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Scheetz TE, Tollefson MR, Roos BR, Boese EA, Pouw AE, Stone EM, Schnieders MJ, Fingert JH. METTL23 Variants and Patients With Normal-Tension Glaucoma. JAMA Ophthalmol 2024:2824091. [PMID: 39325437 DOI: 10.1001/jamaophthalmol.2024.3829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Importance This research confirms and further establishes that pathogenic variants in a fourth gene, METTL23, are associated with autosomal dominant normal-tension glaucoma (NTG). Objective To determine the frequency of glaucoma-causing pathogenic variants in the METTL23 gene in a cohort of patients with NTG from Iowa. Design, Setting, and Participants This case-control study took place at a single tertiary care center in Iowa from January 1997 to January 2024, with analysis occurring between January 2023 and January 2024. Two groups of participants were enrolled from the University of Iowa clinics: 331 patients with NTG and 362 control individuals without glaucoma. Patients with a history of trauma; steroid use; stigmata of pigment dispersion syndrome; exfoliation syndrome; or pathogenic variants in MYOC, TBK1, or OPTN were also excluded. Main Outcomes and Measures Detection of an enrichment of METTL23 pathogenic variants in individuals with NTG compared with control individuals without glaucoma. Results The study included 331 patients with NTG (mean [SD] age, 68.0 [11.7] years; 228 [68.9%] female and 103 [31.1%] male) and 362 control individuals without glaucoma (mean [SD] age, 64.5 [12.6] years; 207 [57.2%] female and 155 [42.8%] male). There were 5 detected instances of 4 unique METTL23 pathogenic variants in patients with NTG. Three METTL23 variants-p.Ala7Val, p.Pro22Arg, and p.Arg63Trp-were judged to be likely pathogenic and were detected in 3 patients (0.91%) with NTG. However, when all detected variants were evaluated with either mutation burden analysis or logistic regression, their frequency was not statistically higher in individuals with NTG than in control individuals without glaucoma (1.5% vs 2.5%; P = .27). Conclusion and Relevance This investigation provides evidence that pathogenic variants in METTL23 are associated with NTG. Within an NTG cohort at a tertiary care center, pathogenic variants were associated with approximately 1% of NTG cases, a frequency similar to that of other known normal-tension glaucoma genes, including optineurin (OPTN), TANK-binding kinase 1 (TBK1), and myocilin (MYOC). The findings suggest that METTL23 pathogenic variants are likely involved in a biologic pathway that is associated with glaucoma that occurs at lower intraocular pressures.
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Affiliation(s)
- Todd E Scheetz
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Mallory R Tollefson
- Deparment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - Ben R Roos
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Erin A Boese
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Andrew E Pouw
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Edwin M Stone
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
| | - Michael J Schnieders
- Institute for Vision Research, University of Iowa, Iowa City
- Deparment of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City
| | - John H Fingert
- Institute for Vision Research, University of Iowa, Iowa City
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City
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Westergaard D, Jørgensen FH, Waaben J, Jung AW, Lademann M, Hansen TF, Cremers J, Ostrowski SR, Pedersen OBV, Reguant R, Jørgensen IF, Fitzgerald T, Birney E, Banasik K, Mortensen L, Brunak S. Uncovering the heritable components of multimorbidities and disease trajectories using a nationwide cohort. Nat Commun 2024; 15:7457. [PMID: 39198472 PMCID: PMC11358290 DOI: 10.1038/s41467-024-51795-8] [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: 08/21/2023] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
Quantifying the contribution of genetics and environmental effects on disease initiation and progression, as well as the shared genetics of different diseases, is vital for the understanding of the disease etiology of multimorbidities. In this study, we leverage nationwide Danish registries to provide a granular atlas of the genetic origin of disease phenotypes for a cohort of all Danes 1978-2018 with partially known pedigree (n = 6.3 million). We estimate the heritability and genetic correlation between thousands of disease phenotypes using a novel approach that can be scaled to nationwide data. Our findings confirm the importance of genetics for a number of known associations and increase the resolution of heritability by adding numerous associations, some of which point to shared biologically origin of different phenotypes. We also establish the heritability of disease trajectories and the importance of sex-specific genetic contributions. Results can be accessed at https://h2.cpr.ku.dk/ .
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Affiliation(s)
- David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | | | - Jens Waaben
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Wolfgang Jung
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Mette Lademann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jolien Cremers
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Roc Reguant
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, New South Wales, Sydney, Australia
| | - Isabella Friis Jørgensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tom Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laust Mortensen
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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3
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Mackey DA, Bigirimana D, Staffieri SE. Integrating Genetics in Glaucoma Screening. J Glaucoma 2024; 33:S49-S53. [PMID: 39149951 PMCID: PMC11332373 DOI: 10.1097/ijg.0000000000002425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/02/2024] [Indexed: 08/17/2024]
Abstract
PRCIS As additional glaucoma genes are identified and classified, polygenic risk scores will be refined, facilitating early diagnosis and treatment. Ensuring genetic research is equitable to prevent glaucoma blindness worldwide is crucial. PURPOSE To review the progress in glaucoma genetics over the past 25 years, including the identification of genes with varying contributions to the disease and the development of polygenic risk scores. METHODS/RESULTS Over the last 2 and a half decades, glaucoma genetics has evolved from identifying genes with Mendelian inheritance patterns, such as myocilin and CYP1B1, to the discovery of hundreds of genes associated with the disease. Polygenic risk scores have been developed, primarily based on research in Northern European populations, and efforts to refine these scores are ongoing. However, there is a question regarding their applicability to other ethnic groups, especially those at higher risk of primary open angle glaucoma, like individuals of African ancestry. Glaucoma is highly heritable and family history can be used for cascade clinical screening programs, but these will not be feasible in all populations. Thus, cascade genetic testing using well-established genes such as myocilin may help improve glaucoma diagnosis. In addition, ongoing investigations seek to identify pathogenic genetic variants within genes like myocilin. CONCLUSIONS The expanding availability of genetic testing for various diseases and early access to genetic risk information necessitates further research to determine when and how to act on specific genetic results. Polygenic risk scores involving multiple genes with subtle effects will require continuous refinement to improve clinical utility. This is crucial for effectively interpreting an individual's risk of developing glaucoma and preventing blindness.
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Affiliation(s)
| | - Deus Bigirimana
- Glaucoma Investigation and Research Unit, Royal Victorian Eye and Ear Hospital
| | - Sandra Elfride Staffieri
- Centre for Eye Research Australia Ltd., Royal Victorian Eye and Ear Hospital
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Australia
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4
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McGuire D, Markus H, Yang L, Xu J, Montgomery A, Berg A, Li Q, Carrel L, Liu DJ, Jiang B. Dissecting heritability, environmental risk, and air pollution causal effects using > 50 million individuals in MarketScan. Nat Commun 2024; 15:5357. [PMID: 38918381 PMCID: PMC11199552 DOI: 10.1038/s41467-024-49566-6] [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: 09/09/2021] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Large national-level electronic health record (EHR) datasets offer new opportunities for disentangling the role of genes and environment through deep phenotype information and approximate pedigree structures. Here we use the approximate geographical locations of patients as a proxy for spatially correlated community-level environmental risk factors. We develop a spatial mixed linear effect (SMILE) model that incorporates both genetics and environmental contribution. We extract EHR and geographical locations from 257,620 nuclear families and compile 1083 disease outcome measurements from the MarketScan dataset. We augment the EHR with publicly available environmental data, including levels of particulate matter 2.5 (PM2.5), nitrogen dioxide (NO2), climate, and sociodemographic data. We refine the estimates of genetic heritability and quantify community-level environmental contributions. We also use wind speed and direction as instrumental variables to assess the causal effects of air pollution. In total, we find PM2.5 or NO2 have statistically significant causal effects on 135 diseases, including respiratory, musculoskeletal, digestive, metabolic, and sleep disorders, where PM2.5 and NO2 tend to affect biologically distinct disease categories. These analyses showcase several robust strategies for jointly modeling genetic and environmental effects on disease risk using large EHR datasets and will benefit upcoming biobank studies in the era of precision medicine.
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Affiliation(s)
- Daniel McGuire
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Havell Markus
- MD/PhD Program, Penn State College of Medicine of Medicine, Hershey, PA, 17033, USA
- Bioinformatics and Genomics PhD Program, Penn State College of Medicine, Hershey, PA, 17033, USA
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Lina Yang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Jingyu Xu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Austin Montgomery
- MD/PhD Program, Penn State College of Medicine of Medicine, Hershey, PA, 17033, USA
| | - Arthur Berg
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Qunhua Li
- Department of Statistics, Penn State University, University Park, PA, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA.
| | - Bibo Jiang
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, 17033, USA.
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5
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Huang X, Kleiman R, Page D, Hebbring S. Automated Family Histories Significantly Improve Risk Prediction in an EHR. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2024; 2024:221-229. [PMID: 38827091 PMCID: PMC11141855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
We recently demonstrated that electronically constructed family pedigrees (e-pedigrees) have great value in epidemiologic research using electronic health record (EHR) data. Prior to this work, it has been well accepted that family health history is a major predictor for a wide spectrum of diseases, reflecting shared effects of genetics, environment, and lifestyle. With the widespread digitalization of patient data via EHRs, there is an unprecedented opportunity to use machine learning algorithms to better predict disease risk. Although predictive models have previously been constructed for a few important diseases, we currently know very little about how accurately the risk for most diseases can be predicted. It is further unknown if the incorporation of e-pedigrees in machine learning can improve the value of these models. In this study, we devised a family pedigree-driven high-throughput machine learning pipeline to simultaneously predict risks for thousands of diagnosis codes using thousands of input features. Models were built to predict future disease risk for three time windows using both Logistic Regression and XGBoost. For example, we achieved average areas under the receiver operating characteristic curves (AUCs) of 0.82, 0.77 and 0.71 for 1, 6, and 24 months, respectively using XGBoost and without e-pedigrees. When adding e-pedigree features to the XGBoost pipeline, AUCs increased to 0.83, 0.79 and 0.74 for the same three time periods, respectively. E-pedigrees similarly improved the predictions when using Logistic Regression. These results emphasize the potential value of incorporating family health history via e-pedigrees into machine learning with no further human time.
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Affiliation(s)
- Xiayuan Huang
- University of Wisconsin-Madison, Madison, Wisconsin, United Sates
| | - Ross Kleiman
- University of Wisconsin-Madison, Madison, Wisconsin, United Sates
| | - David Page
- Duke University, Durham, North Carolina, United States
| | - Scott Hebbring
- Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States
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6
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Yun JS, Jung SH, Lee SN, Jung SM, Won HH, Kim D, Choi JA. Polygenic risk score-based phenome-wide association for glaucoma and its impact on disease susceptibility in two large biobanks. J Transl Med 2024; 22:355. [PMID: 38622600 PMCID: PMC11020996 DOI: 10.1186/s12967-024-05152-4] [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: 01/22/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Glaucoma is a leading cause of worldwide irreversible blindness. Considerable uncertainty remains regarding the association between a variety of phenotypes and the genetic risk of glaucoma, as well as the impact they exert on the glaucoma development. METHODS We investigated the associations of genetic liability for primary open angle glaucoma (POAG) with a wide range of potential risk factors and to assess its impact on the risk of incident glaucoma. The phenome-wide association study (PheWAS) approach was applied to determine the association of POAG polygenic risk score (PRS) with a wide range of phenotypes in 377, 852 participants from the UK Biobank study and 43,623 participants from the Penn Medicine Biobank study, all of European ancestry. Participants were stratified into four risk tiers: low, intermediate, high, and very high-risk. Cox proportional hazard models assessed the relationship of POAG PRS and ocular factors with new glaucoma events. RESULTS In both discovery and replication set in the PheWAS, a higher genetic predisposition to POAG was specifically correlated with ocular disease phenotypes. The POAG PRS exhibited correlations with low corneal hysteresis, refractive error, and ocular hypertension, demonstrating a strong association with the onset of glaucoma. Individuals carrying a high genetic burden exhibited a 9.20-fold, 11.88-fold, and 28.85-fold increase in glaucoma incidence when associated with low corneal hysteresis, high myopia, and elevated intraocular pressure, respectively. CONCLUSION Genetic susceptibility to POAG primarily influences ocular conditions, with limited systemic associations. Notably, the baseline polygenic risk for POAG robustly associates with new glaucoma events, revealing a large combined effect of genetic and ocular risk factors on glaucoma incidents.
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Affiliation(s)
- Jae-Seung Yun
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Su-Nam Lee
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Min Jung
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea.
