1
|
Rivera NV. Big data in sarcoidosis. Curr Opin Pulm Med 2024:00063198-990000000-00180. [PMID: 38967053 DOI: 10.1097/mcp.0000000000001102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
PURPOSE OF REVIEW This review provides an overview of recent advancements in sarcoidosis research, focusing on collaborative networks, phenotype characterization, and molecular studies. It highlights the importance of collaborative efforts, phenotype characterization, and the integration of multilevel molecular data for advancing sarcoidosis research and paving the way toward personalized medicine. RECENT FINDINGS Sarcoidosis exhibits heterogeneous clinical manifestations influenced by various factors. Efforts to define sarcoidosis endophenotypes show promise, while technological advancements enable extensive molecular data generation. Collaborative networks and biobanks facilitate large-scale studies, enhancing biomarker discovery and therapeutic protocols. SUMMARY Sarcoidosis presents a complex challenge due to its unknown cause and heterogeneous clinical manifestations. Collaborative networks, comprehensive phenotype delineation, and the utilization of cutting-edge technologies are essential for advancing our understanding of sarcoidosis biology and developing personalized medicine approaches. Leveraging large-scale epidemiological resources and biobanks and integrating multilevel molecular data offer promising avenues for unraveling the disease's heterogeneity and improving patient outcomes.
Collapse
Affiliation(s)
- Natalia V Rivera
- Division of Respiratory Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
2
|
Irvin MR, Ge T, Patki A, Srinivasasainagendra V, Armstrong ND, Davis B, Jones AC, Perez E, Stalbow L, Lebo M, Kenny E, Loos RJ, Ng MC, Smoller JW, Meigs JB, Lange LA, Karlson EW, Limdi NA, Tiwari HK. Polygenic Risk for Type 2 Diabetes in African Americans. Diabetes 2024; 73:993-1001. [PMID: 38470993 PMCID: PMC11109789 DOI: 10.2337/db23-0232] [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: 03/25/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
African Americans (AAs) have been underrepresented in polygenic risk score (PRS) studies. Here, we integrated genome-wide data from multiple observational studies on type 2 diabetes (T2D), encompassing a total of 101,987 AAs, to train and optimize an AA-focused T2D PRS (PRSAA), using a Bayesian polygenic modeling method. We further tested the score in three independent studies with a total of 7,275 AAs and compared the PRSAA with other published scores. Results show that a 1-SD increase in the PRSAA was associated with 40-60% increase in the odds of T2D (odds ratio [OR] 1.60, 95% CI 1.37-1.88; OR 1.40, 95% CI 1.16-1.70; and OR 1.45, 95% CI 1.30-1.62) across three testing cohorts. These models captured 1.0-2.6% of the variance (R2) in T2D on the liability scale. The positive predictive values for three calculated score thresholds (the top 2%, 5%, and 10%) ranged from 14 to 35%. The PRSAA, in general, performed similarly to existing T2D PRS. The need remains for larger data sets to continue to evaluate the utility of within-ancestry scores in the AA population. ARTICLE HIGHLIGHTS
Collapse
Affiliation(s)
- Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Nicole D. Armstrong
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Brittney Davis
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Alana C. Jones
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Emma Perez
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Mass General Brigham Personalized Medicine, Boston, MA
| | - Lauren Stalbow
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Matthew Lebo
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
- Mass General Brigham Personalized Medicine, Boston, MA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Eimear Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Maggie C.Y. Ng
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Jordan W. Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - James B. Meigs
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Massachusetts General Hospital, Boston, MA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Leslie A. Lange
- Department of Epidemiology, University of Colorado School of Public Health, Aurora, CO
| | - Elizabeth W. Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
- Mass General Brigham Personalized Medicine, Boston, MA
| | - Nita A. Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Hemant K. Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| |
Collapse
|
3
|
Stewart DR. Genomic ascertainment of primary central nervous system cancers in adolescents and young adults. Neurooncol Adv 2024; 6:vdae048. [PMID: 38800695 PMCID: PMC11125399 DOI: 10.1093/noajnl/vdae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024] Open
Abstract
Genomic ascertainment is the inversion of the traditional phenotype-first approach; with a "genome-first" approach, a cohort linked to electronic health records (EHR) undergoes germline sequencing (array, panel, exome, and genome) and deleterious variation of interest in a gene (or set of genes) are identified. Phenotype is then queried from the linked EHR and from call-back investigation and estimates of variant prevalence, disease penetrance, and phenotype can be determined. This should permit a better estimate of the full phenotypic spectrum, severity, and penetrance linked to a deleterious variant. For now, given the modest size, limited EHR, and age of participants in sequenced cohorts, genomic ascertainment approaches to investigate cancer in children and young adults will likely be restricted to descriptive studies and complement traditional phenotype-first work. Another issue is the ascertainment of the cohort itself: Participants need to survive long enough to enroll. Not accounting for this may lead to bias and incorrect estimates of variant prevalence. Adult-focused cohorts with EHR extending back into childhood, linked to cancer registries, and/or studies that permit recontact with participants may facilitate genomic ascertainment in pediatric cancer research. In summary, genomic ascertainment in pediatric primary brain cancer research remains largely untapped and merits further investigation.
