in T cells, compared to DR3/DR4. Non-DR3/DR4 T1D cases were poorly classified based on an existing genetic risk score GRS2, and we created a new GRS which highly discriminated non-DR3/DR4 T1D from both non-diabetes and T2D. In total we identified heterogeneity in T1D genetic risk and disease mechanisms dependent on high-risk HLA haplotype and which enabled accurate classification of T1D across HLA background.
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Affiliation(s)
- Carolyn McGrail
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla, CA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla, CA
| | - Ruth Elgamal
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla, CA
| | - Amber M Luckett
- University of Exeter College of Medicine and Health, Exeter, UK
| | - Richard A Oram
- University of Exeter College of Medicine and Health, Exeter, UK
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
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20
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Butler-Laporte G, Farjoun J, Nakanishi T, Lu T, Abner E, Chen Y, Hultström M, Metspalu A, Milani L, Mägi R, Nelis M, Hudjashov G, Yoshiji S, Ilboudo Y, Liang KYH, Su CY, Willet JDS, Esko T, Zhou S, Forgetta V, Taliun D, Richards JB. HLA allele-calling using multi-ancestry whole-exome sequencing from the UK Biobank identifies 129 novel associations in 11 autoimmune diseases. Commun Biol 2023; 6:1113. [PMID: 37923823 PMCID: PMC10624861 DOI: 10.1038/s42003-023-05496-5] [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: 06/09/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
The human leukocyte antigen (HLA) region on chromosome 6 is strongly associated with many immune-mediated and infection-related diseases. Due to its highly polymorphic nature and complex linkage disequilibrium patterns, traditional genetic association studies of single nucleotide polymorphisms do not perform well in this region. Instead, the field has adopted the assessment of the association of HLA alleles (i.e., entire HLA gene haplotypes) with disease. Often based on genotyping arrays, these association studies impute HLA alleles, decreasing accuracy and thus statistical power for rare alleles and in non-European ancestries. Here, we use whole-exome sequencing (WES) from 454,824 UK Biobank (UKB) participants to directly call HLA alleles using the HLA-HD algorithm. We show this method is more accurate than imputing HLA alleles and harness the improved statistical power to identify 360 associations for 11 auto-immune phenotypes (at least 129 likely novel), leading to better insights into the specific coding polymorphisms that underlie these diseases. We show that HLA alleles with synonymous variants, often overlooked in HLA studies, can significantly influence these phenotypes. Lastly, we show that HLA sequencing may improve polygenic risk scores accuracy across ancestries. These findings allow better characterization of the role of the HLA region in human disease.
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada.
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada.
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Joseph Farjoun
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Tianyuan Lu
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Erik Abner
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yiheng Chen
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mari Nelis
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Georgi Hudjashov
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Satoshi Yoshiji
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Yann Ilboudo
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Kevin Y H Liang
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Chen-Yang Su
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Julian D S Willet
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
| | - Daniel Taliun
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- Department of Twin Research, King's College London, London, UK
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
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21
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Lee YH, Thaweethai T, Sheu YH, Feng YCA, Karlson EW, Ge T, Kraft P, Smoller JW. Impact of selection bias on polygenic risk score estimates in healthcare settings. Psychol Med 2023; 53:7435-7445. [PMID: 37226828 DOI: 10.1017/s0033291723001186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Hospital-based biobanks are being increasingly considered as a resource for translating polygenic risk scores (PRS) into clinical practice. However, since these biobanks originate from patient populations, there is a possibility of bias in polygenic risk estimation due to overrepresentation of patients with higher frequency of healthcare interactions. METHODS PRS for schizophrenia, bipolar disorder, and depression were calculated using summary statistics from the largest available genomic studies for a sample of 24 153 European ancestry participants in the Mass General Brigham (MGB) Biobank. To correct for selection bias, we fitted logistic regression models with inverse probability (IP) weights, which were estimated using 1839 sociodemographic, clinical, and healthcare utilization features extracted from electronic health records of 1 546 440 non-Hispanic White patients eligible to participate in the Biobank study at their first visit to the MGB-affiliated hospitals. RESULTS Case prevalence of bipolar disorder among participants in the top decile of bipolar disorder PRS was 10.0% (95% CI 8.8-11.2%) in the unweighted analysis but only 6.2% (5.0-7.5%) when selection bias was accounted for using IP weights. Similarly, case prevalence of depression among those in the top decile of depression PRS was reduced from 33.5% (31.7-35.4%) to 28.9% (25.8-31.9%) after IP weighting. CONCLUSIONS Non-random selection of participants into volunteer biobanks may induce clinically relevant selection bias that could impact implementation of PRS in research and clinical settings. As efforts to integrate PRS in medical practice expand, recognition and mitigation of these biases should be considered and may need to be optimized in a context-specific manner.
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Affiliation(s)
- Younga Heather Lee
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Tanayott Thaweethai
- Harvard Medical School, Boston, Massachusetts, USA
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yi-Han Sheu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Yen-Chen Anne Feng
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Biostatistics and Data Science, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Elizabeth W Karlson
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, Immunity, and Inflammation, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
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22
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Luterbacher F, Blouin JL, Schwitzgebel VM. Atypical diabetes with spontaneous remission associated with systemic lupus erythematosus in an adolescent girl of African ancestry, a case report. BMC Endocr Disord 2023; 23:228. [PMID: 37864241 PMCID: PMC10588024 DOI: 10.1186/s12902-023-01478-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND New-onset diabetes in youth encompasses type 1 diabetes, type 2 diabetes, monogenic diabetes, and rarer subtypes like Type B insulin resistance syndrome and ketosis-prone atypical diabetes in African populations. Some cases defy classification, posing management challenges. Here, we present a case of a unique, reversible diabetes subtype. CASE PRESENTATION We describe an adolescent African girl recently diagnosed with systemic lupus erythematosus. At age 15, she presented with ketoacidosis, HbA1c of 108.7 mmol/mol (12.1%), and positive anti-insulin antibodies. Initially diagnosed with type 1 diabetes, insulin was prescribed. Due to the presence of obesity and signs of insulin resistance, we added metformin. Concurrently, she received treatment for lupus with hydroxychloroquine, mycophenolate mofetil, and prednisone. After discharge, she stopped insulin due to cultural beliefs. Five months later, her glycemia and HbA1c normalized (37 mmol/mol or 5.5%) without insulin, despite corticosteroid therapy and weight gain. Autoantibodies normalized, and lupus activity decreased. Genetic testing for monogenic diabetes was negative, and the type 1 genetic risk score was exceptionally low. CONCLUSIONS We present a complex, reversible diabetes subtype. Features suggest an autoimmune origin, possibly influenced by overlapping HLA risk haplotypes with lupus. Lupus treatment or immunomodulation may have impacted diabetes remission. Ancestry-tailored genetic risk scores are currently designed to improve diagnostic accuracy.
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Affiliation(s)
- Fanny Luterbacher
- Pediatric Endocrinology and Diabetology, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Rue Willy-Donzé 6, 1205, Geneva, Switzerland
| | - Jean-Louis Blouin
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
- Department of Diagnostics, University Hospitals of Geneva, 1211, Geneva, Switzerland
| | - Valerie M Schwitzgebel
- Pediatric Endocrinology and Diabetology, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Rue Willy-Donzé 6, 1205, Geneva, Switzerland.
- Diabetes Center of the Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.
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23
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You L, Ferrat LA, Oram RA, Parikh HM, Steck AK, Krischer J, Redondo MJ. Type 1 Diabetes Risk Phenotypes Using Cluster Analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.10.23296375. [PMID: 37873281 PMCID: PMC10593014 DOI: 10.1101/2023.10.10.23296375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Although statistical models for predicting type 1 diabetes risk have been developed, approaches that reveal clinically meaningful clusters in the at-risk population and allow for non-linear relationships between predictors are lacking. We aimed to identify and characterize clusters of islet autoantibody-positive individuals that share similar characteristics and type 1 diabetes risk. Methods We tested a novel outcome-guided clustering method in initially non-diabetic autoantibody-positive relatives of individuals with type 1 diabetes, using the TrialNet Pathway to Prevention (PTP) study data (n=1127). The outcome of the analysis was time to type 1 diabetes and variables in the model included demographics, genetics, metabolic factors and islet autoantibodies. An independent dataset (Diabetes Prevention Trial of Type 1 Diabetes, DPT-1 study) (n=704) was used for validation. Findings The analysis revealed 8 clusters with varying type 1 diabetes risks, categorized into three groups. Group A had three clusters with high glucose levels and high risk. Group B included four clusters with elevated autoantibody titers. Group C had three lower-risk clusters with lower autoantibody titers and glucose levels. Within the groups, the clusters exhibit variations in characteristics such as glucose levels, C-peptide levels, age, and genetic risk. A decision rule for assigning individuals to clusters was developed. The validation dataset confirms that the clusters can identify individuals with similar characteristics. Interpretation Demographic, metabolic, immunological, and genetic markers can be used to identify clusters of distinctive characteristics and different risks of progression to type 1 diabetes among autoantibody-positive individuals with a family history of type 1 diabetes. The results also revealed the heterogeneity in the population and complex interactions between variables.