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jin A Choi
- Department of Ophthalmology, College of Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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7
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Hopper JL, Li S, MacInnis RJ, Dowty JG, Nguyen TL, Bui M, Dite GS, Esser VFC, Ye Z, Makalic E, Schmidt DF, Goudey B, Alpen K, Kapuscinski M, Win AK, Dugué PA, Milne RL, Jayasekara H, Brooks JD, Malta S, Calais-Ferreira L, Campbell AC, Young JT, Nguyen-Dumont T, Sung J, Giles GG, Buchanan D, Winship I, Terry MB, Southey MC, Jenkins MA. Breast and bowel cancers diagnosed in people 'too young to have cancer': A blueprint for research using family and twin studies. Genet Epidemiol 2024. [PMID: 38504141 DOI: 10.1002/gepi.22555] [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: 08/30/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
Abstract
Young breast and bowel cancers (e.g., those diagnosed before age 40 or 50 years) have far greater morbidity and mortality in terms of years of life lost, and are increasing in incidence, but have been less studied. For breast and bowel cancers, the familial relative risks, and therefore the familial variances in age-specific log(incidence), are much greater at younger ages, but little of these familial variances has been explained. Studies of families and twins can address questions not easily answered by studies of unrelated individuals alone. We describe existing and emerging family and twin data that can provide special opportunities for discovery. We present designs and statistical analyses, including novel ideas such as the VALID (Variance in Age-specific Log Incidence Decomposition) model for causes of variation in risk, the DEPTH (DEPendency of association on the number of Top Hits) and other approaches to analyse genome-wide association study data, and the within-pair, ICE FALCON (Inference about Causation from Examining FAmiliaL CONfounding) and ICE CRISTAL (Inference about Causation from Examining Changes in Regression coefficients and Innovative STatistical AnaLysis) approaches to causation and familial confounding. Example applications to breast and colorectal cancer are presented. Motivated by the availability of the resources of the Breast and Colon Cancer Family Registries, we also present some ideas for future studies that could be applied to, and compared with, cancers diagnosed at older ages and address the challenges posed by young breast and bowel cancers.
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Affiliation(s)
- John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Shuai Li
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Robert J MacInnis
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Tuong L Nguyen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Gillian S Dite
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Genetic Technologies Ltd., Fitzroy, Victoria, Australia
| | - Vivienne F C Esser
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Zhoufeng Ye
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Daniel F Schmidt
- Department of Data Science and AI, Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Benjamin Goudey
- ARC Training Centre in Cognitive Computing for Medical Technologies, University of Melbourne, Carlton, Victoria, Australia
- The Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Karen Alpen
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Miroslaw Kapuscinski
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
- Genetic Medicine, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Pierre-Antoine Dugué
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Harindra Jayasekara
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Jennifer D Brooks
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sue Malta
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Lucas Calais-Ferreira
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
| | - Alexander C Campbell
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Jesse T Young
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Institute for Mental Health Policy Research, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Centre for Adolescent Health, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
- Justice Health Group, Curtin School of Population Health, Curtin University, Perth, Western Australia, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Joohon Sung
- Department of Public Health Sciences, Division of Genome and Health Big Data, Graduate School of Public Health, Seoul National University, Seoul, South Korea
- Genome Medicine Institute, Seoul National University, Seoul, South Korea
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Daniel Buchanan
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ingrid Winship
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
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8
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Zhang H, Jethani N, Jones S, Genes N, Major VJ, Jaffe IS, Cardillo AB, Heilenbach N, Ali NF, Bonanni LJ, Clayburn AJ, Khera Z, Sadler EC, Prasad J, Schlacter J, Liu K, Silva B, Montgomery S, Kim EJ, Lester J, Hill TM, Avoricani A, Chervonski E, Davydov J, Small W, Chakravartty E, Grover H, Dodson JA, Brody AA, Aphinyanaphongs Y, Masurkar A, Razavian N. Evaluating Large Language Models in Extracting Cognitive Exam Dates and Scores. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.07.10.23292373. [PMID: 38405784 PMCID: PMC10888985 DOI: 10.1101/2023.07.10.23292373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Importance Large language models (LLMs) are crucial for medical tasks. Ensuring their reliability is vital to avoid false results. Our study assesses two state-of-the-art LLMs (ChatGPT and LlaMA-2) for extracting clinical information, focusing on cognitive tests like MMSE and CDR. Objective Evaluate ChatGPT and LlaMA-2 performance in extracting MMSE and CDR scores, including their associated dates. Methods Our data consisted of 135,307 clinical notes (Jan 12th, 2010 to May 24th, 2023) mentioning MMSE, CDR, or MoCA. After applying inclusion criteria 34,465 notes remained, of which 765 underwent ChatGPT (GPT-4) and LlaMA-2, and 22 experts reviewed the responses. ChatGPT successfully extracted MMSE and CDR instances with dates from 742 notes. We used 20 notes for fine-tuning and training the reviewers. The remaining 722 were assigned to reviewers, with 309 each assigned to two reviewers simultaneously. Inter-rater-agreement (Fleiss' Kappa), precision, recall, true/false negative rates, and accuracy were calculated. Our study follows TRIPOD reporting guidelines for model validation. Results For MMSE information extraction, ChatGPT (vs. LlaMA-2) achieved accuracy of 83% (vs. 66.4%), sensitivity of 89.7% (vs. 69.9%), true-negative rates of 96% (vs 60.0%), and precision of 82.7% (vs 62.2%). For CDR the results were lower overall, with accuracy of 87.1% (vs. 74.5%), sensitivity of 84.3% (vs. 39.7%), true-negative rates of 99.8% (98.4%), and precision of 48.3% (vs. 16.1%). We qualitatively evaluated the MMSE errors of ChatGPT and LlaMA-2 on double-reviewed notes. LlaMA-2 errors included 27 cases of total hallucination, 19 cases of reporting other scores instead of MMSE, 25 missed scores, and 23 cases of reporting only the wrong date. In comparison, ChatGPT's errors included only 3 cases of total hallucination, 17 cases of wrong test reported instead of MMSE, and 19 cases of reporting a wrong date. Conclusions In this diagnostic/prognostic study of ChatGPT and LlaMA-2 for extracting cognitive exam dates and scores from clinical notes, ChatGPT exhibited high accuracy, with better performance compared to LlaMA-2. The use of LLMs could benefit dementia research and clinical care, by identifying eligible patients for treatments initialization or clinical trial enrollments. Rigorous evaluation of LLMs is crucial to understanding their capabilities and limitations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Abraham A Brody
- NYU Rory Meyers College of Nursing, NYU Grossman School of Medicine
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9
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Mackey DA, Staffieri SE. Making glaucoma genetic studies more diverse. Cell 2024; 187:273-275. [PMID: 38242084 DOI: 10.1016/j.cell.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]
Abstract
Although the blinding eye disease glaucoma is more common in people of African ancestry, previous genetic studies predominantly involved European subjects. In this issue of Cell, O'Brien et al. report a genome-wide association study for glaucoma in individuals of African ancestry, showing overlap with European studies and refining an African polygenic risk score.
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Affiliation(s)
- David A Mackey
- Lions Eye Institute, University of Western Australia, Perth, WA, Australia; Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Sandra E Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Parkville, VIC, Australia
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10
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Brown KL, Ramlall V, Zietz M, Gisladottir U, Tatonetti NP. Estimating the heritability of SARS-CoV-2 susceptibility and COVID-19 severity. Nat Commun 2024; 15:367. [PMID: 38191623 PMCID: PMC10774300 DOI: 10.1038/s41467-023-44250-7] [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: 08/01/2022] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
SARS-CoV-2 has infected over 340 million people, prompting therapeutic research. While genetic studies can highlight potential drug targets, understanding the heritability of SARS-CoV-2 susceptibility and COVID-19 severity can contextualize their results. To date, loci from meta-analyses explain 1.2% and 5.8% of variation in susceptibility and severity respectively. Here we estimate the importance of shared environment and additive genetic variation to SARS-CoV-2 susceptibility and COVID-19 severity using pedigree data, PCR results, and hospitalization information. The relative importance of genetics and shared environment for susceptibility shifted during the study, with heritability ranging from 33% (95% CI: 20%-46%) to 70% (95% CI: 63%-74%). Heritability was greater for days hospitalized with COVID-19 (41%, 95% CI: 33%-57%) compared to shared environment (33%, 95% CI: 24%-38%). While our estimates suggest these genetic architectures are not fully understood, the shift in susceptibility estimates highlights the challenge of estimation during a pandemic, given environmental fluctuations and vaccine introduction.
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Affiliation(s)
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Department of Physiology & Cellular Biophysics, Columbia University, New York, NY, USA
| | - Michael Zietz
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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11
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Barak-Corren Y, Tsurel D, Keidar D, Gofer I, Shahaf D, Leventer-Roberts M, Barda N, Reis BY. The value of parental medical records for the prediction of diabetes and cardiovascular disease: a novel method for generating and incorporating family histories. J Am Med Inform Assoc 2023; 30:1915-1924. [PMID: 37535812 PMCID: PMC10654871 DOI: 10.1093/jamia/ocad154] [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: 05/01/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
OBJECTIVE To determine whether data-driven family histories (DDFH) derived from linked EHRs of patients and their parents can improve prediction of patients' 10-year risk of diabetes and atherosclerotic cardiovascular disease (ASCVD). MATERIALS AND METHODS A retrospective cohort study using data from Israel's largest healthcare organization. A random sample of 200 000 subjects aged 40-60 years on the index date (January 1, 2010) was included. Subjects with insufficient history (<1 year) or insufficient follow-up (<10 years) were excluded. Two separate XGBoost models were developed-1 for diabetes and 1 for ASCVD-to predict the 10-year risk for each outcome based on data available prior to the index date of January 1, 2010. RESULTS Overall, the study included 110 734 subject-father-mother triplets. There were 22 153 cases of diabetes (20%) and 11 715 cases of ASCVD (10.6%). The addition of parental information significantly improved prediction of diabetes risk (P < .001), but not ASCVD risk. For both outcomes, maternal medical history was more predictive than paternal medical history. A binary variable summarizing parental disease state delivered similar predictive results to the full parental EHR. DISCUSSION The increasing availability of EHRs for multiple family generations makes DDFH possible and can assist in delivering more personalized and precise medicine to patients. Consent frameworks must be established to enable sharing of information across generations, and the results suggest that sharing the full records may not be necessary. CONCLUSION DDFH can address limitations of patient self-reported family history, and it improves clinical predictions for some conditions, but not for all, and particularly among younger adults.
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Affiliation(s)
- Yuval Barak-Corren
- Predictive Medicine Group, Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - David Tsurel
- Predictive Medicine Group, Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, USA
- Clalit Research Institute, Ramat Gan, Israel
- The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daphna Keidar
- Predictive Medicine Group, Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, USA
- Clalit Research Institute, Ramat Gan, Israel
| | - Ilan Gofer
- Clalit Research Institute, Ramat Gan, Israel
| | - Dafna Shahaf
- The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maya Leventer-Roberts
- Clalit Research Institute, Ramat Gan, Israel
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Noam Barda
- Clalit Research Institute, Ramat Gan, Israel
| | - Ben Y Reis
- Predictive Medicine Group, Computational Health Informatics Program, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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12
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Foy BH, Petherbridge R, Roth M, Mow C, Patel HR, Patel CH, Ho SN, Lam E, Karczewski KJ, Tozzo V, Higgins JM. Hematologic setpoints are a stable and patient-specific deep phenotype. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.26.23296146. [PMID: 37808854 PMCID: PMC10557837 DOI: 10.1101/2023.09.26.23296146] [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
The complete blood count is an important screening tool for healthy adults and is the most commonly ordered test at periodic physical exams. However, results are usually interpreted relative to one-size-fits-all reference intervals, undermining the goal of precision medicine to tailor medical care to the needs of individual patients based on their unique characteristics. Here we show that standard complete blood count indices in healthy adults have robust homeostatic setpoints that are patient-specific and stable, with the typical healthy adult's set of 9 blood count setpoints distinguishable from 98% of others, and with these differences persisting for decades. These setpoints reflect a deep physiologic phenotype, enabling improved detection of both acquired and genetic determinants of hematologic regulation, including discovery of multiple novel loci via GWAS analyses. Patient-specific reference intervals derived from setpoints enable more accurate personalized risk assessment, and the setpoints themselves are significantly correlated with mortality risk, providing new opportunities to enhance patient-specific screening and early intervention. This study shows complete blood count setpoints are sufficiently stable and patient-specific to help realize the promise of precision medicine for healthy adults.