Collapse
Affiliation(s)
- Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland, USA
| |
Collapse
|
4
|
Nadkarni GN, Stapleton S, Takale D, Edwards K, Moran K, Mosoyan G, Hansen MK, Donovan MJ, Heerspink HJL, Fleming F, Coca SG. Derivation and independent validation of kidneyintelX.dkd: A prognostic test for the assessment of diabetic kidney disease progression. Diabetes Obes Metab 2023; 25:3779-3787. [PMID: 37722962 DOI: 10.1111/dom.15273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/20/2023]
Abstract
AIMS To develop and validate an updated version of KidneyIntelX (kidneyintelX.dkd) to stratify patients for risk of progression of diabetic kidney disease (DKD) stages 1 to 3, to simplify the test for clinical adoption and support an application to the US Food and Drug Administration regulatory pathway. METHODS We used plasma biomarkers and clinical data from the Penn Medicine Biobank (PMBB) for training, and independent cohorts (BioMe and CANVAS) for validation. The primary outcome was progressive decline in kidney function (PDKF), defined by a ≥40% sustained decline in estimated glomerular filtration rate or end-stage kidney disease within 5 years of follow-up. RESULTS In 573 PMBB participants with DKD, 15.4% experienced PDKF over a median of 3.7 years. We trained a random forest model using biomarkers and clinical variables. Among 657 BioMe participants and 1197 CANVAS participants, 11.7% and 7.5%, respectively, experienced PDKF. Based on training cut-offs, 57%, 35% and 8% of BioMe participants, and 56%, 38% and 6% of CANVAS participants were classified as having low-, moderate- and high-risk levels, respectively. The cumulative incidence at these risk levels was 5.9%, 21.2% and 66.9% in BioMe and 6.7%, 13.1% and 59.6% in CANVAS. After clinical risk factor adjustment, the adjusted hazard ratios were 7.7 (95% confidence interval [CI] 3.0-19.6) and 3.7 (95% CI 2.0-6.8) in BioMe, and 5.4 (95% CI 2.5-11.9) and 2.3 (95% CI 1.4-3.9) in CANVAS, for high- versus low-risk and moderate- versus low-risk levels, respectively. CONCLUSIONS Using two independent cohorts and a clinical trial population, we validated an updated KidneyIntelX test (named kidneyintelX.dkd), which significantly enhanced risk stratification in patients with DKD for PDKF, independently from known risk factors for progression.
Collapse
Affiliation(s)
- Girish N Nadkarni
- Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Digital and Data Driven Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | - Kara Moran
- Renalytix AI, PLC, New York, New York, USA
| | - Gohar Mosoyan
- Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael K Hansen
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | - Hiddo J L Heerspink
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, Groningen, The Netherlands
| | | | - Steven G Coca
- Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
5
|
Hoffmann TJ, Graff RE, Madduri RK, Rodriguez AA, Cario CL, Feng K, Jiang Y, Wang A, Klein RJ, Pierce BL, Eggener S, Tong L, Blot W, Long J, Rebbeck T, Lachance J, Andrews C, Adebiyi AO, Adusei B, Aisuodionoe-Shadrach OI, Fernandez PW, Jalloh M, Janivara R, Chen WC, Mensah JE, Agalliu I, Berndt SI, Shelley JP, Schaffer K, Machiela MJ, Freedman ND, Huang WY, Li SA, Goodman PJ, Till C, Thompson I, Lilja H, Van Den Eeden SK, Chanock SJ, Mosley JD, Conti DV, Haiman CA, Justice AC, Kachuri L, Witte JS. Genome-wide association study of prostate-specific antigen levels in 392,522 men identifies new loci and improves cross-ancestry prediction. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.27.23297676. [PMID: 37961155 PMCID: PMC10635224 DOI: 10.1101/2023.10.27.23297676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
We conducted a multi-ancestry genome-wide association study of prostate-specific antigen (PSA) levels in 296,754 men (211,342 European ancestry; 58,236 African ancestry; 23,546 Hispanic/Latino; 3,630 Asian ancestry; 96.5% of participants were from the Million Veteran Program). We identified 318 independent genome-wide significant (p≤5e-8) variants, 184 of which were novel. Most demonstrated evidence of replication in an independent cohort (n=95,768). Meta-analyzing discovery and replication (n=392,522) identified 447 variants, of which a further 111 were novel. Out-of-sample variance in PSA explained by our new polygenic risk score reached 16.9% (95% CI=16.1%-17.8%) in European ancestry, 9.5% (95% CI=7.0%-12.2%) in African ancestry, 18.6% (95% CI=15.8%-21.4%) in Hispanic/Latino, and 15.3% (95% CI=12.7%-18.1%) in Asian ancestry, and lower for higher age. Our study highlights how including proportionally more participants from underrepresented populations improves genetic prediction of PSA levels, with potential to personalize prostate cancer screening.