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Affiliation(s)
- Lu You
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | | | | | - Hemang M Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Andrea K Steck
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jeffrey Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Maria J Redondo
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
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24
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Srinivasan S, Wu P, Mercader JM, Udler MS, Porneala BC, Bartz TM, Floyd JS, Sitlani C, Guo X, Haessler J, Kooperberg C, Liu J, Ahmad S, van Duijn C, Liu CT, Goodarzi MO, Florez JC, Meigs JB, Rotter JI, Rich SS, Dupuis J, Leong A. A Type 1 Diabetes Polygenic Score Is Not Associated With Prevalent Type 2 Diabetes in Large Population Studies. J Endocr Soc 2023; 7:bvad123. [PMID: 37841955 PMCID: PMC10576255 DOI: 10.1210/jendso/bvad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Indexed: 10/17/2023] Open
Abstract
Context Both type 1 diabetes (T1D) and type 2 diabetes (T2D) have significant genetic contributions to risk and understanding their overlap can offer clinical insight. Objective We examined whether a T1D polygenic score (PS) was associated with a diagnosis of T2D in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. Methods We constructed a T1D PS using 79 known single nucleotide polymorphisms associated with T1D risk. We analyzed 13 792 T2D cases and 14 169 controls from CHARGE cohorts to determine the association between the T1D PS and T2D prevalence. We validated findings in an independent sample of 2256 T2D cases and 27 052 controls from the Mass General Brigham Biobank (MGB Biobank). As secondary analyses in 5228 T2D cases from CHARGE, we used multivariable regression models to assess the association of the T1D PS with clinical outcomes associated with T1D. Results The T1D PS was not associated with T2D both in CHARGE (P = .15) and in the MGB Biobank (P = .87). The partitioned human leukocyte antigens only PS was associated with T2D in CHARGE (OR 1.02 per 1 SD increase in PS, 95% CI 1.01-1.03, P = .006) but not in the MGB Biobank. The T1D PS was weakly associated with insulin use (OR 1.007, 95% CI 1.001-1.012, P = .03) in CHARGE T2D cases but not with other outcomes. Conclusion In large biobank samples, a common variant PS for T1D was not consistently associated with prevalent T2D. However, possible heterogeneity in T2D cannot be ruled out and future studies are needed do subphenotyping.
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Affiliation(s)
- Shylaja Srinivasan
- Division of Pediatric Endocrinology, University of California at San Francisco, San Francisco, CA 94158, USA
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02215, USA
| | - Josep M Mercader
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Miriam S Udler
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bianca C Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Colleen Sitlani
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Xiquing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jun Liu
- Department of Epidemiology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford OX1 2JD, UK
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford OX1 2JD, UK
| | - Ching-Ti Liu
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jose C Florez
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - James B Meigs
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard & Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02215, USA
| | - Aaron Leong
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
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25
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Koch S, Schmidtke J, Krawczak M, Caliebe A. Clinical utility of polygenic risk scores: a critical 2023 appraisal. J Community Genet 2023; 14:471-487. [PMID: 37133683 PMCID: PMC10576695 DOI: 10.1007/s12687-023-00645-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/31/2023] [Indexed: 05/04/2023] Open
Abstract
Since their first appearance in the context of schizophrenia and bipolar disorder in 2009, polygenic risk scores (PRSs) have been described for a large number of common complex diseases. However, the clinical utility of PRSs in disease risk assessment or therapeutic decision making is likely limited because PRSs usually only account for the heritable component of a trait and ignore the etiological role of environment and lifestyle. We surveyed the current state of PRSs for various diseases, including breast cancer, diabetes, prostate cancer, coronary artery disease, and Parkinson disease, with an extra focus upon the potential improvement of clinical scores by their combination with PRSs. We observed that the diagnostic and prognostic performance of PRSs alone is consistently low, as expected. Moreover, combining a PRS with a clinical score at best led to moderate improvement of the power of either risk marker. Despite the large number of PRSs reported in the scientific literature, prospective studies of their clinical utility, particularly of the PRS-associated improvement of standard screening or therapeutic procedures, are still rare. In conclusion, the benefit to individual patients or the health care system in general of PRS-based extensions of existing diagnostic or treatment regimens is still difficult to judge.
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Affiliation(s)
- Sebastian Koch
- Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität zu Kiel, Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Jörg Schmidtke
- Amedes MVZ Wagnerstibbe, Hannover, Germany
- Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover, Germany
| | - Michael Krawczak
- Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität zu Kiel, Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Amke Caliebe
- Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität zu Kiel, Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany.
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26
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Sacks DB, Arnold M, Bakris GL, Bruns DE, Horvath AR, Lernmark Å, Metzger BE, Nathan DM, Kirkman MS. Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus. Diabetes Care 2023; 46:e151-e199. [PMID: 37471273 PMCID: PMC10516260 DOI: 10.2337/dci23-0036] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/11/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Numerous laboratory tests are used in the diagnosis and management of diabetes mellitus. The quality of the scientific evidence supporting the use of these assays varies substantially. APPROACH An expert committee compiled evidence-based recommendations for laboratory analysis in screening, diagnosis, or monitoring of diabetes. The overall quality of the evidence and the strength of the recommendations were evaluated. The draft consensus recommendations were evaluated by invited reviewers and presented for public comment. Suggestions were incorporated as deemed appropriate by the authors (see Acknowledgments). The guidelines were reviewed by the Evidence Based Laboratory Medicine Committee and the Board of Directors of the American Association for Clinical Chemistry and by the Professional Practice Committee of the American Diabetes Association. CONTENT Diabetes can be diagnosed by demonstrating increased concentrations of glucose in venous plasma or increased hemoglobin A1c (HbA1c) in the blood. Glycemic control is monitored by the people with diabetes measuring their own blood glucose with meters and/or with continuous interstitial glucose monitoring (CGM) devices and also by laboratory analysis of HbA1c. The potential roles of noninvasive glucose monitoring, genetic testing, and measurement of ketones, autoantibodies, urine albumin, insulin, proinsulin, and C-peptide are addressed. SUMMARY The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.
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Affiliation(s)
- David B. Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD
| | - Mark Arnold
- Department of Chemistry, University of Iowa, Iowa City, IA
| | - George L. Bakris
- Department of Medicine, American Heart Association Comprehensive Hypertension Center, Section of Endocrinology, Diabetes and Metabolism, University of Chicago Medicine, Chicago, IL
| | - David E. Bruns
- Department of Pathology, University of Virginia Medical School, Charlottesville, VA
| | - Andrea R. Horvath
- New South Wales Health Pathology Department of Chemical Pathology, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital Malmö, Malmö, Sweden
| | - Boyd E. Metzger
- Division of Endocrinology, Northwestern University, The Feinberg School of Medicine, Chicago, IL
| | - David M. Nathan
- Massachusetts General Hospital Diabetes Center and Harvard Medical School, Boston, MA
| | - M. Sue Kirkman
- Department of Medicine, University of North Carolina, Chapel Hill, NC
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27
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Siddiqui K, Nawaz SS. Exploration of Immune Targets for Type 1 Diabetes and Latent Autoimmune Disease Immunotherapy. Immunotargets Ther 2023; 12:91-103. [PMID: 37795196 PMCID: PMC10546931 DOI: 10.2147/itt.s417917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 09/09/2023] [Indexed: 10/06/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that destroys pancreatic beta cells, which produce insulin in the islets of Langerhans. The risk of developing T1D is influenced by environmental factors, genetics, and autoantibodies. Latent autoimmune diabetes in adults (LADA) is a type of T1D that is genetically and phenotypically distinct from classic T1D. This review summarizes the accumulated information on the risk factors for T1D and LADA, and immunotherapy trials that offer insights into potential future combined therapeutic interventions for both T1D and LADA to slow the rate of islet cell loss and preserve beta cell function. Future research should also focus on improving intervention doses, conducting more thorough examinations of intervention responders, and/or combining minimally effective single-target immunotherapies to slow the rate of islet cell loss and preserve beta cell function.
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Affiliation(s)
- Khalid Siddiqui
- Strategic Center for Diabetes Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Shaik Sarfaraz Nawaz
- Strategic Center for Diabetes Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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28
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Jones AG, Shields BM, Oram RA, Dabelea DM, Hagopian WA, Lustigova E, Shah AS, Knupp J, Mottl AK, DÀgostino RB, Williams A, Marcovina SM, Pihoker C, Divers J, Redondo MJ. Clinical prediction models combining routine clinical measures identify participants with youth-onset diabetes who maintain insulin secretion in the range associated with type 2 diabetes: The SEARCH for Diabetes in Youth Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.27.23296128. [PMID: 37808789 PMCID: PMC10557841 DOI: 10.1101/2023.09.27.23296128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Objective With the high prevalence of pediatric obesity and overlapping features between diabetes subtypes, accurately classifying youth-onset diabetes can be challenging. We aimed to develop prediction models that, using characteristics available at diabetes diagnosis, can identify youth who will retain endogenous insulin secretion at levels consistent with type 2 diabetes (T2D). Methods We studied 2,966 youth with diabetes in the prospective SEARCH study (diagnosis age ≤19 years) to develop prediction models to identify participants with fasting c-peptide ≥250 pmol/L (≥0.75ng/ml) after >3 years (median 74 months) of diabetes duration. Models included clinical measures at baseline visit, at a mean diabetes duration of 11 months (age, BMI, sex, waist circumference, HDL-C), with and without islet autoantibodies (GADA, IA-2A) and a Type 1 Diabetes Genetic Risk Score (T1DGRS). Results Models using routine clinical measures with or without autoantibodies and T1DGRS were highly accurate in identifying participants with c-peptide ≥0.75 ng/ml (17% of participants; 2.3% and 53% of those with and without positive autoantibodies) (area under receiver operator curve [AUCROC] 0.95-0.98). In internal validation, optimism was very low, with excellent calibration (slope=0.995-0.999). Models retained high performance for predicting retained c-peptide in older youth with obesity (AUCROC 0.88-0.96), and in subgroups defined by self-reported race/ethnicity (AUCROC 0.88-0.97), autoantibody status (AUCROC 0.87-0.96), and clinically diagnosed diabetes types (AUCROC 0.81-0.92). Conclusion Prediction models combining routine clinical measures at diabetes diagnosis, with or without islet autoantibodies or T1DGRS, can accurately identify youth with diabetes who maintain endogenous insulin secretion in the range associated with type 2 diabetes.