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Affiliation(s)
- Brody H Foy
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Rachel Petherbridge
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Maxwell Roth
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher Mow
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Mass General Brigham Enterprise Research IS, Boston, MA, USA
| | - Hasmukh R Patel
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Chhaya H Patel
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Samantha N Ho
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Evie Lam
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Veronica Tozzo
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - John M Higgins
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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13
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Krefman AE, Ghamsari F, Turner DR, Lu A, Borsje M, Wood CW, Petito LC, Polubriaginof FCG, Schneider D, Ahmad F, Allen NB. Using electronic health record data to link families: an illustrative example using intergenerational patterns of obesity. J Am Med Inform Assoc 2023; 30:915-922. [PMID: 36857086 PMCID: PMC10114127 DOI: 10.1093/jamia/ocad028] [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: 08/14/2022] [Revised: 02/03/2023] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
OBJECTIVE Electronic health record (EHR) data are a valuable resource for population health research but lack critical information such as relationships between individuals. Emergency contacts in EHRs can be used to link family members, creating a population that is more representative of a community than traditional family cohorts. MATERIALS AND METHODS We revised a published algorithm: relationship inference from the electronic health record (RIFTEHR). Our version, Pythonic RIFTEHR (P-RIFTEHR), identifies a patient's emergency contacts, matches them to existing patients (when available) using network graphs, checks for conflicts, and infers new relationships. P-RIFTEHR was run on December 15, 2021 in the Northwestern Medicine Electronic Data Warehouse (NMEDW) on approximately 2.95 million individuals and was validated using the existing link between children born at NM hospitals and their mothers. As proof-of-concept, we modeled the association between parent and child obesity using logistic regression. RESULTS The P-RIFTEHR algorithm matched 1 157 454 individuals in 448 278 families. The median family size was 2, the largest was 32 persons, and 247 families spanned 4 generations or more. Validation of the mother-child pairs resulted in 95.1% sensitivity. Children were 2 times more likely to be obese if a parent is obese (OR: 2.30; 95% CI, 2.23-2.37). CONCLUSION P-RIFTEHR can identify familiar relationships in a large, diverse population in an integrated health system. Estimates of parent-child inheritability of obesity using family structures identified by the algorithm were consistent with previously published estimates from traditional cohort studies.
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Affiliation(s)
- Amy E Krefman
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Farhad Ghamsari
- Department of Internal Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Daniel R Turner
- IT Research Computing Services, Northwestern University, Evanston, Illinois, USA
| | - Alice Lu
- Northwestern Medicine Enterprise Data Warehouse, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Martin Borsje
- Northwestern Medicine Enterprise Data Warehouse, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Colby Witherup Wood
- IT Research Computing Services, Northwestern University, Evanston, Illinois, USA
| | - Lucia C Petito
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Daniel Schneider
- Northwestern Medicine Enterprise Data Warehouse, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Faraz Ahmad
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Norrina B Allen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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14
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Waksmunski AR, Kinzy TG, Cruz LA, Nealon CL, Halladay CW, Anthony SA, Greenberg PB, Sullivan JM, Wu WC, Iyengar SK, Crawford DC, Peachey NS, Cooke Bailey JN. Diversity is key for cross-ancestry transferability of glaucoma genetic risk scores in Hispanic Veterans in the Million Veteran Program. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2023; 28:413-424. [PMID: 36540996 PMCID: PMC9997528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A major goal of precision medicine is to stratify patients based on their genetic risk for a disease to inform future screening and intervention strategies. For conditions like primary open-angle glaucoma (POAG), the genetic risk architecture is complicated with multiple variants contributing small effects on risk. Following the tepid success of genome-wide association studies for high-effect disease risk variant discovery, genetic risk scores (GRS), which collate effects from multiple genetic variants into a single measure, have shown promise for disease risk stratification. We assessed the application of GRS for POAG risk stratification in Hispanic-descent (HIS) and European-descent (EUR) Veterans in the Million Veteran Program. Unweighted and cross-ancestry meta-weighted GRS were calculated based on 127 genomic variants identified in the most recent report of cross-ancestry POAG meta-analyses. We found that both GRS types were associated with POAG case-control status and performed similarly in HIS and EUR Veterans. This trend was also seen in our subset analysis of HIS Veterans with less than 50% EUR global genetic ancestry. Our findings highlight the importance of evaluating GRS based on known POAG risk variants in different ancestry groups and emphasize the need for more multi-ancestry POAG genetic studies.
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Affiliation(s)
- Andrea R Waksmunski
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH 44106, USA,
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15
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Quezada-Sánchez AD, Espín-Arellano I, Morales-Carmona E, Molina-Vélez D, Palacio-Mejía LS, González-González EL, Alvarez Aceves M, Hernández-Ávila JE. Implementation and validation of a probabilistic linkage method for population databases without identification variables. Heliyon 2022; 8:e12311. [PMID: 36582715 PMCID: PMC9793263 DOI: 10.1016/j.heliyon.2022.e12311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/16/2022] Open
Abstract
Linking records of the same person from different sources makes it possible to build administrative cohorts and perform longitudinal analyzes, as an alternative to traditional cohort studies, and have important practical implications in producing knowledge in public health. We implemented the Fellegi-Sunter probabilistic linkage method to a sample of records from the Mexican Automated System for Hospital Discharges and the Statistical and Epidemiological System for Deaths and evaluated its performance. The records in each source were randomly divided into a training sample (25%) and a validation sample (75%). We evaluated different types of blocking in terms of complexity reduction and pairs completeness, and record linkage in terms of sensitivity and positive predictive value. In the validation sample, a blocking scheme based on trigrams of the full name achieved 95.76% pairs completeness and 99.9996% complexity reduction. After pairs classification, we achieved a sensitivity of 90.72% and a positive predictive value of 97.10% in the validation sample. Both values were about one percentage point higher than that obtained in the automatic classification without clerical review of potential pairs. We concluded that the linkage algorithm achieved a good performance in terms of sensitivity and positive predictive value and can be used to build administrative cohorts for the epidemiological analysis of populations with records in health information systems.
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Affiliation(s)
- Amado D. Quezada-Sánchez
- Center for Evaluation and Surveys Research, National Institute of Public Health. Av. Universidad 655 Col. Sta. María Ahuacatitlán. C.P. 62100. Cuernavaca, Morelos, Mexico
| | - Iván Espín-Arellano
- Center for Evaluation and Surveys Research, National Institute of Public Health. Av. Universidad 655 Col. Sta. María Ahuacatitlán. C.P. 62100. Cuernavaca, Morelos, Mexico
| | - Evangelina Morales-Carmona
- Center for Evaluation and Surveys Research, National Institute of Public Health. Av. Universidad 655 Col. Sta. María Ahuacatitlán. C.P. 62100. Cuernavaca, Morelos, Mexico
| | - Diana Molina-Vélez
- Center for Evaluation and Surveys Research, National Institute of Public Health. Av. Universidad 655 Col. Sta. María Ahuacatitlán. C.P. 62100. Cuernavaca, Morelos, Mexico
| | - Lina Sofía Palacio-Mejía
- Conacyt - National Institute of Public Health, Av. Universidad 655 Col., Sta. María Ahuacatitlán, C.P. 62100 Cuernavaca, Morelos, Mexico
| | - Edgar Leonel González-González
- Center for Evaluation and Surveys Research, National Institute of Public Health. Av. Universidad 655 Col. Sta. María Ahuacatitlán. C.P. 62100. Cuernavaca, Morelos, Mexico
| | - Mariana Alvarez Aceves
- Conacyt - National Institute of Public Health, Av. Universidad 655 Col., Sta. María Ahuacatitlán, C.P. 62100 Cuernavaca, Morelos, Mexico
| | - Juan Eugenio Hernández-Ávila
- Center for Evaluation and Surveys Research, National Institute of Public Health. Av. Universidad 655 Col. Sta. María Ahuacatitlán. C.P. 62100. Cuernavaca, Morelos, Mexico,Corresponding author.
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16
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Nealon CL, Halladay CW, Kinzy TG, Simpson P, Canania RL, Anthony SA, Roncone DP, Sawicki Rogers LR, Leber JN, Dougherty JM, Sullivan JM, Wu WC, Greenberg PB, Iyengar SK, Crawford DC, Peachey NS, Bailey JNC. Development and Evaluation of a Rules-based Algorithm for Primary Open-Angle Glaucoma in the VA Million Veteran Program. Ophthalmic Epidemiol 2022; 29:640-648. [PMID: 34822319 PMCID: PMC9583190 DOI: 10.1080/09286586.2021.1992784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/20/2021] [Accepted: 10/09/2021] [Indexed: 10/19/2022]
Abstract
The availability of electronic health record (EHR)-linked biobank data for research presents opportunities to better understand complex ocular diseases. Developing accurate computable phenotypes for ocular diseases for which gold standard diagnosis includes imaging remains inaccessible in most biobank-linked EHRs. The objective of this study was to develop and validate a computable phenotype to identify primary open-angle glaucoma (POAG) through accessing the Department of Veterans Affairs (VA) Computerized Patient Record System (CPRS) and Million Veteran Program (MVP) biobank. Accessing CPRS clinical ophthalmology data from VA Medical Center Eye Clinic (VAMCEC) patients, we developed and iteratively refined POAG case and control algorithms based on clinical, prescription, and structured diagnosis data (ICD-CM codes). Refinement was performed via detailed chart review, initially at a single VAMCEC (n = 200) and validated at two additional VAMCECs (n = 100 each). Positive and negative predictive values (PPV, NPV) were computed as the proportion of CPRS patients correctly classified with POAG or without POAG, respectively, by the algorithms, validated by ophthalmologists and optometrists with access to gold-standard clinical diagnosis data. The final algorithms performed better than previously reported approaches in assuring the accuracy and reproducibility of POAG classification (PPV >83% and NPV >97%) with consistent performance in Black or African American and in White Veterans. Applied to the MVP to identify cases and controls, genetic analysis of a known POAG-associated locus further validated the algorithms. We conclude that ours is a viable approach to use combined EHR-genetic data to study patients with complex diseases that require imaging confirmation.
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Affiliation(s)
| | | | - Tyler G. Kinzy
- VA Northeast Ohio Healthcare System, Cleveland, OH
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH
| | | | | | | | | | | | - Jenna N. Leber
- Ophthalmology Section, VA Western NY Health Care System, Buffalo NY
| | | | - Jack M. Sullivan
- Ophthalmology Section, VA Western NY Health Care System, Buffalo NY
| | - Wen-Chih Wu
- Cardiology Section, Medical Service, Providence VA Medical Center, Providence, RI
| | - Paul B. Greenberg
- Ophthalmology Section, Providence VA Medical Center, Providence, RI
- Division of Ophthalmology, Alpert Medical School, Brown University, Providence, RI
| | - Sudha K. Iyengar
- VA Northeast Ohio Healthcare System, Cleveland, OH
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Dana C. Crawford
- VA Northeast Ohio Healthcare System, Cleveland, OH
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Neal S. Peachey
- VA Northeast Ohio Healthcare System, Cleveland, OH
- Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, OH
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH
| | - Jessica N. Cooke Bailey
- VA Northeast Ohio Healthcare System, Cleveland, OH
- Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH
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17
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Freda PJ, Kranzler HR, Moore JH. Novel digital approaches to the assessment of problematic opioid use. BioData Min 2022; 15:14. [PMID: 35840990 PMCID: PMC9284824 DOI: 10.1186/s13040-022-00301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
The opioid epidemic continues to contribute to loss of life through overdose and significant social and economic burdens. Many individuals who develop problematic opioid use (POU) do so after being exposed to prescribed opioid analgesics. Therefore, it is important to accurately identify and classify risk factors for POU. In this review, we discuss the etiology of POU and highlight novel approaches to identifying its risk factors. These approaches include the application of polygenic risk scores (PRS) and diverse machine learning (ML) algorithms used in tandem with data from electronic health records (EHR), clinical notes, patient demographics, and digital footprints. The implementation and synergy of these types of data and approaches can greatly assist in reducing the incidence of POU and opioid-related mortality by increasing the knowledge base of patient-related risk factors, which can help to improve prescribing practices for opioid analgesics.
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Affiliation(s)
- Philip J Freda
- Cedars-Sinai Medical Center, Department of Computational Biomedicine, 700 N. San Vicente Blvd., Pacific Design Center Suite G540, West Hollywood, CA, 90069, USA.
| | - Henry R Kranzler
- University of Pennsylvania, Center for Studies of Addiction, 3535 Market St., Suite 500 and Crescenz VAMC, 3800 Woodland Ave., Philadelphia, PA, 19104, USA
| | - Jason H Moore
- Cedars-Sinai Medical Center, Department of Computational Biomedicine, 700 N. San Vicente Blvd., Pacific Design Center Suite G540, West Hollywood, CA, 90069, USA
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18
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Glaucoma Cascade Screening in a High Risk Afro-Caribbean Haitian Population: A Pilot Study. J Glaucoma 2022; 31:584-589. [PMID: 35131981 PMCID: PMC9232278 DOI: 10.1097/ijg.0000000000001996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/12/2022] [Indexed: 01/31/2023]
Abstract
PRCIS Glaucoma cascade screening in first-degree relatives (FDRs) of young Haitian glaucoma patients had high yield for diagnosing manifest and suspected glaucoma in 30.8% of those screened despite modest participation. PURPOSE To evaluate the outcomes of glaucoma cascade screening in FDRs (parents, siblings, and offspring) of Haitian juvenile open-angle glaucoma (JOAG) patients. PATIENTS AND METHODS Consecutive index patients (Haitians with JOAG) were identified, and the number/type of FDRs residing in South Florida were recorded. These FDRs were invited for free glaucoma screening, which included a comprehensive ophthalmic exam, gonioscopy, automated visual field testing and optical coherence tomographic analysis of the retinal nerve fiber layers. FDR characteristics and clinical findings from screening are reported. RESULTS A total of 77 FDRs were invited, 26 (33.8%) agreed to undergo screening (18 females, 9 males), which revealed 2 (7.7%) with manifest glaucoma (mean age 77.5 y; one of whom was previously unaware of his glaucoma diagnosis), 6 (23.1%) with suspected glaucoma (mean age 29.8±18.3 y), and 18 (69.2%) without manifest or suspected glaucoma (mean age 37.2±21.8 y). Siblings of index patients were least likely to participate in cascade glaucoma screening when compared with index patients' parents or offspring. FDR eyes with manifest glaucoma had significantly worse best-corrected visual acuities, higher intraocular pressures, thinner central corneal thicknesses, and thinner circumferential papillary retinal nerve fiber layer thicknesses than those without glaucoma. CONCLUSION Glaucoma cascade screening of Haitian JOAG patients' FDRs revealed that 30.8% had suspected or manifest glaucoma. Future efforts centered on provider-initiated recruitment and improving public glaucoma awareness and education may increase screening participation.