Collapse
|
6
|
Forrest IS, O’Neal AJ, Pedra JHF, Do R. Cholesterol Contributes to Risk, Severity, and Machine Learning-Driven Diagnosis of Lyme Disease. Clin Infect Dis 2023; 77:839-847. [PMID: 37227948 PMCID: PMC10506776 DOI: 10.1093/cid/ciad307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Lyme disease is the most prevalent vector-borne disease in the US, yet its host factors are poorly understood and diagnostic tests are limited. We evaluated patients in a large health system to uncover cholesterol's role in the susceptibility, severity, and machine learning-based diagnosis of Lyme disease. METHODS A longitudinal health system cohort comprised 1 019 175 individuals with electronic health record data and 50 329 with linked genetic data. Associations of blood cholesterol level, cholesterol genetic scores comprising common genetic variants, and burden of rare loss-of-function (LoF) variants in cholesterol metabolism genes with Lyme disease were investigated. A portable machine learning model was constructed and tested to predict Lyme disease using routine lipid and clinical measurements. RESULTS There were 3832 cases of Lyme disease. Increasing cholesterol was associated with greater risk of Lyme disease and hypercholesterolemia was more prevalent in Lyme disease cases than in controls. Cholesterol genetic scores and rare LoF variants in CD36 and LDLR were associated with Lyme disease risk. Serological profiling of cases revealed parallel trajectories of rising cholesterol and immunoglobulin levels over the disease course, including marked increases in individuals with LoF variants and high cholesterol genetic scores. The machine learning model predicted Lyme disease solely using routine lipid panel, blood count, and metabolic measurements. CONCLUSIONS These results demonstrate the value of large-scale genetic and clinical data to reveal host factors underlying infectious disease biology, risk, and prognosis and the potential for their clinical translation to machine learning diagnostics that do not need specialized assays.
Collapse
Affiliation(s)
- Iain S Forrest
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anya J O’Neal
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Joao H F Pedra
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ron Do
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
7
|
Chen F, Madduri RK, Rodriguez AA, Darst BF, Chou A, Sheng X, Wang A, Shen J, Saunders EJ, Rhie SK, Bensen JT, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Sanderson M, John EM, Park JY, Xu J, Wang Y, Berndt SI, Huff CD, Yeboah ED, Tettey Y, Lachance J, Tang W, Rentsch CT, Cho K, Mcmahon BH, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Sellers TA, Yamoah K, Murphy AB, Crawford DC, Patel AV, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas CM, Stern MC, Kote-Jarai Z, Govindasami K, Cook MB, Chokkalingam AP, Hsing AW, Goodman PJ, Hoffmann TJ, Drake BF, Hu JJ, Keaton JM, Hellwege JN, Clark PE, Jalloh M, Gueye SM, Niang L, Ogunbiyi O, Idowu MO, Popoola O, Adebiyi AO, Aisuodionoe-Shadrach OI, Ajibola HO, Jamda MA, Oluwole OP, Nwegbu M, Adusei B, Mante S, Darkwa-Abrahams A, Mensah JE, Diop H, Van Den Eeden SK, Blanchet P, Fowke JH, Casey G, Hennis AJ, Lubwama A, Thompson IM, Leach R, Easton DF, Preuss MH, Loos RJ, Gundell SM, Wan P, Mohler JL, Fontham ET, Smith GJ, Taylor JA, Srivastava S, Eeles RA, Carpten JD, Kibel AS, Multigner L, Parent MÉ, Menegaux F, Cancel-Tassin G, Klein EA, Andrews C, Rebbeck TR, Brureau L, Ambs S, Edwards TL, Watya S, Chanock SJ, Witte JS, Blot WJ, Michael Gaziano J, Justice AC, Conti DV, Haiman CA. Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry. Eur Urol 2023; 84:13-21. [PMID: 36872133 PMCID: PMC10424812 DOI: 10.1016/j.eururo.2023.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/14/2022] [Accepted: 01/24/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND Genetic factors play an important role in prostate cancer (PCa) susceptibility. OBJECTIVE To discover common genetic variants contributing to the risk of PCa in men of African ancestry. DESIGN, SETTING, AND PARTICIPANTS We conducted a meta-analysis of ten genome-wide association studies consisting of 19378 cases and 61620 controls of African ancestry. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Common genotyped and imputed variants were tested for their association with PCa risk. Novel susceptibility loci were identified and incorporated into a multiancestry polygenic risk score (PRS). The PRS was evaluated for associations with PCa risk and disease aggressiveness. RESULTS AND LIMITATIONS Nine novel susceptibility loci for PCa were identified, of which seven were only found or substantially more common in men of African ancestry, including an African-specific stop-gain variant in the prostate-specific gene anoctamin 7 (ANO7). A multiancestry PRS of 278 risk variants conferred strong associations with PCa risk in African ancestry studies (odds ratios [ORs] >3 and >5 for men in the top PRS decile and percentile, respectively). More importantly, compared with men in the 40-60% PRS category, men in the top PRS decile had a significantly higher risk of aggressive PCa (OR = 1.23, 95% confidence interval = 1.10-1.38, p = 4.4 × 10-4). CONCLUSIONS This study demonstrates the importance of large-scale genetic studies in men of African ancestry for a better understanding of PCa susceptibility in this high-risk population and suggests a potential clinical utility of PRS in differentiating between the risks of developing aggressive and nonaggressive disease in men of African ancestry. PATIENT SUMMARY In this large genetic study in men of African ancestry, we discovered nine novel prostate cancer (PCa) risk variants. We also showed that a multiancestry polygenic risk score was effective in stratifying PCa risk, and was able to differentiate risk of aggressive and nonaggressive disease.