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Affiliation(s)
| | | | | | | | | | | | - Amy S Shah
- University of Cincinnati & Cincinnati Children's Hospital Medical Center
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29
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Shapiro MR, Dong X, Perry DJ, McNichols JM, Thirawatananond P, Posgai AL, Peters LD, Motwani K, Musca RS, Muir A, Concannon P, Jacobsen LM, Mathews CE, Wasserfall CH, Haller MJ, Schatz DA, Atkinson MA, Brusko MA, Bacher R, Brusko TM. Human immune phenotyping reveals accelerated aging in type 1 diabetes. JCI Insight 2023; 8:e170767. [PMID: 37498686 PMCID: PMC10544250 DOI: 10.1172/jci.insight.170767] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023] Open
Abstract
The proportions and phenotypes of immune cell subsets in peripheral blood undergo continual and dramatic remodeling throughout the human life span, which complicates efforts to identify disease-associated immune signatures in type 1 diabetes (T1D). We conducted cross-sectional flow cytometric immune profiling on peripheral blood from 826 individuals (stage 3 T1D, their first-degree relatives, those with ≥2 islet autoantibodies, and autoantibody-negative unaffected controls). We constructed an immune age predictive model in unaffected participants and observed accelerated immune aging in T1D. We used generalized additive models for location, shape, and scale to obtain age-corrected data for flow cytometry and complete blood count readouts, which can be visualized in our interactive portal (ImmScape); 46 parameters were significantly associated with age only, 25 with T1D only, and 23 with both age and T1D. Phenotypes associated with accelerated immunological aging in T1D included increased CXCR3+ and programmed cell death 1-positive (PD-1+) frequencies in naive and memory T cell subsets, despite reduced PD-1 expression levels on memory T cells. Phenotypes associated with T1D after age correction were predictive of T1D status. Our findings demonstrate advanced immune aging in T1D and highlight disease-associated phenotypes for biomarker monitoring and therapeutic interventions.
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Affiliation(s)
- Melanie R. Shapiro
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Xiaoru Dong
- Diabetes Institute and
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Daniel J. Perry
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - James M. McNichols
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Puchong Thirawatananond
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Amanda L. Posgai
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Leeana D. Peters
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Keshav Motwani
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Richard S. Musca
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Andrew Muir
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Patrick Concannon
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Genetics Institute and
| | - Laura M. Jacobsen
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Clive H. Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Michael J. Haller
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Desmond A. Schatz
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mark A. Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Maigan A. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
| | - Rhonda Bacher
- Diabetes Institute and
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Todd M. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and
- Diabetes Institute and
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, USA
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30
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Szczerbinski L, Mandla R, Schroeder P, Porneala BC, Li JH, Florez JC, Mercader JM, Manning AK, Udler MS. Algorithms for the identification of prevalent diabetes in the All of Us Research Program validated using polygenic scores - a new resource for diabetes precision medicine. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.05.23295061. [PMID: 37732265 PMCID: PMC10508798 DOI: 10.1101/2023.09.05.23295061] [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: 09/22/2023]
Abstract
OBJECTIVE The study aimed to develop and validate algorithms for identifying people with type 1 and type 2 diabetes in the All of Us Research Program (AoU) cohort, using electronic health record (EHR) and survey data. RESEARCH DESIGN AND METHODS Two sets of algorithms were developed, one using only EHR data (EHR), and the other using a combination of EHR and survey data (EHR+). Their performance was evaluated by testing their association with polygenic scores for both type 1 and type 2 diabetes. RESULTS For type 1 diabetes, the EHR-only algorithm showed a stronger association with T1D polygenic score (p=3×10-5) than the EHR+. For type 2 diabetes, the EHR+ algorithm outperformed both the EHR-only and the existing AoU definition, identifying additional cases (25.79% and 22.57% more, respectively) and showing stronger association with T2D polygenic score (DeLong p=0.03 and 1×10-4, respectively). CONCLUSIONS We provide new validated definitions of type 1 and type 2 diabetes in AoU, and make them available for researchers. These algorithms, by ensuring consistent diabetes definitions, pave the way for high-quality diabetes research and future clinical discoveries.
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Affiliation(s)
- Lukasz Szczerbinski
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Ravi Mandla
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, USA
- Cardiology Division, Department of Medicine and Cardiovascular Research Institute, University of California, San Francisco, USA
| | - Philip Schroeder
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Bianca C. Porneala
- Division of General Internal Medicine, Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Josephine H. Li
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jose C. Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Josep M. Mercader
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alisa K. Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General+ Hospital, Boston, USA
| | - Miriam S. Udler
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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31
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Luckett AM, Weedon MN, Hawkes G, Leslie RD, Oram RA, Grant SFA. Utility of genetic risk scores in type 1 diabetes. Diabetologia 2023; 66:1589-1600. [PMID: 37439792 PMCID: PMC10390619 DOI: 10.1007/s00125-023-05955-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023]
Abstract
Iterative advances in understanding of the genetics of type 1 diabetes have identified >70 genetic regions associated with risk of the disease, including strong associations across the HLA class II region that account for >50% of heritability. The increased availability of genetic data combined with the decreased costs of generating these data, have facilitated the development of polygenic scores that aggregate risk variants from associated loci into a single number: either a genetic risk score (GRS) or a polygenic risk score (PRS). PRSs incorporate the risk of many possibly correlated variants from across the genome, even if they do not reach genome-wide significance, whereas GRSs estimate the cumulative contribution of a smaller subset of genetic variants that reach genome-wide significance. Type 1 diabetes GRSs have utility in diabetes classification, aiding discrimination between type 1 diabetes, type 2 diabetes and MODY. Type 1 diabetes GRSs are also being used in newborn screening studies to identify infants at risk of future presentation of the disease. Most early studies of type 1 diabetes genetics have been conducted in European ancestry populations, but, to develop accurate GRSs across diverse ancestries, large case-control cohorts from non-European populations are still needed. The current barriers to GRS implementation within healthcare are mainly related to a lack of guidance and knowledge on integration with other biomarkers and clinical variables. Once these limitations are addressed, there is huge potential for 'test and treat' approaches to be used to tailor care for individuals with type 1 diabetes.
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Affiliation(s)
- Amber M Luckett
- University of Exeter College of Medicine and Health, Exeter, UK
| | | | - Gareth Hawkes
- University of Exeter College of Medicine and Health, Exeter, UK
| | - R David Leslie
- Blizard Institute, Queen Mary University of London, London, UK.
| | - Richard A Oram
- University of Exeter College of Medicine and Health, Exeter, UK.
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK.
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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32
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Connolly JJ, Berner ES, Smith M, Levy S, Terek S, Harr M, Karavite D, Suckiel S, Holm IA, Dufendach K, Nelson C, Khan A, Chisholm RL, Allworth A, Wei WQ, Bland HT, Clayton EW, Soper ER, Linder JE, Limdi NA, Miller A, Nigbur S, Bangash H, Hamed M, Sherafati A, Lewis ACF, Perez E, Orlando LA, Rakhra-Burris TK, Al-Dulaimi M, Cifric S, Scherr CL, Wynn J, Hakonarson H, Sabatello M. Education and electronic medical records and genomics network, challenges, and lessons learned from a large-scale clinical trial using polygenic risk scores. Genet Med 2023; 25:100906. [PMID: 37246632 PMCID: PMC10527667 DOI: 10.1016/j.gim.2023.100906] [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: 02/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/30/2023] Open
Abstract
Polygenic risk scores (PRS) have potential to improve health care by identifying individuals that have elevated risk for common complex conditions. Use of PRS in clinical practice, however, requires careful assessment of the needs and capabilities of patients, providers, and health care systems. The electronic Medical Records and Genomics (eMERGE) network is conducting a collaborative study which will return PRS to 25,000 pediatric and adult participants. All participants will receive a risk report, potentially classifying them as high risk (∼2-10% per condition) for 1 or more of 10 conditions based on PRS. The study population is enriched by participants from racial and ethnic minority populations, underserved populations, and populations who experience poorer medical outcomes. All 10 eMERGE clinical sites conducted focus groups, interviews, and/or surveys to understand educational needs among key stakeholders-participants, providers, and/or study staff. Together, these studies highlighted the need for tools that address the perceived benefit/value of PRS, types of education/support needed, accessibility, and PRS-related knowledge and understanding. Based on findings from these preliminary studies, the network harmonized training initiatives and formal/informal educational resources. This paper summarizes eMERGE's collective approach to assessing educational needs and developing educational approaches for primary stakeholders. It discusses challenges encountered and solutions provided.