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Daniszewski M, Senabouth A, Liang HH, Han X, Lidgerwood GE, Hernández D, Sivakumaran P, Clarke JE, Lim SY, Lees JG, Rooney L, Gulluyan L, Souzeau E, Graham SL, Chan CL, Nguyen U, Farbehi N, Gnanasambandapillai V, McCloy RA, Clarke L, Kearns LS, Mackey DA, Craig JE, MacGregor S, Powell JE, Pébay A, Hewitt AW. Retinal ganglion cell-specific genetic regulation in primary open-angle glaucoma. CELL GENOMICS 2022; 2:100142. [PMID: 36778138 PMCID: PMC9903700 DOI: 10.1016/j.xgen.2022.100142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 03/08/2021] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
To assess the transcriptomic profile of disease-specific cell populations, fibroblasts from patients with primary open-angle glaucoma (POAG) were reprogrammed into induced pluripotent stem cells (iPSCs) before being differentiated into retinal organoids and compared with those from healthy individuals. We performed single-cell RNA sequencing of a total of 247,520 cells and identified cluster-specific molecular signatures. Comparing the gene expression profile between cases and controls, we identified novel genetic associations for this blinding disease. Expression quantitative trait mapping identified a total of 4,443 significant loci across all cell types, 312 of which are specific to the retinal ganglion cell subpopulations, which ultimately degenerate in POAG. Transcriptome-wide association analysis identified genes at loci previously associated with POAG, and analysis, conditional on disease status, implicated 97 statistically significant retinal ganglion cell-specific expression quantitative trait loci. This work highlights the power of large-scale iPSC studies to uncover context-specific profiles for a genetically complex disease.
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Affiliation(s)
- Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Anne Senabouth
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Helena H. Liang
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Xikun Han
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Grace E. Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Priyadharshini Sivakumaran
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Jordan E. Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Shiang Y. Lim
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,O’Brien Institute Department of St Vincent’s Institute of Medical Research, Melbourne, Fitzroy, VIC 3065, Australia
| | - Jarmon G. Lees
- O’Brien Institute Department of St Vincent’s Institute of Medical Research, Melbourne, Fitzroy, VIC 3065, Australia,Department of Medicine, St Vincent’s Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Louise Rooney
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Lerna Gulluyan
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Stuart L. Graham
- Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Chia-Ling Chan
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Uyen Nguyen
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Nona Farbehi
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Vikkitharan Gnanasambandapillai
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Rachael A. McCloy
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Lisa S. Kearns
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - David A. Mackey
- Lions Eye Institute, Centre for Vision Sciences, University of Western Australia, Crawley, WA 6009, Australia,School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Joseph E. Powell
- Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW 2010, Australia,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW 2052, Australia,Corresponding author
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010, Australia,Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia,Corresponding author
| | - Alex W. Hewitt
- Department of Surgery, The University of Melbourne, Parkville, VIC 3010, Australia,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia,School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7005, Australia,Corresponding author
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20
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ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 2022; 606:358-367. [PMID: 35477154 PMCID: PMC9157047 DOI: 10.1038/s41586-022-04769-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/19/2022] [Indexed: 12/12/2022]
Abstract
The composition of the intestinal microbiome varies considerably between individuals and is correlated with health1. Understanding the extent to which, and how, host genetics contributes to this variation is essential yet has proved to be difficult, as few associations have been replicated, particularly in humans2. Here we study the effect of host genotype on the composition of the intestinal microbiota in a large mosaic pig population. We show that, under conditions of exacerbated genetic diversity and environmental uniformity, microbiota composition and the abundance of specific taxa are heritable. We map a quantitative trait locus affecting the abundance of Erysipelotrichaceae species and show that it is caused by a 2.3 kb deletion in the gene encoding N-acetyl-galactosaminyl-transferase that underpins the ABO blood group in humans. We show that this deletion is a ≥3.5-million-year-old trans-species polymorphism under balancing selection. We demonstrate that it decreases the concentrations of N-acetyl-galactosamine in the gut, and thereby reduces the abundance of Erysipelotrichaceae that can import and catabolize N-acetyl-galactosamine. Our results provide very strong evidence for an effect of the host genotype on the abundance of specific bacteria in the intestine combined with insights into the molecular mechanisms that underpin this association. Our data pave the way towards identifying the same effect in rural human populations. The host blood-type-associated ABO genotype affects the abundance of specific bacteria in the pig intestine.
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21
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Wang Z, Wiggs JL, Aung T, Khawaja AP, Khor CC. The genetic basis for adult onset glaucoma: Recent advances and future directions. Prog Retin Eye Res 2022; 90:101066. [PMID: 35589495 DOI: 10.1016/j.preteyeres.2022.101066] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/26/2022]
Abstract
Glaucoma, a diverse group of eye disorders that results in the degeneration of retinal ganglion cells, is the world's leading cause of irreversible blindness. Apart from age and ancestry, the major risk factor for glaucoma is increased intraocular pressure (IOP). In primary open-angle glaucoma (POAG), the anterior chamber angle is open but there is resistance to aqueous outflow. In primary angle-closure glaucoma (PACG), crowding of the anterior chamber angle due to anatomical alterations impede aqueous drainage through the angle. In exfoliation syndrome and exfoliation glaucoma, deposition of white flaky material throughout the anterior chamber directly interfere with aqueous outflow. Observational studies have established that there is a strong hereditable component for glaucoma onset and progression. Indeed, a succession of genome wide association studies (GWAS) that were centered upon single nucleotide polymorphisms (SNP) have yielded more than a hundred genetic markers associated with glaucoma risk. However, a shortcoming of GWAS studies is the difficulty in identifying the actual effector genes responsible for disease pathogenesis. Building on the foundation laid by GWAS studies, research groups have recently begun to perform whole exome-sequencing to evaluate the contribution of protein-changing, coding sequence genetic variants to glaucoma risk. The adoption of this technology in both large population-based studies as well as family studies are revealing the presence of novel, protein-changing genetic variants that could enrich our understanding of the pathogenesis of glaucoma. This review will cover recent advances in the genetics of primary open-angle glaucoma, primary angle-closure glaucoma and exfoliation glaucoma, which collectively make up the vast majority of all glaucoma cases in the world today. We will discuss how recent advances in research methodology have uncovered new risk genes, and how follow up biological investigations could be undertaken in order to define how the risk encoded by a genetic sequence variant comes into play in patients. We will also hypothesise how data arising from characterising these genetic variants could be utilized to predict glaucoma risk and the manner in which new therapeutic strategies might be informed.
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Affiliation(s)
- Zhenxun Wang
- Duke-NUS Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Tin Aung
- Duke-NUS Medical School, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Chiea Chuen Khor
- Duke-NUS Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore; Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
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22
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Kamran M, Bibi F, ur. Rehman A, Morris DW. Major Depressive Disorder: Existing Hypotheses about Pathophysiological Mechanisms and New Genetic Findings. Genes (Basel) 2022; 13:646. [PMID: 35456452 PMCID: PMC9025468 DOI: 10.3390/genes13040646] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 01/08/2023] Open
Abstract
Major depressive disorder (MDD) is a common mental disorder generally characterized by symptoms associated with mood, pleasure and effectiveness in daily life activities. MDD is ranked as a major contributor to worldwide disability. The complex pathogenesis of MDD is not yet understood, and this is a major cause of failure to develop new therapies and MDD recurrence. Here we summarize the literature on existing hypotheses about the pathophysiological mechanisms of MDD. We describe the different approaches undertaken to understand the molecular mechanism of MDD using genetic data. Hundreds of loci have now been identified by large genome-wide association studies (GWAS). We describe these studies and how they have provided information on the biological processes, cell types, tissues and druggable targets that are enriched for MDD risk genes. We detail our understanding of the genetic correlations and causal relationships between MDD and many psychiatric and non-psychiatric disorders and traits. We highlight the challenges associated with genetic studies, including the complexity of MDD genetics in diverse populations and the need for a study of rare variants and new studies of gene-environment interactions.
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Affiliation(s)
- Muhammad Kamran
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.K.); (A.u.R.)
- Centre for Neuroimaging, Cognition and Genomics (NICOG), Discipline of Biochemistry, National University of Ireland Galway, H91 CF50 Galway, Ireland
| | - Farhana Bibi
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan;
| | - Asim. ur. Rehman
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.K.); (A.u.R.)
| | - Derek W. Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), Discipline of Biochemistry, National University of Ireland Galway, H91 CF50 Galway, Ireland
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23
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Helton JJ, Davis JP, Lee DS, Pakdaman S. Expanding adverse child experiences to inequality and racial discrimination. Prev Med 2022; 157:107016. [PMID: 35301044 DOI: 10.1016/j.ypmed.2022.107016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/30/2021] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Abstract
There is a well-established correlation between health and adverse childhood experiences (ACEs). Arguments have been made to expand ACE scales to include indicators of racism and structural inequalities. In this paper, we use nationally representative data to examine the relationships between latent groups of an expanded adversity scale and a broad range of child health outcomes. Data were obtained from a merger of the 2017 and 2018 National Survey of Children's Health (NSCH) and analyzed in 2021 (n = 52,129). Adversities were defined as violent victimization, violence exposure, a range of parental problems, racial discrimination, food insecurity, and unkempt housing. Latent class analysis (LCA) was used to uncover emergent groups of adversities, and logistic regression was used to assess group relationship to global and diagnosed measures of health. Four groups emerged: high all (3.6%), material and food hardship (11.9%), parental problems (10.3%), and low all (74.2%). Results showed the high all groups at greater odds of almost all outcomes. Compared to low all group, high all had particularly higher odds of any special (OR = 2.29) or complex (OR = 2.53) healthcare need, frequent severe headaches (OR = 2.07), and depression (OR = 3.4) or anxiety (OR = 2.11). Our analysis noted separation of experiences based on additional items related to structural inequalities: food insecurity, poverty, and unkempt housing. However, augmenting existing ACE scales with these indicators may be unnecessary as children most at-risk for poor health were a very small group (1 in 28) that experienced multiple forms of violence and parental problems.
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Affiliation(s)
- Jesse J Helton
- College of Public Health and Social Justice, School of Social Work, St. Louis University, St. Louis, MO, United States of America.
| | - Jordan P Davis
- USC Center for Artificial Intelligence in Society, United States of America; USC Center for Mindfulness Science, United States of America; USC Institute for Addiction Science, United States of America; Suzanne Dworak-Peck School of Social Work, University of Southern California, Los Angeles, CA, United States of America
| | - Daniel S Lee
- Suzanne Dworak-Peck School of Social Work, University of Southern California, Los Angeles, CA, United States of America
| | - Sheila Pakdaman
- Suzanne Dworak-Peck School of Social Work, University of Southern California, Los Angeles, CA, United States of America
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24
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Holm E, Holm M, Vilhelmsen K, Andorsdottir G, Vorum H, Simpson A, Roos BR, Fingert JH, Rosenberg T. Prevalence of Open-angle Glaucoma in the Faroese Population. J Glaucoma 2022; 31:72-78. [PMID: 34342283 PMCID: PMC8795462 DOI: 10.1097/ijg.0000000000001921] [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: 04/08/2021] [Accepted: 07/24/2021] [Indexed: 02/03/2023]
Abstract
PURPOSE The Faroe Islands are home to 50,000 genetically isolated people in the North Atlantic. The prevalence of open-angle glaucoma (OAG) in the Faroese population is unknown. Consequently, we conducted a survey to determine the prevalence of OAG in the Faroese population. We also investigated the role of known glaucoma-causing genes in Faroese OAG. MATERIALS AND METHODS We conducted a prospective survey of known and newly diagnosed glaucoma patients at the Faroese National Hospital, Landssjukrahusid, Tórshavn between October 1, 2015 to December 31, 2017. In addition we reviewed the only eye care provider in the Faroese Islands by scrutinizing electronic medical records between 2009 and June 15, 2014, October 1, 2015 and the partly overlapping prescriptions for ocular hypotensive medications in 2016 to identify patients with either a diagnosis of glaucoma, a diagnosis of ocular hypertension or a prescription for ocular hypotensive medications. Next, we prospectively confirmed diagnoses with complete eye examinations. Patient DNA samples were tested for variations in known glaucoma-causing genes [myocilin (MYOC), optineurin (OPTN), and TANK binding kinase 1 (TBK1)]. RESULTS We determined the age-related prevalence of OAG January 1, 2017 in individuals 40 years or older to be 10.7/1000 (1.07%) and highly age-related. A diagnosis of OAG was present in 264 patients, of whom 211 (79.9%) had primary OAG (including normal tension glaucoma), 49 (18.6%) had pseudoexfoliation glaucoma, and 4 (1.5%) had pigmentary glaucoma. Among patients receiving medications for glaucoma, nearly 50% had primary OAG, while the majority of the rest had ocular hypertension or secondary glaucoma. No disease-causing variants were detected in MYOC, OPTN, or TBK1. CONCLUSIONS The calculated prevalence of OAG in the Faroe Islands was 1.07%. The absence of MYOC, OPTN, or TBK1 disease-causing variants in Faroese primary OAG patients suggests that a different, potentially unique set of genes may be contributing to the pathogenesis of glaucoma in this population.