Collapse
Affiliation(s)
- Fei Chen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Burcu F Darst
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alisha Chou
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anqi Wang
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jiayi Shen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sue A Ingles
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Rick A Kittles
- Department of Population Sciences, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Sara S Strom
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Benjamin A Rybicki
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - William B Isaacs
- James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Esther M John
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Jianfeng Xu
- Program for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Ying Wang
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chad D Huff
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Yao Tettey
- Department of Pathology, University of Ghana, Accra, Ghana; Korle Bu Teaching Hospital, Accra, Ghana
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Christopher T Rentsch
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Kelly Cho
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Jamaica Plain, MA, USA
| | - Benjamin H Mcmahon
- Theoretical Biology Division, Los Alamos National Lab, Los Alamos, NM, USA
| | | | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- Korle Bu Teaching Hospital, Accra, Ghana
| | | | | | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Kosj Yamoah
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA; Department of Radiation Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Adam B Murphy
- Department of Urology, Northwestern University, Chicago, IL, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Kennesaw, GA, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Melinda C Aldrich
- Division of Epidemiology, Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Cussenot
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Gyorgy Petrovics
- Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Cullen
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Department of Surgery, Center for Prostate Disease Research, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | - Mariana C Stern
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Ann W Hsing
- Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bettina F Drake
- Division of Public Health Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer J Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Jacob M Keaton
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Nashville, TN, USA
| | - Peter E Clark
- Atrium Health/Levine Cancer Institute, Charlotte, NC, USA
| | | | | | | | - Olufemi Ogunbiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Michael O Idowu
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Olufemi Popoola
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College of Medicine, University of Ibadan and University College Hospital, Ibadan, Nigeria
| | - Oseremen I Aisuodionoe-Shadrach
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Hafees O Ajibola
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Mustapha A Jamda
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Olabode P Oluwole
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | - Maxwell Nwegbu
- College of Health Sciences, University of Abuja, University of Abuja Teaching Hospital and Cancer Science Center, Abuja, Nigeria
| | | | | | | | | | - Halimatou Diop
- Laboratoires Bacteriologie et Virologie, Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente, Northern California, Oakland, CA, USA; Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Pascal Blanchet
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Jay H Fowke
- Department of Preventive Medicine, Division of Epidemiology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Graham Casey
- Department of Public Health Science, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anselm J Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Ian M Thompson
- CHRISTUS Santa Rosa Medical Center Hospital, San Antonio, TX, USA
| | - Robin Leach
- Department of Urology, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susan M Gundell
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Peggy Wan
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James L Mohler
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elizabeth T Fontham
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Gary J Smith
- Department of Urology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Shiv Srivastava
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Rosaline A Eeles
- The Institute of Cancer Research, London, UK; Royal Marsden NHS Foundation Trust, London, UK
| | - John D Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam S Kibel
- Department of Urology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luc Multigner
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | - Marie-Élise Parent
- Epidemiology and Biostatistics Unit, Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC, Canada
| | - Florence Menegaux
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif Cédex, France; Paris-Sud University, Villejuif Cédex, France
| | - Geraldine Cancel-Tassin
- Department of Urology and Predictive Onco-Urology Group, Sorbonne Université, GRC 5 Predictive Onco-Urology, APHP-Sorbonne Université, Paris, France; CeRePP, Tenon Hospital, Paris, France
| | - Eric A Klein
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Caroline Andrews
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA; Glickman Urological & Kidney Institute, Cleveland, OH, USA
| | - Timothy R Rebbeck
- Harvard TH Chan School of Public Health and Division of Population Sciences, Dana Farber Cancer Institute, Boston, MA, USA
| | - Laurent Brureau
- CHU de Pointe-à-Pitre, Univ Antilles, Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Pointe-à-Pitre, Guadeloupe, France
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; International Epidemiology Institute, Rockville, MD, USA
| | - J Michael Gaziano
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Amy C Justice
- Yale School of Medicine, New Haven, CT, USA; VA Connecticut Healthcare System, West Haven, CT, USA
| | - David V Conti
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
8
|
Forrest IS, Petrazzini BO, Duffy Á, Park JK, O'Neal AJ, Jordan DM, Rocheleau G, Nadkarni GN, Cho JH, Blazer AD, Do R. A machine learning model identifies patients in need of autoimmune disease testing using electronic health records. Nat Commun 2023; 14:2385. [PMID: 37169741 PMCID: PMC10130143 DOI: 10.1038/s41467-023-37996-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 04/05/2023] [Indexed: 05/13/2023] Open
Abstract
Systemic autoimmune rheumatic diseases (SARDs) can lead to irreversible damage if left untreated, yet these patients often endure long diagnostic journeys before being diagnosed and treated. Machine learning may help overcome the challenges of diagnosing SARDs and inform clinical decision-making. Here, we developed and tested a machine learning model to identify patients who should receive rheumatological evaluation for SARDs using longitudinal electronic health records of 161,584 individuals from two institutions. The model demonstrated high performance for predicting cases of autoantibody-tested individuals in a validation set, an external test set, and an independent cohort with a broader case definition. This approach identified more individuals for autoantibody testing compared with current clinical standards and a greater proportion of autoantibody carriers among those tested. Diagnoses of SARDs and other autoimmune conditions increased with higher model probabilities. The model detected a need for autoantibody testing and rheumatology encounters up to five years before the test date and assessment date, respectively. Altogether, these findings illustrate that the clinical manifestations of a diverse array of autoimmune conditions are detectable in electronic health records using machine learning, which may help systematize and accelerate autoimmune testing.