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Affiliation(s)
- John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA.
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - Maureen Smith
- Center for Genetic Medicine, Department of Medicine, Northwestern University, Chicago, IL
| | - Samuel Levy
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA
| | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA
| | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, PA
| | - Sabrina Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Kevin Dufendach
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Catrina Nelson
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Aimee Allworth
- Department of Medical Genetics, University of Washington, Seattle, WA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Harris T Bland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Ellen Wright Clayton
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, TN; Vanderbilt University Law School, Nashville, TN
| | - Emily R Soper
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN; Department of Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Scott Nigbur
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Marwan Hamed
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Anna C F Lewis
- Edmond and Lily Safra Center for Ethics, Harvard, MA; Brigham and Women's Hospital, Boston, MA
| | - Emma Perez
- Mass General Brigham Personalized Medicine, Brigham and Women's Hospital, Boston, MA
| | | | | | | | - Selma Cifric
- Department of Biology, The College of Idaho, Caldwell, ID
| | - Courtney Lynam Scherr
- School of Communication | Department of Communication Studies, Northwestern University, Chicago, IL
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maya Sabatello
- Center for Precision Medicine & Genomics, Department of Medicine, Columbia University Irving Medical Center, New York, NY; Division of Ethics, Department of Medical Humanities & Ethics, Columbia University Irving Medical Center, New York, NY.
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Sacks DB, Arnold M, Bakris GL, Bruns DE, Horvath AR, Lernmark Å, Metzger BE, Nathan DM, Kirkman MS. Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus. Clin Chem 2023:hvad080. [PMID: 37473453 DOI: 10.1093/clinchem/hvad080] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/12/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Numerous laboratory tests are used in the diagnosis and management of diabetes mellitus. The quality of the scientific evidence supporting the use of these assays varies substantially. APPROACH An expert committee compiled evidence-based recommendations for laboratory analysis in screening, diagnosis, or monitoring of diabetes. The overall quality of the evidence and the strength of the recommendations were evaluated. The draft consensus recommendations were evaluated by invited reviewers and presented for public comment. Suggestions were incorporated as deemed appropriate by the authors (see Acknowledgments). The guidelines were reviewed by the Evidence Based Laboratory Medicine Committee and the Board of Directors of the American Association of Clinical Chemistry and by the Professional Practice Committee of the American Diabetes Association. CONTENT Diabetes can be diagnosed by demonstrating increased concentrations of glucose in venous plasma or increased hemoglobin A1c (Hb A1c) in the blood. Glycemic control is monitored by the people with diabetes measuring their own blood glucose with meters and/or with continuous interstitial glucose monitoring (CGM) devices and also by laboratory analysis of Hb A1c. The potential roles of noninvasive glucose monitoring, genetic testing, and measurement of ketones, autoantibodies, urine albumin, insulin, proinsulin, and C-peptide are addressed. SUMMARY The guidelines provide specific recommendations based on published data or derived from expert consensus. Several analytes are found to have minimal clinical value at the present time, and measurement of them is not recommended.
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Affiliation(s)
- David B Sacks
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Mark Arnold
- Department of Chemistry, University of Iowa, Iowa City, IA, United States
| | - George L Bakris
- Department of Medicine, American Heart Association Comprehensive Hypertension Center, Section of Endocrinology, Diabetes and Metabolism, University of Chicago Medicine, Chicago, ILUnited States
| | - David E Bruns
- Department of Pathology, University of Virginia Medical School, Charlottesville, VA, United States
| | - Andrea R Horvath
- New South Wales Health Pathology Department of Chemical Pathology, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital Malmö, Malmö, Sweden
| | - Boyd E Metzger
- Division of Endocrinology, Northwestern University, The Feinberg School of Medicine, Chicago, IL, United States
| | - David M Nathan
- Massachusetts General Hospital Diabetes Center and Harvard Medical School, Boston, MA, United States
| | - M Sue Kirkman
- Department of Medicine, University of North Carolina, Chapel Hill, NC, United States
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Lu T, Silveira PP, Greenwood CMT. Development of risk prediction models for depression combining genetic and early life risk factors. Front Neurosci 2023; 17:1143496. [PMID: 37534032 PMCID: PMC10390723 DOI: 10.3389/fnins.2023.1143496] [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: 01/13/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
Background Both genetic and early life risk factors play important roles in the pathogenesis and progression of adult depression. However, the interplay between these risk factors and their added value to risk prediction models have not been fully elucidated. Methods Leveraging a meta-analysis of major depressive disorder genome-wide association studies (N = 45,591 cases and 97,674 controls), we developed and optimized a polygenic risk score for depression using LDpred in a model selection dataset from the UK Biobank (N = 130,092 European ancestry individuals). In a UK Biobank test dataset (N = 278,730 European ancestry individuals), we tested whether the polygenic risk score and early life risk factors were associated with each other and compared their associations with depression phenotypes. Finally, we conducted joint predictive modeling to combine this polygenic risk score with early life risk factors by stepwise regression, and assessed the model performance in identifying individuals at high risk of depression. Results In the UK Biobank test dataset, the polygenic risk score for depression was moderately associated with multiple early life risk factors. For instance, a one standard deviation increase in the polygenic risk score was associated with 1.16-fold increased odds of frequent domestic violence (95% CI: 1.14-1.19) and 1.09-fold increased odds of not having access to medical care as a child (95% CI: 1.05-1.14). However, the polygenic risk score was more strongly associated with depression phenotypes than most early life risk factors. A joint predictive model integrating the polygenic risk score, early life risk factors, age and sex achieved an AUROC of 0.6766 for predicting strictly defined major depressive disorder, while a model without the polygenic risk score and a model without any early life risk factors had an AUROC of 0.6593 and 0.6318, respectively. Conclusion We have developed a polygenic risk score to partly capture the genetic liability to depression. Although genetic and early life risk factors can be correlated, joint predictive models improved risk stratification despite limited improvement in magnitude, and may be explored as tools to better identify individuals at high risk of depression.
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Affiliation(s)
- Tianyuan Lu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Patrícia Pelufo Silveira
- Department of Psychiatry, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Research Center, McGill University, Montreal, QC, Canada
| | - Celia M. T. Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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35
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Sigurdsson AI, Louloudis I, Banasik K, Westergaard D, Winther O, Lund O, Ostrowski S, Erikstrup C, Pedersen O, Nyegaard M, Brunak S, Vilhjálmsson B, Rasmussen S. Deep integrative models for large-scale human genomics. Nucleic Acids Res 2023; 51:e67. [PMID: 37224538 PMCID: PMC10325897 DOI: 10.1093/nar/gkad373] [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: 03/18/2022] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 05/26/2023] Open
Abstract
Polygenic risk scores (PRSs) are expected to play a critical role in precision medicine. Currently, PRS predictors are generally based on linear models using summary statistics, and more recently individual-level data. However, these predictors mainly capture additive relationships and are limited in data modalities they can use. We developed a deep learning framework (EIR) for PRS prediction which includes a model, genome-local-net (GLN), specifically designed for large-scale genomics data. The framework supports multi-task learning, automatic integration of other clinical and biochemical data, and model explainability. When applied to individual-level data from the UK Biobank, the GLN model demonstrated a competitive performance compared to established neural network architectures, particularly for certain traits, showcasing its potential in modeling complex genetic relationships. Furthermore, the GLN model outperformed linear PRS methods for Type 1 Diabetes, likely due to modeling non-additive genetic effects and epistasis. This was supported by our identification of widespread non-additive genetic effects and epistasis in the context of T1D. Finally, we constructed PRS models that integrated genotype, blood, urine, and anthropometric data and found that this improved performance for 93% of the 290 diseases and disorders considered. EIR is available at https://github.com/arnor-sigurdsson/EIR.
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Affiliation(s)
- Arnór I Sigurdsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Louloudis
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ole Winther
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
| | - Ole Lund
- Danish National Genome Center, Ørestads Boulevard 5, 2300 Copenhagen S, Denmark
- DTU Health Tech, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, 8000 Aarhus C, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Immunology, Zealand University Hospital, 4600 Køge, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, DK- 9260 Gistrup, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research (NCRR), Aarhus University, 8000 Aarhus C, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), 8210 Aarhus V, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, 8000 Aarhus C, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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36
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Lehmann B, Mackintosh M, McVean G, Holmes C. Optimal strategies for learning multi-ancestry polygenic scores vary across traits. Nat Commun 2023; 14:4023. [PMID: 37419925 PMCID: PMC10328935 DOI: 10.1038/s41467-023-38930-7] [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: 04/07/2022] [Accepted: 05/22/2023] [Indexed: 07/09/2023] Open
Abstract
Polygenic scores (PGSs) are individual-level measures that aggregate the genome-wide genetic predisposition to a given trait. As PGS have predominantly been developed using European-ancestry samples, trait prediction using such European ancestry-derived PGS is less accurate in non-European ancestry individuals. Although there has been recent progress in combining multiple PGS trained on distinct populations, the problem of how to maximize performance given a multiple-ancestry cohort is largely unexplored. Here, we investigate the effect of sample size and ancestry composition on PGS performance for fifteen traits in UK Biobank. For some traits, PGS estimated using a relatively small African-ancestry training set outperformed, on an African-ancestry test set, PGS estimated using a much larger European-ancestry only training set. We observe similar, but not identical, results when considering other minority-ancestry groups within UK Biobank. Our results emphasise the importance of targeted data collection from underrepresented groups in order to address existing disparities in PGS performance.