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Affiliation(s)
| | | | | | | | - Henrik Vorum
- Department of Ophthalmology, University Hospital, Aalborg
| | - Allie Simpson
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Benjamin R Roos
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA
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Jermy BS, Glanville KP, Coleman JRI, Lewis CM, Vassos E. Exploring the genetic heterogeneity in major depression across diagnostic criteria. Mol Psychiatry 2021; 26:7337-7345. [PMID: 34290369 PMCID: PMC8872976 DOI: 10.1038/s41380-021-01231-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 02/05/2023]
Abstract
Major depressive disorder (MDD) is defined differently across genetic research studies and this may be a key source of heterogeneity. While previous literature highlights differences between minimal and strict phenotypes, the components contributing to this heterogeneity have not been identified. Using the cardinal symptoms (depressed mood/anhedonia) as a baseline, we build MDD phenotypes using five components-(1) five or more symptoms, (2) episode duration, (3) functional impairment, (4) episode persistence, and (5) episode recurrence-to determine the contributors to such heterogeneity. Thirty-two depression phenotypes which systematically incorporate different combinations of MDD components were created using the mental health questionnaire data within the UK Biobank. SNP-based heritabilities and genetic correlations with three previously defined major depression phenotypes were calculated (Psychiatric Genomics Consortium (PGC) defined depression, 23andMe self-reported depression and broad depression) and differences between estimates analysed. All phenotypes were heritable (h2SNP range: 0.102-0.162) and showed substantial genetic correlations with other major depression phenotypes (Rg range: 0.651-0.895 (PGC); 0.652-0.837 (23andMe); 0.699-0.900 (broad depression)). The strongest effect on SNP-based heritability was from the requirement for five or more symptoms (1.4% average increase) and for a long episode duration (2.7% average decrease). No significant differences were noted between genetic correlations. While there is some variation, the two cardinal symptoms largely reflect the genetic aetiology of phenotypes incorporating more MDD components. These components may index severity, however, their impact on heterogeneity in genetic results is likely to be limited.
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Affiliation(s)
- Bradley S Jermy
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK.
| | - Kylie P Glanville
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Jonathan R I Coleman
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
- Department of Medical & Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Evangelos Vassos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
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Kalka IN, Gavrieli A, Shilo S, Rossman H, Artzi NS, Yacovzada NS, Segal E. Estimating heritability of glycaemic response to metformin using nationwide electronic health records and population-sized pedigree. COMMUNICATIONS MEDICINE 2021; 1:55. [PMID: 35602224 PMCID: PMC9053254 DOI: 10.1038/s43856-021-00058-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 11/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Variability of response to medication is a well-known phenomenon, determined by both environmental and genetic factors. Understanding the heritable component of the response to medication is of great interest but challenging due to several reasons, including small study cohorts and computational limitations. Methods Here, we study the heritability of variation in the glycaemic response to metformin, first-line therapeutic agent for type 2 diabetes (T2D), by leveraging 18 years of electronic health records (EHR) data from Israel’s largest healthcare service provider, consisting of over five million patients of diverse ethnicities and socio-economic background. Our cohort consists of 80,788 T2D patients treated with metformin, with an accumulated number of 1,611,591 HbA1C measurements and 4,581,097 metformin prescriptions. We estimate the explained variance of glycated hemoglobin (HbA1c%) reduction due to inheritance by constructing a six-generation population-size pedigree from national registries and linking it to medical health records. Results Using Linear Mixed Model-based framework, a common-practice method for heritability estimation, we calculate a heritability measure of \documentclass[12pt]{minimal}
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\begin{document}$$7.8 \%\! -\!34.4 \%$$\end{document}7.8%−34.4%) for males and \documentclass[12pt]{minimal}
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\begin{document}$$10.0 \%\! -\!35.7 \%$$\end{document}10.0%−35.7%) in females. Results remain unchanged after adjusting for pre-treatment HbA1c%, and in proportional reduction of HbA1c%. Conclusions To the best of our knowledge, our work is the first to estimate heritability of drug response using solely EHR data combining a pedigree-based kinship matrix. We demonstrate that while response to metformin treatment has a heritable component, most of the variation is likely due to other factors, further motivating non-genetic analyses aimed at unraveling metformin’s action mechanism. Individuals in a population might respond differently to the same medication and this phenomenon is commonly attributed to either genes or the environment. Here, we studied the familial aspects of the response to metformin, a medication used in the treatment of type 2 diabetes. We combined information from 18 years of medical records identifying newly treated patients with type 2 diabetes with information about how the trait was inherited within their families. We calculated a metric that tells us how well differences in people’s genes account for differences in their traits, and demonstrate that although the difference in response to metformin is in part explained by the genes people with type 2 diabetes inherit, most of it is not explained by genes. This finding contributes to a better understanding of differences in metformin response and might help inform treatment in future. Kalka and Gavrieli et al. assessed the heritability of variation in the glycaemic response to metformin by leveraging electronic health records data gathered from a large cohort of patients with diabetes and combining it with pedigree information. The authors show that although the variability in this response has a heritable component, most of it is likely non-genetic.
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Hamm NC, Hamad AF, Wall-Wieler E, Roos LL, Plana-Ripoll O, Lix LM. Multigenerational health research using population-based linked databases: an international review. Int J Popul Data Sci 2021; 6:1686. [PMID: 34734126 PMCID: PMC8530190 DOI: 10.23889/ijpds.v6i1.1686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Family health history is a well-established risk factor for many health conditions but the systematic collection of health histories, particularly for multiple generations and multiple family members, can be challenging. Routinely-collected electronic databases in a select number of sites worldwide offer a powerful tool to conduct multigenerational health research for entire populations. At these sites, administrative and healthcare records are used to construct familial relationships and objectively-measured health histories. We review and synthesize published literature to compare the attributes of routinely-collected, linked databases for three European sites (Denmark, Norway, Sweden) and three non-European sites (Canadian province of Manitoba, Taiwan, Australian state of Western Australia) with the capability to conduct population-based multigenerational health research. Our review found that European sites primarily identified family structures using population registries, whereas non-European sites used health insurance registries (Manitoba and Taiwan) or linked data from multiple sources (Western Australia). Information on familial status was reported to be available as early as 1947 (Sweden); Taiwan had the fewest years of data available (1995 onwards). All centres reported near complete coverage of familial relationships for their population catchment regions. Challenges in working with these data include differentiating biological and legal relationships, establishing accurate familial linkages over time, and accurately identifying health conditions. This review provides important insights about the benefits and challenges of using routinely-collected, population-based linked databases for conducting population-based multigenerational health research, and identifies opportunities for future research within and across the data-intensive environments at these six sites.
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Affiliation(s)
- Naomi C Hamm
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, CANADA, R3E 0W3
| | - Amani F Hamad
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, CANADA, R3E 0W3
| | - Elizabeth Wall-Wieler
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, CANADA, R3E 0W3.,Manitoba Centre for Health Policy, University of Manitoba, Winnipeg, MB, CANADA, R3E 3P5
| | - Leslie L Roos
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, CANADA, R3E 0W3.,Manitoba Centre for Health Policy, University of Manitoba, Winnipeg, MB, CANADA, R3E 3P5
| | - Oleguer Plana-Ripoll
- National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, DENMARK, 8210
| | - Lisa M Lix
- Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, CANADA, R3E 0W3
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Huang X, Tatonetti N, LaRow K, Delgoffee B, Mayer J, Page D, Hebbring SJ. E-Pedigrees: a large-scale automatic family pedigree prediction application. Bioinformatics 2021; 37:3966-3968. [PMID: 34086863 PMCID: PMC8570807 DOI: 10.1093/bioinformatics/btab419] [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: 01/21/2021] [Revised: 04/30/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The use and functionality of Electronic Health Records (EHR) have increased rapidly in the past few decades. EHRs are becoming an important depository of patient health information and can capture family data. Pedigree analysis is a longstanding and powerful approach that can gain insight into the underlying genetic and environmental factors in human health, but traditional approaches to identifying and recruiting families are low-throughput and labor-intensive. Therefore, high-throughput methods to automatically construct family pedigrees are needed. RESULTS We developed a stand-alone application: Electronic Pedigrees, or E-Pedigrees, which combines two validated family prediction algorithms into a single software package for high throughput pedigrees construction. The convenient platform considers patients' basic demographic information and/or emergency contact data to infer high-accuracy parent-child relationship. Importantly, E-Pedigrees allows users to layer in additional pedigree data when available and provides options for applying different logical rules to improve accuracy of inferred family relationships. This software is fast and easy to use, is compatible with different EHR data sources, and its output is a standard PED file appropriate for multiple downstream analyses. AVAILABILITY AND IMPLEMENTATION The Python 3.3+ version E-Pedigrees application is freely available on: https://github.com/xiayuan-huang/E-pedigrees.
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Affiliation(s)
- Xiayuan Huang
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicholas Tatonetti
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Katie LaRow
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Brooke Delgoffee
- Office of Research Computing and Analytics, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - John Mayer
- Office of Research Computing and Analytics, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - David Page
- Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Scott J Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
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Kendall KM, Van Assche E, Andlauer TFM, Choi KW, Luykx JJ, Schulte EC, Lu Y. The genetic basis of major depression. Psychol Med 2021; 51:2217-2230. [PMID: 33682643 DOI: 10.1017/s0033291721000441] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Major depressive disorder (MDD) is a common, debilitating, phenotypically heterogeneous disorder with heritability ranges from 30% to 50%. Compared to other psychiatric disorders, its high prevalence, moderate heritability, and strong polygenicity have posed major challenges for gene-mapping in MDD. Studies of common genetic variation in MDD, driven by large international collaborations such as the Psychiatric Genomics Consortium, have confirmed the highly polygenic nature of the disorder and implicated over 100 genetic risk loci to date. Rare copy number variants associated with MDD risk were also recently identified. The goal of this review is to present a broad picture of our current understanding of the epidemiology, genetic epidemiology, molecular genetics, and gene-environment interplay in MDD. Insights into the impact of genetic factors on the aetiology of this complex disorder hold great promise for improving clinical care.
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Affiliation(s)
- K M Kendall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - E Van Assche
- Department of Psychiatry, University of Muenster, Muenster, Germany
| | - T F M Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - K W Choi
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA02114, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA02114, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA02115, USA
| | - J J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Outpatient Second Opinion Clinic, GGNet Mental Health, Warnsveld, The Netherlands
| | - E C Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Y Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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30
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Han IC, Burnight ER, Kaalberg EE, Boyce TM, Stone EM, Fingert JH, Mullins RF, Tucker BA, Wiley LA. Chimeric Helper-Dependent Adenoviruses Transduce Retinal Ganglion Cells and Müller Cells in Human Retinal Explants. J Ocul Pharmacol Ther 2021; 37:575-579. [PMID: 34597181 DOI: 10.1089/jop.2021.0057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Purpose: Despite numerous recent advances in retinal gene therapy using adeno-associated viruses (AAVs) as delivery vectors, there remains a crucial need to identify viral vectors with the ability to transduce specific retinal cell types and that have a larger carrying capacity than AAV. In this study, we evaluate the retinal tropism of 2 chimeric helper-dependent adenoviruses (HDAds), helper-dependent adenovirus serotype 5 (HDAd5)/3 and HDAd5/35, both ex vivo using human retinal explants and in vivo using rats. Methods: We transduced cultured human retinal explants with HDAd5/3 and HDAd5/35 carrying an eGFP vector and evaluated tropism and transduction efficiency using immunohistochemistry. To assess in vivo transduction efficiency, subretinal injections were performed in wild-type Sprague-Dawley rats. For both explants and subretinal injections, we delivered 10 μL (1 × 106 vector genomes/mL) and assessed tropism at 7- and 14-days post-transduction, respectively. Results: HDAd5/3 and HDAd5/35 both transduced human retinal ganglion cells (RGCs) and Müller cells, but not photoreceptors, in human retinal explants. However, subretinal injections in albino rats resulted in transduction of the retinal pigmented epithelium only, highlighting species-specific differences in retinal tropism and the value of a human explant model when testing vectors for eventual human gene therapy. Conclusions: Chimeric HDAds are promising candidates for the delivery of large genes, multiple genes, or neuroprotective factors to Müller cells and RGCs. These vectors may have utility for targeted therapy of neurodegenerative diseases primarily involving retinal ganglion or Müller cell types, such as glaucoma or macular telangiectasia type 2.