Collapse
Affiliation(s)
- Iain S Forrest
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ben O Petrazzini
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Áine Duffy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua K Park
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anya J O'Neal
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Daniel M Jordan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ghislain Rocheleau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashira D Blazer
- Division of Rheumatology, Hospital for Special Surgery, New York, NY, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
9
|
Forrest IS, Petrazzini BO, Duffy Á, Park JK, Marquez-Luna C, Jordan DM, Rocheleau G, Cho JH, Rosenson RS, Narula J, Nadkarni GN, Do R. Machine learning-based marker for coronary artery disease: derivation and validation in two longitudinal cohorts. Lancet 2023; 401:215-225. [PMID: 36563696 PMCID: PMC10069625 DOI: 10.1016/s0140-6736(22)02079-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Binary diagnosis of coronary artery disease does not preserve the complexity of disease or quantify its severity or its associated risk with death; hence, a quantitative marker of coronary artery disease is warranted. We evaluated a quantitative marker of coronary artery disease derived from probabilities of a machine learning model. METHODS In this cohort study, we developed and validated a coronary artery disease-predictive machine learning model using 95 935 electronic health records and assessed its probabilities as in-silico scores for coronary artery disease (ISCAD; range 0 [lowest probability] to 1 [highest probability]) in participants in two longitudinal biobank cohorts. We measured the association of ISCAD with clinical outcomes-namely, coronary artery stenosis, obstructive coronary artery disease, multivessel coronary artery disease, all-cause death, and coronary artery disease sequelae. FINDINGS Among 95 935 participants, 35 749 were from the BioMe Biobank (median age 61 years [IQR 18]; 14 599 [41%] were male and 21 150 [59%] were female; 5130 [14%] were with diagnosed coronary artery disease) and 60 186 were from the UK Biobank (median age 62 [15] years; 25 031 [42%] male and 35 155 [58%] female; 8128 [14%] with diagnosed coronary artery disease). The model predicted coronary artery disease with an area under the receiver operating characteristic curve of 0·95 (95% CI 0·94-0·95; sensitivity of 0·94 [0·94-0·95] and specificity of 0·82 [0·81-0·83]) and 0·93 (0·92-0·93; sensitivity of 0·90 [0·89-0·90] and specificity of 0·88 [0·87-0·88]) in the BioMe validation and holdout sets, respectively, and 0·91 (0·91-0·91; sensitivity of 0·84 [0·83-0·84] and specificity of 0·83 [0·82-0·83]) in the UK Biobank external test set. ISCAD captured coronary artery disease risk from known risk factors, pooled cohort equations, and polygenic risk scores. Coronary artery stenosis increased quantitatively with ascending ISCAD quartiles (increase per quartile of 12 percentage points), including risk of obstructive coronary artery disease, multivessel coronary artery disease, and stenosis of major coronary arteries. Hazard ratios (HRs) and prevalence of all-cause death increased stepwise over ISCAD deciles (decile 1: HR 1·0 [95% CI 1·0-1·0], 0·2% prevalence; decile 6: 11 [3·9-31], 3·1% prevalence; and decile 10: 56 [20-158], 11% prevalence). A similar trend was observed for recurrent myocardial infarction. 12 (46%) undiagnosed individuals with high ISCAD (≥0·9) had clinical evidence of coronary artery disease according to the 2014 American College of Cardiology/American Heart Association Task Force guidelines. INTERPRETATION Electronic health record-based machine learning was used to generate an in-silico marker for coronary artery disease that can non-invasively quantify atherosclerosis and risk of death on a continuous spectrum, and identify underdiagnosed individuals. FUNDING National Institutes of Health.
Collapse
Affiliation(s)
- Iain S Forrest
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ben O Petrazzini
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Áine Duffy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joshua K Park
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carla Marquez-Luna
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel M Jordan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ghislain Rocheleau
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert S Rosenson
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Metabolism and Lipids Unit, Zena and Michael A Wiener Cardiovascular Institute, Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jagat Narula
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Data-Driven and Digital Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
10
|
Loh M, Zhang W, Ng HK, Schmid K, Lamri A, Tong L, Ahmad M, Lee JJ, Ng MCY, Petty LE, Spracklen CN, Takeuchi F, Islam MT, Jasmine F, Kasturiratne A, Kibriya M, Mohlke KL, Paré G, Prasad G, Shahriar M, Chee ML, de Silva HJ, Engert JC, Gerstein HC, Mani KR, Sabanayagam C, Vujkovic M, Wickremasinghe AR, Wong TY, Yajnik CS, Yusuf S, Ahsan H, Bharadwaj D, Anand SS, Below JE, Boehnke M, Bowden DW, Chandak GR, Cheng CY, Kato N, Mahajan A, Sim X, McCarthy MI, Morris AP, Kooner JS, Saleheen D, Chambers JC. Identification of genetic effects underlying type 2 diabetes in South Asian and European populations. Commun Biol 2022; 5:329. [PMID: 35393509 PMCID: PMC8991226 DOI: 10.1038/s42003-022-03248-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/08/2022] [Indexed: 02/08/2023] Open
Abstract
South Asians are at high risk of developing type 2 diabetes (T2D). We carried out a genome-wide association meta-analysis with South Asian T2D cases (n = 16,677) and controls (n = 33,856), followed by combined analyses with Europeans (neff = 231,420). We identify 21 novel genetic loci for significant association with T2D (P = 4.7 × 10-8 to 5.2 × 10-12), to the best of our knowledge at the point of analysis. The loci are enriched for regulatory features, including DNA methylation and gene expression in relevant tissues, and highlight CHMP4B, PDHB, LRIG1 and other genes linked to adiposity and glucose metabolism. A polygenic risk score based on South Asian-derived summary statistics shows ~4-fold higher risk for T2D between the top and bottom quartile. Our results provide further insights into the genetic mechanisms underlying T2D, and highlight the opportunities for discovery from joint analysis of data from across ancestral populations.