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Affiliation(s)
- Brieuc Lehmann
- Department of Statistical Science, University College London, London, UK.
| | | | - Gil McVean
- Big Data Institute, University of Oxford, Oxford, UK
| | - Chris Holmes
- The Alan Turing Institute, London, UK
- Big Data Institute, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
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37
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Pande AK, Dutta D, Singla R. Prevention of Type 1 Diabetes: Current Perspective. Indian J Endocrinol Metab 2023; 27:277-285. [PMID: 37867976 PMCID: PMC10586562 DOI: 10.4103/ijem.ijem_78_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/17/2023] [Accepted: 05/16/2023] [Indexed: 10/24/2023] Open
Abstract
People living with type 1 Diabetes (T1D) and their families have poor perception of health related quality of life. Therapies for T1D are becoming better with time, but they still involve a lot of effort. Prevention of T1D, if successful, has potential to change lives of millions of families across the globe. Type 1 diabetes is an autoimmune disease with underlying genetic predisposition for autoimmunity against beta cell antigens upon exposure to an environmental trigger. Identifying underlying primary antigen responsible for initiating autoimmune cascade, avoiding environmental trigger and modifying immunity has all been used as strategies for preventing or delaying onset of type 1 diabetes. Primary prevention for type 1 diabetes is hindered by difficulty in identifying at-risk population and also due to lack of effective preventive strategy. Secondary prevention, in children with presence of autoimmunity, has recently received a boost with approval of Teplizumab, an immunity modifying drug by its Anti-CD3 action. Application of preventive strategies would also change based on country specific incidence, prevalence and availability of health resources. In current review, an update on preventive strategies for type 1 diabetes is being discussed as well as their applicability in Indian context.
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Affiliation(s)
- Arun K Pande
- Consultant Endocrinologist, Lucknow Endocrine Diabetes and Thyroid Clinic, Lucknow, Uttar Pradesh, India
| | - Deep Dutta
- Consultant Endocrinologist, CEDAR Superspeciality Healthcare, Dwarka, New Delhi, India
| | - Rajiv Singla
- Consultant Endocrinologist, Kalpavriksh Healthcare, Dwarka, Delhi, India
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38
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Quattrin T, Mastrandrea LD, Walker LSK. Type 1 diabetes. Lancet 2023; 401:2149-2162. [PMID: 37030316 DOI: 10.1016/s0140-6736(23)00223-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/03/2022] [Accepted: 01/26/2023] [Indexed: 04/10/2023]
Abstract
Type 1 diabetes is a chronic disease caused by autoimmune destruction of pancreatic β cells. Individuals with type 1 diabetes are reliant on insulin for survival. Despite enhanced knowledge related to the pathophysiology of the disease, including interactions between genetic, immune, and environmental contributions, and major strides in treatment and management, disease burden remains high. Studies aimed at blocking the immune attack on β cells in people at risk or individuals with very early onset type 1 diabetes show promise in preserving endogenous insulin production. This Seminar will review the field of type 1 diabetes, highlighting recent progress within the past 5 years, challenges to clinical care, and future directions in research, including strategies to prevent, manage, and cure the disease.
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Affiliation(s)
- Teresa Quattrin
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA; Diabetes Center, John R Oishei Children's Hospital, Buffalo, NY, USA.
| | - Lucy D Mastrandrea
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA; Diabetes Center, John R Oishei Children's Hospital, Buffalo, NY, USA
| | - Lucy S K Walker
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
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39
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Xia Y, Chen Y, Li X, Luo S, Lin J, Huang G, Xiao Y, Chen Z, Xie Z, Zhou Z. HLA Class I Association With Autoimmune Diabetes in Chinese People: Distinct Implications in Classic Type 1 Diabetes and LADA. J Clin Endocrinol Metab 2023; 108:e404-e414. [PMID: 36652403 DOI: 10.1210/clinem/dgad006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
CONTEXT We aimed to investigate whether human leukocyte antigen (HLA) Class I loci differentially modulated the risk for and clinical features of Chinese people with classic type 1 diabetes (T1D) and latent autoimmune diabetes in adults (LADA). METHODS In this case-control study, genotypes of HLA-A, -B, -C, -DRB1, -DQA1, and -DQB1 loci were obtained from 1067 cases with classic T1D, 1062 cases with LADA, and 1107 normal controls using next-generation sequencing. RESULTS Despite 4 alleles shared between classic T1D and LADA (protective: A*02:07 and B*46:01; susceptible: B*54:01 and C*08:01), 7 Class I alleles conferred risk exclusively for classic T1D (A*24:02, B*15:02, B*15:18, B*39:01, B*40:06, B*48:01, and C*07:02) whereas only A*02:01 was an additional risk factor for LADA. Class I alleles affected a wide spectrum of T1D clinical features, including positive rate of protein tyrosine phosphatase autoantibody and zinc transporter 8 autoantibody (A*24:02), C-peptide levels (A*24:02), and age at diagnosis (B*46:01, C*01:02, B*15:02, C*07:02, and C*08:01). By contrast, except for the detrimental effect of C*08:01 on C-peptide concentrations in LADA, no other Class I associations with clinical characteristics of LADA could be reported. The addition of Class I alleles refined the risk model consisting only of DR-DQ data in classic T1D while the overall predictive value of the LADA risk model comprising both Class I and II information was relatively low. CONCLUSION The attenuated HLA Class I susceptibility to LADA was indicative of a less deleterious immunogenetic nature compared with classic T1D. These autoimmune diabetes-related Class I variants might serve as additional markers in future screening among Chinese people.
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Affiliation(s)
- Ying Xia
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Yan Chen
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Yang Xiao
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Zhiying Chen
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
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Goyal S, Rani J, Bhat MA, Vanita V. Genetics of diabetes. World J Diabetes 2023; 14:656-679. [PMID: 37383588 PMCID: PMC10294065 DOI: 10.4239/wjd.v14.i6.656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/13/2023] [Accepted: 04/17/2023] [Indexed: 06/14/2023] Open
Abstract
Diabetes mellitus is a complicated disease characterized by a complex interplay of genetic, epigenetic, and environmental variables. It is one of the world's fastest-growing diseases, with 783 million adults expected to be affected by 2045. Devastating macrovascular consequences (cerebrovascular disease, cardiovascular disease, and peripheral vascular disease) and microvascular complications (like retinopathy, nephropathy, and neuropathy) increase mortality, blindness, kidney failure, and overall quality of life in individuals with diabetes. Clinical risk factors and glycemic management alone cannot predict the development of vascular problems; multiple genetic investigations have revealed a clear hereditary component to both diabetes and its related complications. In the twenty-first century, technological advancements (genome-wide association studies, next-generation sequencing, and exome-sequencing) have led to the identification of genetic variants associated with diabetes, however, these variants can only explain a small proportion of the total heritability of the condition. In this review, we address some of the likely explanations for this "missing heritability", for diabetes such as the significance of uncommon variants, gene-environment interactions, and epigenetics. Current discoveries clinical value, management of diabetes, and future research directions are also discussed.
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Affiliation(s)
- Shiwali Goyal
- Department of Ophthalmic Genetics and Visual Function Branch, National Eye Institute, Rockville, MD 20852, United States
| | - Jyoti Rani
- Department of Human Genetics, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Mohd Akbar Bhat
- Department of Ophthalmology, Georgetown University Medical Center, Washington DC, DC 20057, United States
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar 143005, Punjab, India
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Perry DJ, Shapiro MR, Chamberlain SW, Kusmartseva I, Chamala S, Balzano-Nogueira L, Yang M, Brant JO, Brusko M, Williams MD, McGrail KM, McNichols J, Peters LD, Posgai AL, Kaddis JS, Mathews CE, Wasserfall CH, Webb-Robertson BJM, Campbell-Thompson M, Schatz D, Evans-Molina C, Pugliese A, Concannon P, Anderson MS, German MS, Chamberlain CE, Atkinson MA, Brusko TM. A genomic data archive from the Network for Pancreatic Organ donors with Diabetes. Sci Data 2023; 10:323. [PMID: 37237059 PMCID: PMC10219990 DOI: 10.1038/s41597-023-02244-6] [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: 12/24/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The Network for Pancreatic Organ donors with Diabetes (nPOD) is the largest biorepository of human pancreata and associated immune organs from donors with type 1 diabetes (T1D), maturity-onset diabetes of the young (MODY), cystic fibrosis-related diabetes (CFRD), type 2 diabetes (T2D), gestational diabetes, islet autoantibody positivity (AAb+), and without diabetes. nPOD recovers, processes, analyzes, and distributes high-quality biospecimens, collected using optimized standard operating procedures, and associated de-identified data/metadata to researchers around the world. Herein describes the release of high-parameter genotyping data from this collection. 372 donors were genotyped using a custom precision medicine single nucleotide polymorphism (SNP) microarray. Data were technically validated using published algorithms to evaluate donor relatedness, ancestry, imputed HLA, and T1D genetic risk score. Additionally, 207 donors were assessed for rare known and novel coding region variants via whole exome sequencing (WES). These data are publicly-available to enable genotype-specific sample requests and the study of novel genotype:phenotype associations, aiding in the mission of nPOD to enhance understanding of diabetes pathogenesis to promote the development of novel therapies.