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Affiliation(s)
- Ian C Han
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Erin R Burnight
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Emily E Kaalberg
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Timothy M Boyce
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Edwin M Stone
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - John H Fingert
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Robert F Mullins
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Budd A Tucker
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Luke A Wiley
- The University of Iowa Institute for Vision Research, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
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Major Depressive Disorder and Lifestyle: Correlated Genetic Effects in Extended Twin Pedigrees. Genes (Basel) 2021; 12:genes12101509. [PMID: 34680904 PMCID: PMC8535260 DOI: 10.3390/genes12101509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/27/2022] Open
Abstract
In recent years, evidence has accumulated with regard to the ubiquity of pleiotropy across the genome, and shared genetic etiology is thought to play a large role in the widespread comorbidity among psychiatric disorders and risk factors. Recent methods investigate pleiotropy by estimating genetic correlation from genome-wide association summary statistics. More comprehensive estimates can be derived from the known relatedness between genetic relatives. Analysis of extended twin pedigree data allows for the estimation of genetic correlation for additive and non-additive genetic effects, as well as a shared household effect. Here we conduct a series of bivariate genetic analyses in extended twin pedigree data on lifetime major depressive disorder (MDD) and three indicators of lifestyle, namely smoking behavior, physical inactivity, and obesity, decomposing phenotypic variance and covariance into genetic and environmental components. We analyze lifetime MDD and lifestyle data in a large multigenerational dataset of 19,496 individuals by variance component analysis in the ‘Mendel’ software. We find genetic correlations for MDD and smoking behavior (rG = 0.249), physical inactivity (rG = 0.161), body-mass index (rG = 0.081), and obesity (rG = 0.155), which were primarily driven by additive genetic effects. These outcomes provide evidence in favor of a shared genetic etiology between MDD and the lifestyle factors.
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Cohen NM, Schwartzman O, Jaschek R, Lifshitz A, Hoichman M, Balicer R, Shlush LI, Barbash G, Tanay A. Personalized lab test models to quantify disease potentials in healthy individuals. Nat Med 2021; 27:1582-1591. [PMID: 34426707 DOI: 10.1038/s41591-021-01468-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 07/12/2021] [Indexed: 12/27/2022]
Abstract
Standardized lab tests are central for patient evaluation, differential diagnosis and treatment. Interpretation of these data is nevertheless lacking quantitative and personalized metrics. Here we report on the modeling of 2.1 billion lab measurements of 92 different lab tests from 2.8 million adults over a span of 18 years. Following unsupervised filtering of 131 chronic conditions and 5,223 drug-test pairs we performed a virtual survey of lab tests distributions in healthy individuals. Age and sex alone explain less than 10% of the within-normal test variance in 89 out of 92 tests. Personalized models based on patients' history explain 60% of the variance for 17 tests and over 36% for half of the tests. This allows for systematic stratification of the risk for future abnormal test levels and subsequent emerging disease. Multivariate modeling of within-normal lab tests can be readily implemented as a basis for quantitative patient evaluation.
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Affiliation(s)
| | - Omer Schwartzman
- Department of Mathematics and Computer Science, Weizmann Institute, Rehovot, Israel.,The Division of Internal Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Ram Jaschek
- Department of Mathematics and Computer Science, Weizmann Institute, Rehovot, Israel
| | - Aviezer Lifshitz
- Department of Mathematics and Computer Science, Weizmann Institute, Rehovot, Israel
| | - Michael Hoichman
- Department of Mathematics and Computer Science, Weizmann Institute, Rehovot, Israel
| | - Ran Balicer
- Innovation Division, Clalit Research Institute, Clalit Health Services, Tel Aviv, Israel
| | - Liran I Shlush
- Department of Immunology, Weizmann Institute, Rehovot, Israel
| | - Gabi Barbash
- Bench to Bedside Program, Weizmann Institute, Rehovot, Israel
| | - Amos Tanay
- Department of Mathematics and Computer Science, Weizmann Institute, Rehovot, Israel.
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He K, Yao L, Zhang J, Li Y, Li C. Construction of Genealogical Knowledge Graphs From Obituaries: Multitask Neural Network Extraction System. J Med Internet Res 2021; 23:e25670. [PMID: 34346903 PMCID: PMC8374669 DOI: 10.2196/25670] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/26/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Background Genealogical information, such as that found in family trees, is imperative for biomedical research such as disease heritability and risk prediction. Researchers have used policyholder and their dependent information in medical claims data and emergency contacts in electronic health records (EHRs) to infer family relationships at a large scale. We have previously demonstrated that online obituaries can be a novel data source for building more complete and accurate family trees. Objective Aiming at supplementing EHR data with family relationships for biomedical research, we built an end-to-end information extraction system using a multitask-based artificial neural network model to construct genealogical knowledge graphs (GKGs) from online obituaries. GKGs are enriched family trees with detailed information including age, gender, death and birth dates, and residence. Methods Built on a predefined family relationship map consisting of 4 types of entities (eg, people’s name, residence, birth date, and death date) and 71 types of relationships, we curated a corpus containing 1700 online obituaries from the metropolitan area of Minneapolis and St Paul in Minnesota. We also adopted data augmentation technology to generate additional synthetic data to alleviate the issue of data scarcity for rare family relationships. A multitask-based artificial neural network model was then built to simultaneously detect names, extract relationships between them, and assign attributes (eg, birth dates and death dates, residence, age, and gender) to each individual. In the end, we assemble related GKGs into larger ones by identifying people appearing in multiple obituaries. Results Our system achieved satisfying precision (94.79%), recall (91.45%), and F-1 measures (93.09%) on 10-fold cross-validation. We also constructed 12,407 GKGs, with the largest one made up of 4 generations and 30 people. Conclusions In this work, we discussed the meaning of GKGs for biomedical research, presented a new version of a corpus with a predefined family relationship map and augmented training data, and proposed a multitask deep neural system to construct and assemble GKGs. The results show our system can extract and demonstrate the potential of enriching EHR data for more genetic research. We share the source codes and system with the entire scientific community on GitHub without the corpus for privacy protection.
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Affiliation(s)
- Kai He
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China.,National Engineering Lab for Big Data Analytics, Xi'an Jiaotong University, Xi'an, China.,Shanxi Province Key Laboratory of Satellite and Terrestrial Network Technology Research and Development, Xian, China
| | - Lixia Yao
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - JiaWei Zhang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China.,National Engineering Lab for Big Data Analytics, Xi'an Jiaotong University, Xi'an, China.,Shanxi Province Key Laboratory of Satellite and Terrestrial Network Technology Research and Development, Xian, China
| | - Yufei Li
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China.,National Engineering Lab for Big Data Analytics, Xi'an Jiaotong University, Xi'an, China.,Shanxi Province Key Laboratory of Satellite and Terrestrial Network Technology Research and Development, Xian, China
| | - Chen Li
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China.,National Engineering Lab for Big Data Analytics, Xi'an Jiaotong University, Xi'an, China.,Shanxi Province Key Laboratory of Satellite and Terrestrial Network Technology Research and Development, Xian, China
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Chung MK, Rappaport SM, Wheelock CE, Nguyen VK, van der Meer TP, Miller GW, Vermeulen R, Patel CJ. Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:85001. [PMID: 34435882 PMCID: PMC8388254 DOI: 10.1289/ehp8327] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/28/2021] [Accepted: 07/13/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Recent developments in technologies have offered opportunities to measure the exposome with unprecedented accuracy and scale. However, because most investigations have targeted only a few exposures at a time, it is hypothesized that the majority of the environmental determinants of chronic diseases remain unknown. OBJECTIVES We describe a functional exposome concept and explain how it can leverage existing bioassays and high-resolution mass spectrometry for exploratory study. We discuss how such an approach can address well-known barriers to interpret exposures and present a vision of next-generation exposomics. DISCUSSION The exposome is vast. Instead of trying to capture all exposures, we can reduce the complexity by measuring the functional exposome-the totality of the biologically active exposures relevant to disease development-through coupling biochemical receptor-binding assays with affinity purification-mass spectrometry. We claim the idea of capturing exposures with functional biomolecules opens new opportunities to solve critical problems in exposomics, including low-dose detection, unknown annotations, and complex mixtures of exposures. Although novel, biology-based measurement can make use of the existing data processing and bioinformatics pipelines. The functional exposome concept also complements conventional targeted and untargeted approaches for understanding exposure-disease relationships. CONCLUSIONS Although measurement technology has advanced, critical technological, analytical, and inferential barriers impede the detection of many environmental exposures relevant to chronic-disease etiology. Through biology-driven exposomics, it is possible to simultaneously scale up discovery of these causal environmental factors. https://doi.org/10.1289/EHP8327.
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Affiliation(s)
- Ming Kei Chung
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen M. Rappaport
- Program in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Craig E. Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Vy Kim Nguyen
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas P. van der Meer
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Gary W. Miller
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Roel Vermeulen
- Utrecht University & Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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35
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Shang N, Khan A, Polubriaginof F, Zanoni F, Mehl K, Fasel D, Drawz PE, Carrol RJ, Denny JC, Hathcock MA, Arruda-Olson AM, Peissig PL, Dart RA, Brilliant MH, Larson EB, Carrell DS, Pendergrass S, Verma SS, Ritchie MD, Benoit B, Gainer VS, Karlson EW, Gordon AS, Jarvik GP, Stanaway IB, Crosslin DR, Mohan S, Ionita-Laza I, Tatonetti NP, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical records-based chronic kidney disease phenotype for clinical care and "big data" observational and genetic studies. NPJ Digit Med 2021; 4:70. [PMID: 33850243 PMCID: PMC8044136 DOI: 10.1038/s41746-021-00428-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Chronic Kidney Disease (CKD) represents a slowly progressive disorder that is typically silent until late stages, but early intervention can significantly delay its progression. We designed a portable and scalable electronic CKD phenotype to facilitate early disease recognition and empower large-scale observational and genetic studies of kidney traits. The algorithm uses a combination of rule-based and machine-learning methods to automatically place patients on the staging grid of albuminuria by glomerular filtration rate ("A-by-G" grid). We manually validated the algorithm by 451 chart reviews across three medical systems, demonstrating overall positive predictive value of 95% for CKD cases and 97% for healthy controls. Independent case-control validation using 2350 patient records demonstrated diagnostic specificity of 97% and sensitivity of 87%. Application of the phenotype to 1.3 million patients demonstrated that over 80% of CKD cases are undetected using ICD codes alone. We also demonstrated several large-scale applications of the phenotype, including identifying stage-specific kidney disease comorbidities, in silico estimation of kidney trait heritability in thousands of pedigrees reconstructed from medical records, and biobank-based multicenter genome-wide and phenome-wide association studies.
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Affiliation(s)
- Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Fernanda Polubriaginof
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Francesca Zanoni
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Karla Mehl
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - David Fasel
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Paul E Drawz
- Department of Medicine, University of Minnesota, Minnesota, MN, USA
| | - Robert J Carrol
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
- Departments of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | | | | | - Richard A Dart
- Marshfield Clinic Research Institute, Marshfield, WI, USA
| | | | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | | | | | | | | | | | | | - Adam S Gordon
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ian B Stanaway
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David R Crosslin
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Sumit Mohan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, USA.
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Guo J, Yuan C, Shang N, Zheng T, Bello NA, Kiryluk K, Weng C, Wang S. Similarity-based health risk prediction using Domain Fusion and electronic health records data. J Biomed Inform 2021; 116:103711. [PMID: 33610881 PMCID: PMC8569826 DOI: 10.1016/j.jbi.2021.103711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/01/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
Electronic Health Record (EHR) data represents a valuable resource for individualized prospective prediction of health conditions. Statistical methods have been developed to measure patient similarity using EHR data, mostly using clinical attributes. Only a handful of recent methods have combined clinical analytics with other forms of similarity analytics, and no unified framework exists yet to measure comprehensive patient similarity. Here, we developed a generic framework named Patient similarity based on Domain Fusion (PsDF). PsDF performs patient similarity assessment on each available domain data separately, and then integrate the affinity information over various domains into a comprehensive similarity metric. We used the integrated patient similarity to support outcome prediction by assigning a risk score to each patient. With extensive simulations, we demonstrated that PsDF outperformed existing risk prediction methods including a random forest classifier, a regression-based model, and a naïve similarity method, especially when heterogeneous signals exist across different domains. Using PsDF and EHR data extracted from the data warehouse of Columbia University Irving Medical Center, we developed two different clinical prediction tools for two different clinical outcomes: incident cases of end stage kidney disease (ESKD) and severe aortic stenosis (AS) requiring valve replacement. We demonstrated that our new prediction method is scalable to large datasets, robust to random missingness, and generalizable to diverse clinical outcomes.