Collapse
Affiliation(s)
- Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Katharina Schmid
- Institute of Computational Biology, Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, 85748, Garching bei München, Neuherberg, Germany
| | - Amel Lamri
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Lin Tong
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Meraj Ahmad
- Genomic Research on Complex diseases, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Jung-Jin Lee
- Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Mayo Hospital, Lahore, Pakistan
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, 37215, USA
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Cassandra N Spracklen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Md Tariqul Islam
- U Chicago Research Bangladesh, House#4, Road#2b, Sector#4, Uttara, Dhaka, 1230, Bangladesh
| | - Farzana Jasmine
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Anuradhani Kasturiratne
- Department of Public Health, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | - Muhammad Kibriya
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Guillaume Paré
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Gauri Prasad
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohammad Shahriar
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Miao Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | - James C Engert
- Department of Medicine, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Hertzel C Gerstein
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - K Radha Mani
- Genomic Research on Complex diseases, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Marijana Vujkovic
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Ananda R Wickremasinghe
- Department of Public Health, Faculty of Medicine, University of Kelaniya, Kelaniya, Sri Lanka
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Salim Yusuf
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Habibul Ahsan
- The University of Chicago, Biological Sciences Division, Public Health Sciences, 5841 South Maryland Avenue, MC2000, Chicago, IL, 60637, USA
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology Campus, New Delhi, 110020, India
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sonia S Anand
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Donald W Bowden
- Department of Medicine, Mayo Hospital, Lahore, Pakistan
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 37215, USA
| | - Giriraj R Chandak
- Genomic Research on Complex diseases, CSIR-Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India
- JSS Academy of Health Education of Research, Mysuru, India
- Science and Engineering Research Board, Department of Science and Technology, Ministry of Science and technology, Government of India, New Delhi, India
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Anubha Mahajan
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hosptial, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK.
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK.
- MRC-PHE Centre for Enviroment and Health, Imperial College London, London, W2 1PG, UK.
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK.
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan.
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
- Department of Cardiology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - John C Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
- Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, UK.
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UB1 3HW, UK.
- Imperial College Healthcare NHS Trust, Imperial College London, London, W12 0HS, UK.
- MRC-PHE Centre for Enviroment and Health, Imperial College London, London, W2 1PG, UK.
| |
Collapse
|
11
|
DiCorpo D, LeClair J, Cole JB, Sarnowski C, Ahmadizar F, Bielak LF, Blokstra A, Bottinger EP, Chaker L, Chen YDI, Chen Y, de Vries PS, Faquih T, Ghanbari M, Gudmundsdottir V, Guo X, Hasbani NR, Ibi D, Ikram MA, Kavousi M, Leonard HL, Leong A, Mercader JM, Morrison AC, Nadkarni GN, Nalls MA, Noordam R, Preuss M, Smith JA, Trompet S, Vissink P, Yao J, Zhao W, Boerwinkle E, Goodarzi MO, Gudnason V, Jukema JW, Kardia SL, Loos RJ, Liu CT, Manning AK, Mook-Kanamori D, Pankow JS, Picavet HSJ, Sattar N, Simonsick EM, Verschuren WM, Willems van Dijk K, Florez JC, Rotter JI, Meigs JB, Dupuis J, Udler MS. Type 2 Diabetes Partitioned Polygenic Scores Associate With Disease Outcomes in 454,193 Individuals Across 13 Cohorts. Diabetes Care 2022; 45:674-683. [PMID: 35085396 PMCID: PMC8918228 DOI: 10.2337/dc21-1395] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/15/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Type 2 diabetes (T2D) has heterogeneous patient clinical characteristics and outcomes. In previous work, we investigated the genetic basis of this heterogeneity by clustering 94 T2D genetic loci using their associations with 47 diabetes-related traits and identified five clusters, termed β-cell, proinsulin, obesity, lipodystrophy, and liver/lipid. The relationship between these clusters and individual-level metabolic disease outcomes has not been assessed. RESEARCH DESIGN AND METHODS Here we constructed individual-level partitioned polygenic scores (pPS) for these five clusters in 12 studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank (n = 454,193) and tested for cross-sectional association with T2D-related outcomes, including blood pressure, renal function, insulin use, age at T2D diagnosis, and coronary artery disease (CAD). RESULTS Despite all clusters containing T2D risk-increasing alleles, they had differential associations with metabolic outcomes. Increased obesity and lipodystrophy cluster pPS, which had opposite directions of association with measures of adiposity, were both significantly associated with increased blood pressure and hypertension. The lipodystrophy and liver/lipid cluster pPS were each associated with CAD, with increasing and decreasing effects, respectively. An increased liver/lipid cluster pPS was also significantly associated with reduced renal function. The liver/lipid cluster includes known loci linked to liver lipid metabolism (e.g., GCKR, PNPLA3, and TM6SF2), and these findings suggest that cardiovascular disease risk and renal function may be impacted by these loci through their shared disease pathway. CONCLUSIONS Our findings support that genetically driven pathways leading to T2D also predispose differentially to clinical outcomes.