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Affiliation(s)
- Daniel J Perry
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Melanie R Shapiro
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Sonya W Chamberlain
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Irina Kusmartseva
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Srikar Chamala
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Leandro Balzano-Nogueira
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Mingder Yang
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jason O Brant
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL, 32610, USA
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - MacKenzie D Williams
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Kieran M McGrail
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - James McNichols
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Leeana D Peters
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Amanda L Posgai
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - John S Kaddis
- Department of Diabetes and Cancer Discovery Science, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Clayton E Mathews
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Clive H Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Bobbie-Jo M Webb-Robertson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Department of Biomedical Engineering, College of Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Desmond Schatz
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Carmella Evans-Molina
- Center for Diabetes and Metabolic Diseases and the Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, 33021, USA
| | - Patrick Concannon
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32601, USA
| | - Mark S Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Michael S German
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Chester E Chamberlain
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA.
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA.
- Department of Pediatrics, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
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Mameli C, Triolo TM, Chiarelli F, Rewers M, Zuccotti G, Simmons KM. Lessons and Gaps in the Prediction and Prevention of Type 1 Diabetes. Pharmacol Res 2023; 193:106792. [PMID: 37201589 DOI: 10.1016/j.phrs.2023.106792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Type 1 diabetes (T1D) is a serious chronic autoimmune condition. Even though the root cause of T1D development has yet to be determined, enough is known about the natural history of T1D pathogenesis to allow study of interventions that may delay or even prevent the onset of hyperglycemia and clinical T1D. Primary prevention aims to prevent the onset of beta cell autoimmunity in asymptomatic people at high genetic risk for T1D. Secondary prevention strategies aim to preserve functional beta cells once autoimmunity is present, and tertiary prevention aims to initiate and extend partial remission of beta cell destruction after the clinical onset of T1D. The approval of teplizumab in the United States to delay the onset of clinical T1D marks an impressive milestone in diabetes care. This treatment opens the door to a paradigm shift in T1D care. People with T1D risk need to be identified early by measuring T1D related islet autoantibodies. Identifying people with T1D before they have symptoms will facilitate better understanding of pre-symptomatic T1D progression and T1D prevention strategies that may be effective.
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Affiliation(s)
- Chiara Mameli
- Department of Pediatrics, V. Buzzi Children's Hospital, Milan, Italy; Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
| | - Taylor M Triolo
- Barbara Davis Center for Diabetes, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045
| | | | - Marian Rewers
- Barbara Davis Center for Diabetes, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Gianvincenzo Zuccotti
- Department of Pediatrics, V. Buzzi Children's Hospital, Milan, Italy; Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Kimber M Simmons
- Barbara Davis Center for Diabetes, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045
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Gomes MB, Rodrigues V, Santos DC, Bôas PRV, Silva DA, de Sousa Azulay RS, Dib SA, Pavin EJ, Fernandes VO, Montenegro Junior RM, Felicio JS, Réa R, Negrato CA, Porto LC. Association between HLA Class II Alleles/Haplotypes and Genomic Ancestry in Brazilian Patients with Type 1 Diabetes: A Nationwide Exploratory Study. Genes (Basel) 2023; 14:genes14050991. [PMID: 37239351 DOI: 10.3390/genes14050991] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
We aimed to identify HLA-DRB1, -DQA1, and -DQB1 alleles/haplotypes associated with European, African, or Native American genomic ancestry (GA) in admixed Brazilian patients with type 1 diabetes (T1D). This exploratory nationwide study enrolled 1599 participants. GA percentage was inferred using a panel of 46 ancestry informative marker-insertion/deletion. Receiver operating characteristic curve analysis (ROC) was applied to identify HLA class II alleles related to European, African, or Native American GA, and showed significant (p < 0.05) accuracy for identifying HLA risk alleles related to European GA: for DRB1*03:01, the area under the curve was (AUC) 0.533; for DRB1*04:01 AUC = 0.558, for DRB1*04:02 AUC = 0.545. A better accuracy for identifying African GA was observed for the risk allele DRB1*09:01AUC = 0.679 and for the protective alleles DRB1*03:02 AUC = 0.649, DRB1*11:02 AUC = 0.636, and DRB1*15:03 AUC = 0.690. Higher percentage of European GA was observed in patients with risk haplotypes (p < 0.05). African GA percentage was higher in patients with protective haplotypes (p < 0.05). Risk alleles and haplotypes were related to European GA and protective alleles/haplotypes to African GA. Future studies with other ancestry markers are warranted to fill the gap in knowledge regarding the genetic origin of T1D in highly admixed populations such as that found in Brazil.
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Affiliation(s)
- Marília Brito Gomes
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Vandilson Rodrigues
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís 65080-805, Brazil
| | - Deborah Conte Santos
- Department of Internal Medicine, Diabetes Unit, Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Paulo Ricardo Villas Bôas
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
| | - Dayse A Silva
- DNA Diagnostic Laboratory (LDD), Rio de Janeiro State University (UERJ), Rio de Janeiro 20550-900, Brazil
| | - Rossana Santiago de Sousa Azulay
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís 65080-805, Brazil
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), São Luís 65020-070, Brazil
| | - Sergio Atala Dib
- Endocrinology Division, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Elizabeth João Pavin
- Endocrinology Division, School of Medical Sciences, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil
| | - Virgínia Oliveira Fernandes
- Department of Clinical Medicine, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Department of Community Health, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Clinical Research Unit, Walter Cantídio University Hospital, Federal University of Ceará (UFC/EBSERH), Fortaleza 60430-372, Brazil
| | - Renan Magalhães Montenegro Junior
- Department of Clinical Medicine, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Department of Community Health, Federal University of Ceará (UFC), Fortaleza 60430-275, Brazil
- Clinical Research Unit, Walter Cantídio University Hospital, Federal University of Ceará (UFC/EBSERH), Fortaleza 60430-372, Brazil
| | - João Soares Felicio
- Endocrinology Division, João de Barros Barreto University Hospital, Federal University of Pará (UFPA), Belém 66073-000, Brazil
| | - Rosangela Réa
- Endocrinology Unit, Federal University of Paraná (UFPR), Curitiba 80060-900, Brazil
| | - Carlos Antonio Negrato
- Medical Doctor Program, School of Dentistry, University of São Paulo (USP), Bauru 17012-901, Brazil
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro 20950-003, Brazil
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Ghalwash M, Anand V, Lou O, Martin F, Rewers M, Ziegler AG, Toppari J, Hagopian WA, Veijola R. Islet autoantibody screening in at-risk adolescents to predict type 1 diabetes until young adulthood: a prospective cohort study. THE LANCET. CHILD & ADOLESCENT HEALTH 2023; 7:261-268. [PMID: 36681087 PMCID: PMC10038928 DOI: 10.1016/s2352-4642(22)00350-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND Screening for islet autoantibodies in children and adolescents identifies individuals who will later develop type 1 diabetes, allowing patient and family education to prevent diabetic ketoacidosis at onset and to enable consideration of preventive therapies. We aimed to assess whether islet autoantibody screening is effective for predicting type 1 diabetes in adolescents aged 10-18 years with an increased risk of developing type 1 diabetes. METHODS Data were harmonised from prospective studies from Finland (the Diabetes Prediction and Prevention study), Germany (the BABYDIAB study), and the USA (Diabetes Autoimmunity Study in the Young and the Diabetes Evaluation in Washington study). Autoantibodies against insulin, glutamic acid decarboxylase, and insulinoma-associated protein 2 were measured at each follow-up visit. Children who were lost to follow-up or diagnosed with type 1 diabetes before 10 years of age were excluded. Inverse probability censoring weighting was used to include data from remaining participants. Sensitivity and the positive predictive value of these autoantibodies, tested at one or two ages, to predict type 1 diabetes by the age of 18 years were the main outcomes. FINDINGS Of 20 303 children with an increased type 1 diabetes risk, 8682 were included for the analysis with inverse probability censoring weighting. 1890 were followed up to 18 years of age or developed type 1 diabetes between the ages of 10 years and 18 years, and their median follow-up was 18·3 years (IQR 14·5-20·3). 442 (23·4%) of 1890 adolescents were positive for at least one islet autoantibody, and 262 (13·9%) developed type 1 diabetes. Time from seroconversion to diabetes diagnosis increased by 0·64 years (95% CI 0·34-0·95) for each 1-year increment of diagnosis age (Pearson's correlation coefficient 0·88, 95% CI 0·50-0·97, p=0·0020). The median interval between the last prediagnostic sample and diagnosis was 0·3 years (IQR 0·1-1·3) in the 227 participants who were autoantibody positive and 6·8 years (1·6-9·9) for the 35 who were autoantibody negative. Single screening at the age of 10 years was 90% (95% CI 86-95) sensitive, with a positive predictive value of 66% (60-72) for clinical diabetes. Screening at two ages (10 years and 14 years) increased sensitivity to 93% (95% CI 89-97) but lowered the positive predictive value to 55% (49-60). INTERPRETATION Screening of adolescents at risk for type 1 diabetes only once at 10 years of age for islet autoantibodies was highly effective to detect type 1 diabetes by the age of 18 years, which in turn could enable prevention of diabetic ketoacidosis and participation in secondary prevention trials. FUNDING JDRF International.