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Affiliation(s)
- Jia Guo
- Department of Biostatistics, Mailman School of Public Health, Columbia University, United States
| | - Chi Yuan
- Department of Biomedical Informatics, Columbia University, United States
| | - Ning Shang
- Department of Biomedical Informatics, Columbia University, United States
| | - Tian Zheng
- Department of Statistics, Columbia University, United States
| | | | | | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, United States
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, United States
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Sivesind TE, Runion T, Branda M, Schilling LM, Dellavalle RP. Dermatologic Research Potential of the Observational Health Data Sciences and Informatics (OHDSI) Network. Dermatology 2021; 238:44-52. [PMID: 33735862 DOI: 10.1159/000514536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/18/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The Observational Health Data Sciences and Informatics (OHDSI) network enables access to billions of deidentified, standardized health records and built-in analytics software for observational health research, with numerous potential applications to dermatology. While the use of the OHDSI has increased steadily over the past several years, review of the literature reveals few studies utilizing OHDSI in dermatology. To our knowledge, the University of Colorado School of Medicine is unique in its use of OHDSI for dermatology big data research. SUMMARY A PubMed search was conducted in August 2020, followed by a literature review, with 24 of the 72 screened articles selected for inclusion. In this review, we discuss the ways OHDSI has been used to compile and analyze data, improve prediction and estimation capabilities, and inform treatment guidelines across specialties. We also discuss the potential for OHDSI in dermatology - specifically, ways that it could reveal adherence to available guidelines, establish standardized protocols, and ensure health equity. Key Messages: OHDSI has demonstrated broad utility in medicine. Adoption of OHDSI by the field of dermatology would facilitate big data research, allow for examination of current prescribing and treatment patterns without clear best practice guidelines, improve the dermatologic knowledge base and, by extension, improve patient outcomes.
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Affiliation(s)
- Torunn Elise Sivesind
- Department of Dermatology, University of Colorado School of Medicine, Aurora, Colorado, USA,
| | - Taylor Runion
- Rocky Vista University College of Osteopathic Medicine, Parker, Colorado, USA
| | - Megan Branda
- Department of Biostatistics and Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Lisa M Schilling
- Department of Medicine, Data Science to Patient Value Program Aurora, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Robert P Dellavalle
- Department of Dermatology, University of Colorado School of Medicine, Aurora, Colorado, USA
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Campbell-Salome G, Jones LK, Masnick MF, Walton NA, Ahmed CD, Buchanan AH, Brangan A, Esplin ED, Kann DG, Ladd IG, Kelly MA, Kindt I, Kirchner HL, McGowan MP, McMinn MN, Morales A, Myers KD, Oetjens MT, Rahm AK, Schmidlen TJ, Sheldon A, Simmons E, Snir M, Strande NT, Walters NL, Wilemon K, Williams MS, Gidding SS, Sturm AC. Developing and Optimizing Innovative Tools to Address Familial Hypercholesterolemia Underdiagnosis: Identification Methods, Patient Activation, and Cascade Testing for Familial Hypercholesterolemia. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e003120. [PMID: 33480803 PMCID: PMC7892261 DOI: 10.1161/circgen.120.003120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background: Familial hypercholesterolemia (FH) is the most common cardiovascular genetic disorder and, if left untreated, is associated with increased risk of premature atherosclerotic cardiovascular disease, the leading cause of preventable death in the United States. Although FH is common, fatal, and treatable, it is underdiagnosed and undertreated due to a lack of systematic methods to identify individuals with FH and limited uptake of cascade testing. Methods and Results: This mixed-method, multi-stage study will optimize, test, and implement innovative approaches for both FH identification and cascade testing in 3 aims. To improve identification of individuals with FH, in Aim 1, we will compare and refine automated phenotype-based and genomic approaches to identify individuals likely to have FH. To improve cascade testing uptake for at-risk individuals, in Aim 2, we will use a patient-centered design thinking process to optimize and develop novel, active family communication methods. Using a prospective, observational pragmatic trial, we will assess uptake and effectiveness of each family communication method on cascade testing. Guided by an implementation science framework, in Aim 3, we will develop a comprehensive guide to identify individuals with FH. Using the Conceptual Model for Implementation Research, we will evaluate implementation outcomes including feasibility, acceptability, and perceived sustainability as well as health outcomes related to the optimized methods and tools developed in Aims 1 and 2. Conclusions: Data generated from this study will address barriers and gaps in care related to underdiagnosis of FH by developing and optimizing tools to improve FH identification and cascade testing.
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Affiliation(s)
- Gemme Campbell-Salome
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Laney K Jones
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Max F Masnick
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Nephi A Walton
- Intermountain Precision Genomics, Intermountain Healthcare, St. George, UT (N.A.W.)
| | - Catherine D Ahmed
- The Familial Hypercholesterolemia Foundation, Pasadena, CA (C.D.A., M.P.M., K.D.M., A.S., K.W.)
| | - Adam H Buchanan
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Andrew Brangan
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | | | - David G Kann
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Ilene G Ladd
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Melissa A Kelly
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | | | - H Lester Kirchner
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Mary P McGowan
- The Familial Hypercholesterolemia Foundation, Pasadena, CA (C.D.A., M.P.M., K.D.M., A.S., K.W.).,Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, NH (M.P.M.)
| | - Megan N McMinn
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Ana Morales
- Invitae, San Francisco, CA (E.D.E., A.M., E.S., M.S.)
| | - Kelly D Myers
- The Familial Hypercholesterolemia Foundation, Pasadena, CA (C.D.A., M.P.M., K.D.M., A.S., K.W.)
| | - Matthew T Oetjens
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Alanna Kulchak Rahm
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Tara J Schmidlen
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Amanda Sheldon
- The Familial Hypercholesterolemia Foundation, Pasadena, CA (C.D.A., M.P.M., K.D.M., A.S., K.W.)
| | | | - Moran Snir
- Invitae, San Francisco, CA (E.D.E., A.M., E.S., M.S.)
| | - Natasha T Strande
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Nicole L Walters
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Katherine Wilemon
- The Familial Hypercholesterolemia Foundation, Pasadena, CA (C.D.A., M.P.M., K.D.M., A.S., K.W.)
| | - Marc S Williams
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Samuel S Gidding
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
| | - Amy C Sturm
- Geisinger, Danville, PA (G.C.-S., L.K.J., M.F.M., A.H.B., A.B., D.G.K., I.G.L., M.A.K., H.L.K., M.N.M., M.T.O., A.K.R., T.J.S., N.T.S., N.L.W., M.S.W., S.S.G., A.C.S.)
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Silventoinen K, Konttinen H. Obesity and eating behavior from the perspective of twin and genetic research. Neurosci Biobehav Rev 2021; 109:150-165. [PMID: 31959301 DOI: 10.1016/j.neubiorev.2019.12.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/11/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
Abstract
Obesity has dramatically increased during the last decades and is currently one of the most serious global health problems. We present a hypothesis that obesity is a neuro-behavioral disease having a strong genetic background mediated largely by eating behavior and is sensitive to the macro-environment; we study this hypothesis from the perspective of genetic research. Genetic family and genome-wide-association studies have shown well that body mass index (BMI, kg/m2) is a highly heritable and polygenic trait. New genetic variation of BMI emerges after early childhood. Candidate genes of BMI notably express in brain tissue, supporting that this new variation is related to behavior. Obesogenic environments at both childhood family and societal levels reinforce the genetic susceptibility to obesity. Genetic factors have a clear influence on macro-nutrient intake and appetite-related eating behavior traits. Results on the gene-by-diet interactions in obesity are mixed, but emerging evidence suggests that eating behavior traits partly mediate the effect of genes on BMI. However, more rigorous prospective study designs controlling for measurement bias are still needed.
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Affiliation(s)
- Karri Silventoinen
- Department of Social Research, University of Helsinki, Helsinki, Finland; Department of Public Health, University of Helsinki, Helsinki, Finland.
| | - Hanna Konttinen
- Department of Social Research, University of Helsinki, Helsinki, Finland
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40
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Thangaraj PM, Kummer BR, Lorberbaum T, Elkind MSV, Tatonetti NP. Comparative analysis, applications, and interpretation of electronic health record-based stroke phenotyping methods. BioData Min 2020; 13:21. [PMID: 33372632 PMCID: PMC7720570 DOI: 10.1186/s13040-020-00230-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 11/15/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Accurate identification of acute ischemic stroke (AIS) patient cohorts is essential for a wide range of clinical investigations. Automated phenotyping methods that leverage electronic health records (EHRs) represent a fundamentally new approach cohort identification without current laborious and ungeneralizable generation of phenotyping algorithms. We systematically compared and evaluated the ability of machine learning algorithms and case-control combinations to phenotype acute ischemic stroke patients using data from an EHR. MATERIALS AND METHODS Using structured patient data from the EHR at a tertiary-care hospital system, we built and evaluated machine learning models to identify patients with AIS based on 75 different case-control and classifier combinations. We then estimated the prevalence of AIS patients across the EHR. Finally, we externally validated the ability of the models to detect AIS patients without AIS diagnosis codes using the UK Biobank. RESULTS Across all models, we found that the mean AUROC for detecting AIS was 0.963 ± 0.0520 and average precision score 0.790 ± 0.196 with minimal feature processing. Classifiers trained with cases with AIS diagnosis codes and controls with no cerebrovascular disease codes had the best average F1 score (0.832 ± 0.0383). In the external validation, we found that the top probabilities from a model-predicted AIS cohort were significantly enriched for AIS patients without AIS diagnosis codes (60-150 fold over expected). CONCLUSIONS Our findings support machine learning algorithms as a generalizable way to accurately identify AIS patients without using process-intensive manual feature curation. When a set of AIS patients is unavailable, diagnosis codes may be used to train classifier models.
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Affiliation(s)
- Phyllis M Thangaraj
- Department of Biomedical Informatics, Columbia University, 622 W 168th St., PH-20, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Benjamin R Kummer
- Department of Neurology, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - Tal Lorberbaum
- Department of Biomedical Informatics, Columbia University, 622 W 168th St., PH-20, New York, NY, 10032, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Mitchell S V Elkind
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Columbia University, 622 W 168th St., PH-20, New York, NY, 10032, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA.
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Zhang Q, Liu Z, Li J, Liu G. Identifying Diabetic Macular Edema and Other Retinal Diseases by Optical Coherence Tomography Image and Multiscale Deep Learning. Diabetes Metab Syndr Obes 2020; 13:4787-4800. [PMID: 33304104 PMCID: PMC7723239 DOI: 10.2147/dmso.s288419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/21/2020] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Diabetic Macular Edema has been one of the research hotspots all over the world. But as the global population continues to grow, the number of OCT images requiring manual analysis is becoming increasingly unaffordable. Medical images are often fuzzy due to the inherent physical processes of acquiring them. It is difficult for traditional algorithms to use low-quality data. And traditional algorithms usually only provide diagnostic results, which makes the reliability and interpretability of the model face challenges. To solve problem above, we proposed a more intuitive and robust diagnosis model with self-enhancement ability and clinical triage patients' ability. METHODS We used 38,057 OCT images (Drusen, DME, CNV and Normal) to establish and evaluate the model. All data are OCT images of fundus retina. There were 37,457 samples in the training dataset and 600 samples in the validation dataset. In order to diagnose these images accurately, we propose a multiscale transfer learning algorithm. Firstly, the sample is sent to the automatic self-enhancement module for edge detection and enhancement. Then, the processed data are sent to the image diagnosis module to determine the disease type. This process makes more data more effective and can be accurately classified. Finally, we calculated the accuracy, precision, sensitivity and specificity of the model, and verified the performance of the model from the perspective of clinical application. RESULTS The model proposed in this paper can provide the diagnosis results and display the detection targets more intuitively. The model reached 94.5% accuracy, 97.2% precision, 97.7% sensitivity and 97% specificity in the independent testing dataset. CONCLUSION Comparing the performance of relevant work and ablation test, our model achieved relatively good performance. It is proved that the model proposed in this paper has a stronger ability to recognize diseases even in the face of low-quality images. Experiment results also demonstrate its clinical referral capability. It can reduce the workload of medical staff and save the precious time of patients.