Collapse
Affiliation(s)
- Daniel DiCorpo
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Jessica LeClair
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Joanne B. Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA
| | - Chloé Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Fariba Ahmadizar
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Julius Global Health, University Utrecht Medical Center, Utrecht, the Netherlands
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Anneke Blokstra
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Erwin P. Bottinger
- Hasso Plattner Institute Digital Health, Potsdam, Germany
- Mount Sinai Health System, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Layal Chaker
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine, Division of Endocrinology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Yii-Der I. Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Ye Chen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Tariq Faquih
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Valborg Gudmundsdottir
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Natalie R. Hasbani
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Dorina Ibi
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hampton L. Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
- Data Tecnica International, Glen Echo, MD
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD
| | - Aaron Leong
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Josep M. Mercader
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Alanna C. Morrison
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | - Girish N. Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD
- Data Tecnica International, Glen Echo, MD
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, MD
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI
| | - Stella Trompet
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Petra Vissink
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - J. Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Netherlands Heart Institute, Utrecht, the Netherlands
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Ruth J.F. Loos
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Alisa K. Manning
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | - Dennis Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN
| | - H. Susan J. Picavet
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Naveed Sattar
- British Heart Foundation Glasgow Cardiovascular Research Centre, Faculty of Medicine, Glasgow, U.K
| | - Eleanor M. Simonsick
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD
| | - W.M. Monique Verschuren
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ko Willems van Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jose C. Florez
- Department of Medicine, Harvard Medical School, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA
| | - James B. Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Miriam S. Udler
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Endocrine Division, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| |
Collapse
|
12
|
Landi I, Kaji DA, Cotter L, Van Vleck T, Belbin G, Preuss M, Loos RJF, Kenny E, Glicksberg BS, Beckmann ND, O'Reilly P, Schadt EE, Achtyes ED, Buckley PF, Lehrer D, Malaspina DP, McCarroll SA, Rapaport MH, Fanous AH, Pato MT, Pato CN, Bigdeli TB, Nadkarni GN, Charney AW. Prognostic value of polygenic risk scores for adults with psychosis. Nat Med 2021; 27:1576-1581. [PMID: 34489608 PMCID: PMC8446329 DOI: 10.1038/s41591-021-01475-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/22/2021] [Indexed: 12/31/2022]
Abstract
Polygenic risk scores (PRS) summarize genetic liability to a disease at the individual level, and the aim is to use them as biomarkers of disease and poor outcomes in real-world clinical practice. To date, few studies have assessed the prognostic value of PRS relative to standards of care. Schizophrenia (SCZ), the archetypal psychotic illness, is an ideal test case for this because the predictive power of the SCZ PRS exceeds that of most other common diseases. Here, we analyzed clinical and genetic data from two multi-ethnic cohorts totaling 8,541 adults with SCZ and related psychotic disorders, to assess whether the SCZ PRS improves the prediction of poor outcomes relative to clinical features captured in a standard psychiatric interview. For all outcomes investigated, the SCZ PRS did not improve the performance of predictive models, an observation that was generally robust to divergent case ascertainment strategies and the ancestral background of the study participants.
Collapse
Affiliation(s)
- Isotta Landi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Deepak A Kaji
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liam Cotter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tielman Van Vleck
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gillian Belbin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Preuss
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Eric D Achtyes
- Cherry Health, Grand Rapids, MI, USA
- Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Peter F Buckley
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Douglas Lehrer
- Department of Psychiatry, Wright State University, Dayton, OH, USA
| | - Dolores P Malaspina
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mark H Rapaport
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Ayman H Fanous
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, USA
| | - Michele T Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Carlos N Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Tim B Bigdeli
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY, USA
- VA New York Harbor Healthcare System, Brooklyn, NY, USA
| | - Girish N Nadkarni
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
13
|
Chan L, Nadkarni GN, Fleming F, McCullough JR, Connolly P, Mosoyan G, El Salem F, Kattan MW, Vassalotti JA, Murphy B, Donovan MJ, Coca SG, Damrauer SM. Derivation and validation of a machine learning risk score using biomarker and electronic patient data to predict progression of diabetic kidney disease. Diabetologia 2021; 64:1504-1515. [PMID: 33797560 PMCID: PMC8187208 DOI: 10.1007/s00125-021-05444-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/27/2021] [Indexed: 12/17/2022]
Abstract
AIM Predicting progression in diabetic kidney disease (DKD) is critical to improving outcomes. We sought to develop/validate a machine-learned, prognostic risk score (KidneyIntelX™) combining electronic health records (EHR) and biomarkers. METHODS This is an observational cohort study of patients with prevalent DKD/banked plasma from two EHR-linked biobanks. A random forest model was trained, and performance (AUC, positive and negative predictive values [PPV/NPV], and net reclassification index [NRI]) was compared with that of a clinical model and Kidney Disease: Improving Global Outcomes (KDIGO) categories for predicting a composite outcome of eGFR decline of ≥5 ml/min per year, ≥40% sustained decline, or kidney failure within 5 years. RESULTS In 1146 patients, the median age was 63 years, 51% were female, the baseline eGFR was 54 ml min-1 [1.73 m]-2, the urine albumin to creatinine ratio (uACR) was 6.9 mg/mmol, follow-up was 4.3 years and 21% had the composite endpoint. On cross-validation in derivation (n = 686), KidneyIntelX had an AUC of 0.77 (95% CI 0.74, 0.79). In validation (n = 460), the AUC was 0.77 (95% CI 0.76, 0.79). By comparison, the AUC for the clinical model was 0.62 (95% CI 0.61, 0.63) in derivation and 0.61 (95% CI 0.60, 0.63) in validation. Using derivation cut-offs, KidneyIntelX stratified 46%, 37% and 17% of the validation cohort into low-, intermediate- and high-risk groups for the composite kidney endpoint, respectively. The PPV for progressive decline in kidney function in the high-risk group was 61% for KidneyIntelX vs 40% for the highest risk strata by KDIGO categorisation (p < 0.001). Only 10% of those scored as low risk by KidneyIntelX experienced progression (i.e., NPV of 90%). The NRIevent for the high-risk group was 41% (p < 0.05). CONCLUSIONS KidneyIntelX improved prediction of kidney outcomes over KDIGO and clinical models in individuals with early stages of DKD.