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Affiliation(s)
- Mohamed Ghalwash
- Center for Computational Health, IBM Research, Yorktown Heights, NY, USA; Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Vibha Anand
- Center for Computational Health, IBM Research, Cambridge, MA, USA
| | | | | | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado, Denver, CO, USA
| | - Anette-G Ziegler
- Forschergruppe Diabetes and Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany der TU München, Munich, Germany
| | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Centre for Population Health Research, University of Turku, Turku, Finland; Department of Pediatrics, Turku University Hospital, Turku, Finland
| | | | - Riitta Veijola
- Department of Pediatrics, Research Unit of Clinical Medicine, Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland.
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Kim DH, Jensen A, Jones K, Raghavan S, Phillips LS, Hung A, Sun YV, Li G, Reaven P, Zhou H, Zhou JJ. A platform for phenotyping disease progression and associated longitudinal risk factors in large-scale EHRs, with application to incident diabetes complications in the UK Biobank. JAMIA Open 2023; 6:ooad006. [PMID: 36789288 PMCID: PMC9912368 DOI: 10.1093/jamiaopen/ooad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Objective Modern healthcare data reflect massive multi-level and multi-scale information collected over many years. The majority of the existing phenotyping algorithms use case-control definitions of disease. This paper aims to study the time to disease onset and progression and identify the time-varying risk factors that drive them. Materials and Methods We developed an algorithmic approach to phenotyping the incidence of diseases by consolidating data sources from the UK Biobank (UKB), including primary care electronic health records (EHRs). We focused on defining events, event dates, and their censoring time, including relevant terms and existing phenotypes, excluding generic, rare, or semantically distant terms, forward-mapping terminology terms, and expert review. We applied our approach to phenotyping diabetes complications, including a composite cardiovascular disease (CVD) outcome, diabetic kidney disease (DKD), and diabetic retinopathy (DR), in the UKB study. Results We identified 49 049 participants with diabetes. Among them, 1023 had type 1 diabetes (T1D), and 40 193 had type 2 diabetes (T2D). A total of 23 833 diabetes subjects had linked primary care records. There were 3237, 3113, and 4922 patients with CVD, DKD, and DR events, respectively. The risk prediction performance for each outcome was assessed, and our results are consistent with the prediction area under the ROC (receiver operating characteristic) curve (AUC) of standard risk prediction models using cohort studies. Discussion and Conclusion Our publicly available pipeline and platform enable streamlined curation of incidence events, identification of time-varying risk factors underlying disease progression, and the definition of a relevant cohort for time-to-event analyses. These important steps need to be considered simultaneously to study disease progression.
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Affiliation(s)
- Do Hyun Kim
- Department of Biostatistics, University of California, Los Angeles, California, USA
| | - Aubrey Jensen
- Department of Biostatistics, University of California, Los Angeles, California, USA
| | - Kelly Jones
- Department of Computer Science, Columbia University, New York, New York, USA
| | - Sridharan Raghavan
- Division of Hospital Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
- Rocky Mountain Regional VA Medical Center, Aurora, Colorado, USA
| | - Lawrence S Phillips
- Division of Endocrinology, Emory University School of Medicine, Atlanta, Georgia, USA
- Atlanta VA Medical Center, Decatur, Georgia, USA
| | - Adriana Hung
- VA Tennessee Valley Healthcare System, Nashville, Tennessee, USA
- Vanderbilt University, Nashville, Tennessee, USA
| | - Yan V Sun
- Department of Epidemiology, Emory University, Atlanta, Georgia, USA
| | - Gang Li
- Department of Biostatistics, University of California, Los Angeles, California, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Peter Reaven
- Phoenix VA Health Care System, Phoenix, Arizona, USA
| | - Hua Zhou
- Department of Biostatistics, University of California, Los Angeles, California, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jin J Zhou
- Department of Biostatistics, University of California, Los Angeles, California, USA
- Phoenix VA Health Care System, Phoenix, Arizona, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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Deutsch AJ, Stalbow L, Majarian TD, Mercader JM, Manning AK, Florez JC, Loos RJ, Udler MS. Polygenic Scores Help Reduce Racial Disparities in Predictive Accuracy of Automated Type 1 Diabetes Classification Algorithms. Diabetes Care 2023; 46:794-800. [PMID: 36745605 PMCID: PMC10090893 DOI: 10.2337/dc22-1833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/10/2023] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Automated algorithms to identify individuals with type 1 diabetes using electronic health records are increasingly used in biomedical research. It is not known whether the accuracy of these algorithms differs by self-reported race. We investigated whether polygenic scores improve identification of individuals with type 1 diabetes. RESEARCH DESIGN AND METHODS We investigated two large hospital-based biobanks (Mass General Brigham [MGB] and BioMe) and identified individuals with type 1 diabetes using an established automated algorithm. We performed medical record reviews to validate the diagnosis of type 1 diabetes. We implemented two published polygenic scores for type 1 diabetes (developed in individuals of European or African ancestry). We assessed the classification algorithm before and after incorporating polygenic scores. RESULTS The automated algorithm was more likely to incorrectly assign a diagnosis of type 1 diabetes in self-reported non-White individuals than in self-reported White individuals (odds ratio 3.45; 95% CI 1.54-7.69; P = 0.0026). After incorporating polygenic scores into the MGB Biobank, the positive predictive value of the type 1 diabetes algorithm increased from 70 to 97% for self-reported White individuals (meaning that 97% of those predicted to have type 1 diabetes indeed had type 1 diabetes) and from 53 to 100% for self-reported non-White individuals. Similar results were found in BioMe. CONCLUSIONS Automated phenotyping algorithms may exacerbate health disparities because of an increased risk of misclassification of individuals from underrepresented populations. Polygenic scores may be used to improve the performance of phenotyping algorithms and potentially reduce this disparity.
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Affiliation(s)
- Aaron J. Deutsch
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Lauren Stalbow
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Timothy D. Majarian
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Josep M. Mercader
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Alisa K. Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
| | - Jose C. Florez
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Ruth J.F. Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Miriam S. Udler
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
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47
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Michalek DA, Onengut-Gumuscu S, Repaske DR, Rich SS. Precision Medicine in Type 1 Diabetes. J Indian Inst Sci 2023; 103:335-351. [PMID: 37538198 PMCID: PMC10393845 DOI: 10.1007/s41745-023-00356-x] [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: 11/18/2022] [Accepted: 01/04/2023] [Indexed: 03/09/2023]
Abstract
Type 1 diabetes is a complex, chronic disease in which the insulin-producing beta cells in the pancreas are sufficiently altered or impaired to result in requirement of exogenous insulin for survival. The development of type 1 diabetes is thought to be an autoimmune process, in which an environmental (unknown) trigger initiates a T cell-mediated immune response in genetically susceptible individuals. The presence of islet autoantibodies in the blood are signs of type 1 diabetes development, and risk of progressing to clinical type 1 diabetes is correlated with the presence of multiple islet autoantibodies. Currently, a "staging" model of type 1 diabetes proposes discrete components consisting of normal blood glucose but at least two islet autoantibodies (Stage 1), abnormal blood glucose with at least two islet autoantibodies (Stage 2), and clinical diagnosis (Stage 3). While these stages may, in fact, not be discrete and vary by individual, the format suggests important applications of precision medicine to diagnosis, prevention, prognosis, treatment and monitoring. In this paper, applications of precision medicine in type 1 diabetes are discussed, with both opportunities and barriers to global implementation highlighted. Several groups have implemented components of precision medicine, yet the integration of the necessary steps to achieve both short- and long-term solutions will need to involve researchers, patients, families, and healthcare providers to fully impact and reduce the burden of type 1 diabetes.
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Affiliation(s)
- Dominika A. Michalek
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA USA
| | - David R. Repaske
- Division of Endocrinology, Department of Pediatrics, University of Virginia, Charlottesville, VA USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA USA
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48
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Shams H, Shao X, Santaniello A, Kirkish G, Harroud A, Ma Q, Isobe N, Schaefer CA, McCauley JL, Cree BAC, Didonna A, Baranzini SE, Patsopoulos NA, Hauser SL, Barcellos LF, Henry RG, Oksenberg JR. Polygenic risk score association with multiple sclerosis susceptibility and phenotype in Europeans. Brain 2023; 146:645-656. [PMID: 35253861 PMCID: PMC10169285 DOI: 10.1093/brain/awac092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/29/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Polygenic inheritance plays a pivotal role in driving multiple sclerosis susceptibility, an inflammatory demyelinating disease of the CNS. We developed polygenic risk scores (PRS) of multiple sclerosis and assessed associations with both disease status and severity in cohorts of European descent. The largest genome-wide association dataset for multiple sclerosis to date (n = 41 505) was leveraged to generate PRS scores, serving as an informative susceptibility marker, tested in two independent datasets, UK Biobank [area under the curve (AUC) = 0.73, 95% confidence interval (CI): 0.72-0.74, P = 6.41 × 10-146] and Kaiser Permanente in Northern California (KPNC, AUC = 0.8, 95% CI: 0.76-0.82, P = 1.5 × 10-53). Individuals within the top 10% of PRS were at higher than 5-fold increased risk in UK Biobank (95% CI: 4.7-6, P = 2.8 × 10-45) and 15-fold higher risk in KPNC (95% CI: 10.4-24, P = 3.7 × 10-11), relative to the median decile. The cumulative absolute risk of developing multiple sclerosis from age 20 onwards was significantly higher in genetically predisposed individuals according to PRS. Furthermore, inclusion of PRS in clinical risk models increased the risk discrimination by 13% to 26% over models based only on conventional risk factors in UK Biobank and KPNC, respectively. Stratifying disease risk by gene sets representative of curated cellular signalling cascades, nominated promising genetic candidate programmes for functional characterization. These pathways include inflammatory signalling mediation, response to viral infection, oxidative damage, RNA polymerase transcription, and epigenetic regulation of gene expression to be among significant contributors to multiple sclerosis susceptibility. This study also indicates that PRS is a useful measure for estimating susceptibility within related individuals in multicase families. We show a significant association of genetic predisposition with thalamic atrophy within 10 years of disease progression in the UCSF-EPIC cohort (P < 0.001), consistent with a partial overlap between the genetics of susceptibility and end-organ tissue injury. Mendelian randomization analysis suggested an effect of multiple sclerosis susceptibility on thalamic volume, which was further indicated to be through horizontal pleiotropy rather than a causal effect. In summary, this study indicates important, replicable associations of PRS with enhanced risk assessment and radiographic outcomes of tissue injury, potentially informing targeted screening and prevention strategies.