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Affiliation(s)
- Quan Zhang
- College of Electronic Information and Optical Engineering, Nankai University, Tianjin300350, People’s Republic of China
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Nankai University, Tianjin300350, People’s Republic of China
| | - Zhiang Liu
- College of Computer Science, Nankai University, Tianjin300350, People’s Republic of China
| | - Jiaxu Li
- The Second Affiliated Hospital of Harbin Medical University, Department of Plastic and Cosmetic Surgery, Harbin, Heilongjiang, 150081, People’s Republic of China
| | - Guohua Liu
- College of Electronic Information and Optical Engineering, Nankai University, Tianjin300350, People’s Republic of China
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Nankai University, Tianjin300350, People’s Republic of China
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Swietlik EM, Prapa M, Martin JM, Pandya D, Auckland K, Morrell NW, Gräf S. 'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1408. [PMID: 33256119 PMCID: PMC7760524 DOI: 10.3390/genes11121408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.
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Affiliation(s)
- Emilia M. Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matina Prapa
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Jennifer M. Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Kathryn Auckland
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
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Merikangas AK, Almasy L. Using the tools of genetic epidemiology to understand sex differences in neuropsychiatric disorders. GENES BRAIN AND BEHAVIOR 2020; 19:e12660. [PMID: 32348611 PMCID: PMC7507200 DOI: 10.1111/gbb.12660] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/01/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023]
Abstract
Many neuropsychiatric disorders exhibit differences in prevalence, age of onset, symptoms or course of illness between males and females. For the most part, the origins of these differences are not well understood. In this article, we provide an overview of sex differences in psychiatric disorders including autism spectrum disorder (ASD), attention deficit/hyperactivity disorder (ADHD), anxiety, depression, alcohol and substance abuse, schizophrenia, eating disorders and risk of suicide. We discuss both genetic and nongenetic mechanisms that have been hypothesized to underlie these differences, including ascertainment bias, environmental stressors, X‐ or Y‐linked risk loci, and differential liability thresholds in males and females. We then review the use of twin, family and genome‐wide association approaches to study potential genetic mechanisms of sex differences and the extent to which these designs have been employed in studies of psychiatric disorders. We describe the utility of genetic epidemiologic study designs, including classical twin and family studies, large‐scale studies of population registries, derived recurrence risks, and molecular genetic analyses of genome‐wide variation that may enhance our understanding sex differences in neuropsychiatric disorders.
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Affiliation(s)
- Alison K Merikangas
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Penn-CHOP Lifespan Brain Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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DOĞAN İ, DOGAN N. Kalıtım Derecesinin Tahmini ve İnsan Hastalıklarının/Özelliklerinin Kalıtsallığı. DÜZCE ÜNIVERSITESI SAĞLIK BILIMLERI ENSTITÜSÜ DERGISI 2020. [DOI: 10.33631/duzcesbed.679732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Toxo: a library for calculating penetrance tables of high-order epistasis models. BMC Bioinformatics 2020; 21:138. [PMID: 32272874 PMCID: PMC7147067 DOI: 10.1186/s12859-020-3456-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 03/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains the probability of expressing the phenotype under study given a particular allele combination. Available simulators can only create penetrance tables for well-known epistasis models involving a small number of genes and under a large number of limitations. Results Toxo is a MATLAB library designed to calculate penetrance tables of epistasis models of any interaction order which resemble real data more closely. The user specifies the desired heritability (or prevalence) and the program maximizes the table’s prevalence (or heritability) according to the input epistatic model boundaries. Conclusions Toxo extends the capabilities of existing simulators that define epistasis using penetrance tables. These tables can be directly used as input for software simulators such as GAMETES so that they are able to generate data samples with larger interactions and more realistic prevalences/heritabilities.
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Hanson HA, Leiser CL, Madsen MJ, Gardner J, Knight S, Cessna M, Sweeney C, Doherty JA, Smith KR, Bernard PS, Camp NJ. Family Study Designs Informed by Tumor Heterogeneity and Multi-Cancer Pleiotropies: The Power of the Utah Population Database. Cancer Epidemiol Biomarkers Prev 2020; 29:807-815. [PMID: 32098891 PMCID: PMC7168701 DOI: 10.1158/1055-9965.epi-19-0912] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/15/2020] [Accepted: 02/18/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Previously, family-based designs and high-risk pedigrees have illustrated value for the discovery of high- and intermediate-risk germline breast cancer susceptibility genes. However, genetic heterogeneity is a major obstacle hindering progress. New strategies and analytic approaches will be necessary to make further advances. One opportunity with the potential to address heterogeneity via improved characterization of disease is the growing availability of multisource databases. Specific to advances involving family-based designs are resources that include family structure, such as the Utah Population Database (UPDB). To illustrate the broad utility and potential power of multisource databases, we describe two different novel family-based approaches to reduce heterogeneity in the UPDB. METHODS Our first approach focuses on using pedigree-informed breast tumor phenotypes in gene mapping. Our second approach focuses on the identification of families with similar pleiotropies. We use a novel network-inspired clustering technique to explore multi-cancer signatures for high-risk breast cancer families. RESULTS Our first approach identifies a genome-wide significant breast cancer locus at 2q13 [P = 1.6 × 10-8, logarithm of the odds (LOD) equivalent 6.64]. In the region, IL1A and IL1B are of particular interest, key cytokine genes involved in inflammation. Our second approach identifies five multi-cancer risk patterns. These clusters include expected coaggregations (such as breast cancer with prostate cancer, ovarian cancer, and melanoma), and also identify novel patterns, including coaggregation with uterine, thyroid, and bladder cancers. CONCLUSIONS Our results suggest pedigree-informed tumor phenotypes can map genes for breast cancer, and that various different cancer pleiotropies exist for high-risk breast cancer pedigrees. IMPACT Both methods illustrate the potential for decreasing etiologic heterogeneity that large, population-based multisource databases can provide.See all articles in this CEBP Focus section, "Modernizing Population Science."
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Affiliation(s)
- Heidi A Hanson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah.
- Utah Population Database, University of Utah, Salt Lake City, Utah
- Department of Surgery, University of Utah, Salt Lake City, Utah
| | - Claire L Leiser
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Michael J Madsen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - John Gardner
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Melissa Cessna
- Intermountain Biorepository, Intermountain Healthcare, Salt Lake City, Utah
- Department of Pathology, Intermountain Medical Center, Intermountain Healthcare, Salt Lake City, Utah
| | - Carol Sweeney
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Utah Cancer Registry, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jennifer A Doherty
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Utah Cancer Registry, University of Utah, Salt Lake City, Utah
- Department of Population Sciences, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ken R Smith
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Utah Population Database, University of Utah, Salt Lake City, Utah
- Department of Family and Consumer Studies, University of Utah, Salt Lake City, Utah
| | - Philip S Bernard
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Nicola J Camp
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Utah Population Database, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah
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Li R, Chen Y, Ritchie MD, Moore JH. Electronic health records and polygenic risk scores for predicting disease risk. Nat Rev Genet 2020; 21:493-502. [PMID: 32235907 DOI: 10.1038/s41576-020-0224-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2020] [Indexed: 01/03/2023]
Abstract
Accurate prediction of disease risk based on the genetic make-up of an individual is essential for effective prevention and personalized treatment. Nevertheless, to date, individual genetic variants from genome-wide association studies have achieved only moderate prediction of disease risk. The aggregation of genetic variants under a polygenic model shows promising improvements in prediction accuracies. Increasingly, electronic health records (EHRs) are being linked to patient genetic data in biobanks, which provides new opportunities for developing and applying polygenic risk scores in the clinic, to systematically examine and evaluate patient susceptibilities to disease. However, the heterogeneous nature of EHR data brings forth many practical challenges along every step of designing and implementing risk prediction strategies. In this Review, we present the unique considerations for using genotype and phenotype data from biobank-linked EHRs for polygenic risk prediction.
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Affiliation(s)
- Ruowang Li
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason H Moore
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA.
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Krigel A, Tatonetti NP, Neugut AI, Lebwohl B. No Increased Risk of Colorectal Adenomas in Spouses of Patients with Colorectal Neoplasia. Clin Gastroenterol Hepatol 2020; 18:509-510. [PMID: 30928453 PMCID: PMC10855025 DOI: 10.1016/j.cgh.2019.03.038] [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: 12/04/2018] [Revised: 03/18/2019] [Accepted: 03/24/2019] [Indexed: 02/07/2023]
Abstract
Although genetic factors such as family history have been associated with increased risk of developing colorectal cancer (CRC), multiple lifestyle and environmental risk factors for CRC have been identified, including smoking, diet, obesity, and physical activity.1,2 Although couples typically have different genetic backgrounds, spouses are likely to share lifestyle and environmental exposures over the course of years, including similar home environments, geographical locations of residence, dietary exposures, and smoking exposures.3 As such, one might expect that an increased CRC incidence would be seen among spouses of patients with CRC; however, studies on this topic have inconsistent results.3-6 By using a large cohort of spouses who have undergone colonoscopy, we aimed to determine whether the risk of colorectal adenomas is increased among spouses of those with colorectal neoplasia (CRN) on colonoscopy.
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Affiliation(s)
- Anna Krigel
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, New York, New York.
| | - Nicholas P Tatonetti
- Division of Biomedical Informatics, Columbia University Medical Center, New York, New York
| | - Alfred I Neugut
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Benjamin Lebwohl
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, New York, New York; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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Jia G, Li Y, Zhang H, Chattopadhyay I, Boeck Jensen A, Blair DR, Davis L, Robinson PN, Dahlén T, Brunak S, Benson M, Edgren G, Cox NJ, Gao X, Rzhetsky A. Estimating heritability and genetic correlations from large health datasets in the absence of genetic data. Nat Commun 2019; 10:5508. [PMID: 31796735 PMCID: PMC6890770 DOI: 10.1038/s41467-019-13455-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/08/2019] [Indexed: 11/17/2022] Open
Abstract
Typically, estimating genetic parameters, such as disease heritability and between-disease genetic correlations, demands large datasets containing all relevant phenotypic measures and detailed knowledge of family relationships or, alternatively, genotypic and phenotypic data for numerous unrelated individuals. Here, we suggest an alternative, efficient estimation approach through the construction of two disease metrics from large health datasets: temporal disease prevalence curves and low-dimensional disease embeddings. We present eleven thousand heritability estimates corresponding to five study types: twins, traditional family studies, health records-based family studies, single nucleotide polymorphisms, and polygenic risk scores. We also compute over six hundred thousand estimates of genetic, environmental and phenotypic correlations. Furthermore, we find that: (1) disease curve shapes cluster into five general patterns; (2) early-onset diseases tend to have lower prevalence than late-onset diseases (Spearman's ρ = 0.32, p < 10-16); and (3) the disease onset age and heritability are negatively correlated (ρ = -0.46, p < 10-16).
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Affiliation(s)
- Gengjie Jia
- Department of Medicine, Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Yu Li
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Hanxin Zhang
- Department of Medicine, Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
- Committee on Genomics, Genetics, and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Ishanu Chattopadhyay
- Department of Medicine, Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Anders Boeck Jensen
- Institute for Next Generation Healthcare, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - David R Blair
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Lea Davis
- Division of Genetic Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Peter N Robinson
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Torsten Dahlén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1017, Denmark
| | - Mikael Benson
- Centre for Individualized Medicine, Department of Pediatrics, Linkoping University, Linkoping, 58183, Sweden
| | - Gustaf Edgren
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Andrey Rzhetsky
- Department of Medicine, Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
- Committee on Genomics, Genetics, and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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Oliynyk RT. Future Preventive Gene Therapy of Polygenic Diseases from a Population Genetics Perspective. Int J Mol Sci 2019; 20:E5013. [PMID: 31658652 PMCID: PMC6834143 DOI: 10.3390/ijms20205013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
With the accumulation of scientific knowledge of the genetic causes of common diseases and continuous advancement of gene-editing technologies, gene therapies to prevent polygenic diseases may soon become possible. This study endeavored to assess population genetics consequences of such therapies. Computer simulations were used to evaluate the heterogeneity in causal alleles for polygenic diseases that could exist among geographically distinct populations. The results show that although heterogeneity would not be easily detectable by epidemiological studies following population admixture, even significant heterogeneity would not impede the outcomes of preventive gene therapies. Preventive gene therapies designed to correct causal alleles to a naturally-occurring neutral state of nucleotides would lower the prevalence of polygenic early- to middle-age-onset diseases in proportion to the decreased population relative risk attributable to the edited alleles. The outcome would manifest differently for late-onset diseases, for which the therapies would result in a delayed disease onset and decreased lifetime risk; however, the lifetime risk would increase again with prolonging population life expectancy, which is a likely consequence of such therapies. If the preventive heritable gene therapies were to be applied on a large scale, the decreasing frequency of risk alleles in populations would reduce the disease risk or delay the age of onset, even with a fraction of the population receiving such therapies. With ongoing population admixture, all groups would benefit over generations.
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Affiliation(s)
- Roman Teo Oliynyk
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand.
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand.
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