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Affiliation(s)
- Hengameh Shams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA.,Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xiaorong Shao
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Gina Kirkish
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adil Harroud
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Qin Ma
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Noriko Isobe
- Department of Neurology, Graduate School of medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | | | | | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Bruce A C Cree
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alessandro Didonna
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA.,Department of Anatomy and Cell Biology, East Carolina University, Greenville, NC 27834, USA
| | - Sergio E Baranzini
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nikolaos A Patsopoulos
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, 02115 MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lisa F Barcellos
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Roland G Henry
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jorge R Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
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49
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Thomas NJ, Walkey HC, Kaur A, Misra S, Oliver NS, Colclough K, Weedon MN, Johnston DG, Hattersley AT, Patel KA. The relationship between islet autoantibody status and the genetic risk of type 1 diabetes in adult-onset type 1 diabetes. Diabetologia 2023; 66:310-320. [PMID: 36355183 PMCID: PMC9807542 DOI: 10.1007/s00125-022-05823-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022]
Abstract
AIMS/HYPOTHESIS The reason for the observed lower rate of islet autoantibody positivity in clinician-diagnosed adult-onset vs childhood-onset type 1 diabetes is not known. We aimed to explore this by assessing the genetic risk of type 1 diabetes in autoantibody-negative and -positive children and adults. METHODS We analysed GAD autoantibodies, insulinoma-2 antigen autoantibodies and zinc transporter-8 autoantibodies (ZnT8A) and measured type 1 diabetes genetic risk by genotyping 30 type 1 diabetes-associated variants at diagnosis in 1814 individuals with clinician-diagnosed type 1 diabetes (1112 adult-onset, 702 childhood-onset). We compared the overall type 1 diabetes genetic risk score (T1DGRS) and non-HLA and HLA (DR3-DQ2, DR4-DQ8 and DR15-DQ6) components with autoantibody status in those with adult-onset and childhood-onset diabetes. We also measured the T1DGRS in 1924 individuals with type 2 diabetes from the Wellcome Trust Case Control Consortium to represent non-autoimmune diabetes control participants. RESULTS The T1DGRS was similar in autoantibody-negative and autoantibody-positive clinician-diagnosed childhood-onset type 1 diabetes (mean [SD] 0.274 [0.034] vs 0.277 [0.026], p=0.4). In contrast, the T1DGRS in autoantibody-negative adult-onset type 1 diabetes was lower than that in autoantibody-positive adult-onset type 1 diabetes (mean [SD] 0.243 [0.036] vs 0.271 [0.026], p<0.0001) but higher than that in type 2 diabetes (mean [SD] 0.229 [0.034], p<0.0001). Autoantibody-negative adults were more likely to have the more protective HLA DR15-DQ6 genotype (15% vs 3%, p<0.0001), were less likely to have the high-risk HLA DR3-DQ2/DR4-DQ8 genotype (6% vs 19%, p<0.0001) and had a lower non-HLA T1DGRS (p<0.0001) than autoantibody-positive adults. In contrast to children, autoantibody-negative adults were more likely to be male (75% vs 59%), had a higher BMI (27 vs 24 kg/m2) and were less likely to have other autoimmune conditions (2% vs 10%) than autoantibody-positive adults (all p<0.0001). In both adults and children, type 1 diabetes genetic risk was unaffected by the number of autoantibodies (p>0.3). These findings, along with the identification of seven misclassified adults with monogenic diabetes among autoantibody-negative adults and the results of a sensitivity analysis with and without measurement of ZnT8A, suggest that the intermediate type 1 diabetes genetic risk in autoantibody-negative adults is more likely to be explained by the inclusion of misclassified non-autoimmune diabetes (estimated to represent 67% of all antibody-negative adults, 95% CI 61%, 73%) than by the presence of unmeasured autoantibodies or by a discrete form of diabetes. When these estimated individuals with non-autoimmune diabetes were adjusted for, the prevalence of autoantibody positivity in adult-onset type 1 diabetes was similar to that in children (93% vs 91%, p=0.4). CONCLUSIONS/INTERPRETATION The inclusion of non-autoimmune diabetes is the most likely explanation for the observed lower rate of autoantibody positivity in clinician-diagnosed adult-onset type 1 diabetes. Our data support the utility of islet autoantibody measurement in clinician-suspected adult-onset type 1 diabetes in routine clinical practice.
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Affiliation(s)
- Nicholas J Thomas
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
- Department of Diabetes and Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Helen C Walkey
- Faculty of Medicine, Imperial College London, London, UK
| | - Akaal Kaur
- Faculty of Medicine, Imperial College London, London, UK
| | - Shivani Misra
- Faculty of Medicine, Imperial College London, London, UK
| | - Nick S Oliver
- Faculty of Medicine, Imperial College London, London, UK
| | - Kevin Colclough
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
- Department of Diabetes and Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
- Department of Diabetes and Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.
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50
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Jin H, Kim YA, Lee Y, Kwon SH, Do AR, Seo S, Won S, Seo JH. Identification of genetic variants associated with diabetic kidney disease in multiple Korean cohorts via a genome-wide association study mega-analysis. BMC Med 2023; 21:16. [PMID: 36627639 PMCID: PMC9832630 DOI: 10.1186/s12916-022-02723-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The pathogenesis of diabetic kidney disease (DKD) is complex, involving metabolic and hemodynamic factors. Although DKD has been established as a heritable disorder and several genetic studies have been conducted, the identification of unique genetic variants for DKD is limited by its multiplex classification based on the phenotypes of diabetes mellitus (DM) and chronic kidney disease (CKD). Thus, we aimed to identify the genetic variants related to DKD that differentiate it from type 2 DM and CKD. METHODS We conducted a large-scale genome-wide association study mega-analysis, combining Korean multi-cohorts using multinomial logistic regression. A total of 33,879 patients were classified into four groups-normal, DM without CKD, CKD without DM, and DKD-and were further analyzed to identify novel single-nucleotide polymorphisms (SNPs) associated with DKD. Additionally, fine-mapping analysis was conducted to investigate whether the variants of interest contribute to a trait. Conditional analyses adjusting for the effect of type 1 DM (T1D)-associated HLA variants were also performed to remove confounding factors of genetic association with T1D. Moreover, analysis of expression quantitative trait loci (eQTL) was performed using the Genotype-Tissue Expression project. Differentially expressed genes (DEGs) were analyzed using the Gene Expression Omnibus database (GSE30529). The significant eQTL DEGs were used to explore the predicted interaction networks using search tools for the retrieval of interacting genes and proteins. RESULTS We identified three novel SNPs [rs3128852 (P = 8.21×10-25), rs117744700 (P = 8.28×10-10), and rs28366355 (P = 2.04×10-8)] associated with DKD. Moreover, the fine-mapping study validated the causal relationship between rs3128852 and DKD. rs3128852 is an eQTL for TRIM27 in whole blood tissues and HLA-A in adipose-subcutaneous tissues. rs28366355 is an eQTL for HLA-group genes present in most tissues. CONCLUSIONS We successfully identified SNPs (rs3128852, rs117744700, and rs28366355) associated with DKD and verified the causal association between rs3128852 and DKD. According to the in silico analysis, TRIM27 and HLA-A can define DKD pathophysiology and are associated with immune response and autophagy. However, further research is necessary to understand the mechanism of immunity and autophagy in the pathophysiology of DKD and to prevent and treat DKD.
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Affiliation(s)
- Heejin Jin
- Institute of Health and Environment, Seoul National University, Seoul, Korea
| | - Ye An Kim
- Division of Endocrinology, Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Korea
| | - Young Lee
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Jinhwangdo-ro 61-gil 53, Gangdong-gu, Seoul, Korea
| | - Seung-Hyun Kwon
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Jinhwangdo-ro 61-gil 53, Gangdong-gu, Seoul, Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, South Korea
| | - Sujin Seo
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Sungho Won
- Institute of Health and Environment, Seoul National University, Seoul, Korea.,Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul, Korea.,RexSoft Corps, Seoul, Korea
| | - Je Hyun Seo
- Veterans Medical Research Institute, Veterans Health Service Medical Center, Jinhwangdo-ro 61-gil 53, Gangdong-gu, Seoul, Korea.
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