Collapse
Affiliation(s)
- Lili Chan
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Girish N Nadkarni
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fergus Fleming
- Renalytix AI Plc, Cardiff, UK
- Renalytix AI, Inc., New York, NY, USA
| | | | | | - Gohar Mosoyan
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fadi El Salem
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael W Kattan
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland, OH, USA
| | - Joseph A Vassalotti
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara Murphy
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael J Donovan
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven G Coca
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
14
|
Shapiro AJ, Kroener L, Quinn MM. Expanded carrier screening for recessively inherited disorders: economic burden and factors in decision-making when one individual in a couple is identified as a carrier. J Assist Reprod Genet 2021; 38:957-963. [PMID: 33501564 DOI: 10.1007/s10815-021-02084-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/20/2021] [Indexed: 11/27/2022] Open
Abstract
PURPOSE When undergoing expanded carrier screening (ECS), couples are often screened sequentially to reduce need for a second individual's test. It is unknown how often partners of individuals found to be carriers complete the recommended testing with a sequential approach and what factors contribute to decision-making regarding partner testing. Additionally, the economic burden placed on individuals by ECS testing and its effect on partner testing has not been evaluated. METHODS In part 1, all individuals at a university-affiliated reproductive endocrinology and infertility practice identified to be carriers of a recessively inherited mutation using the Counsyl/Foresight ECS were included. Conditions were categorized by severity according to a previously described classification system. In part 2, all individuals who underwent ECS with a single test provider between September 1, 2013 and February 1, 2020 were contacted via email to complete a confidential and anonymized online survey. RESULTS In part 1, a total of 2061 patients were screened. 36.9% were carriers of one or more recessively inherited disorders. Twenty-seven percent of positively screened individuals did not have their partner screened. Carriers of a moderate condition had a trend towards a reduced odds for having their partner screened compared to a profound condition (OR 0.36, 95% CI 0.12-1.05, p = 0.06). Number of conditions was not predictive of subsequent partner screening (OR 0.95, 95% CI 0.72-1.25, p = 0.72). In part 2, the cost of ECS was not covered by insurance for 54.5% (103/189) and most paid over $300 out-of-pocket for testing (47.6%). The most common reason for not completing partner testing was that the results would not alter their course when seeking conception (33.3%). 73.5% of patients knew that the largest benefit of ECS comes from knowing a partner's results as well as their own. CONCLUSIONS Not all carriers of recessively inherited disorders choose to undergo partner screening. Patients found to be carrier of more debilitating genetic disorders may be more likely to screen their reproductive partners. For many, ECS testing is not covered by insurance, and this test may impose a significant economic burden. For some patients, the results of ECS would not change what they would do when seeking conception. Providers should evaluate whether a patient's ECS result would change their treatment course prior to testing.
Collapse
Affiliation(s)
- Alice J Shapiro
- Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Lindsay Kroener
- Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Molly M Quinn
- Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
15
|
Patrinos GP, Pasparakis E, Koiliari E, Pereira AC, Hünemeier T, Pereira LV, Mitropoulou C. Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries. Am J Hum Genet 2020; 107:589-595. [PMID: 33007198 DOI: 10.1016/j.ajhg.2020.08.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In the post-genomic era, genomic medicine interventions as a key component of personalized medicine and tailored-made health care are greatly anticipated following recent scientific and technological advances. Indeed, large-scale sequencing efforts that explore human genomic variation have been initiated in several, mostly developed, countries across the globe, such as the United States, the United Kingdom, and a few others. Here, we highlight the successful implementation of large-scale national genomic initiatives, namely the Genome of Greece (GoGreece) and the DNA do Brasil (DNABr), aiming to emphasize the importance of implementing such initiatives in developing countries. Based on this experience, we also provide a roadmap for replicating these projects in other low-resource settings, thereby bringing genomic medicine in these countries closer to clinical fruition.
Collapse
|
16
|
Hernandez-Nieto C, Alkon-Meadows T, Lee J, Cacchione T, Iyune-Cojab E, Garza-Galvan M, Luna-Rojas M, Copperman AB, Sandler B. Expanded carrier screening for preconception reproductive risk assessment: Prevalence of carrier status in a Mexican population. Prenat Diagn 2020; 40:635-643. [PMID: 32003480 DOI: 10.1002/pd.5656] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/30/2019] [Accepted: 01/21/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Genetic carrier screening has the potential to identify couples at risk of having a child affected with an autosomal recessive or X-linked disorder. However, the current prevalence of carrier status for these conditions in developing countries is not well defined. This study assesses the prevalence of carrier status of selected genetic conditions utilizing an expanded, pan-ethnic genetic carrier screening panel (ECS) in a large population of Mexican patients. METHODS Retrospective chart review of all patients tested with a single ECS panel at an international infertility center from 2012 to 2018 were included, and the prevalence of positive carrier status in a Mexican population was evaluated. RESULTS Eight hundred five individuals were analyzed with ECS testing for 283 genetic conditions. Three hundred fifty-two carriers (43.7%) were identified with 503 pathogenic variants in 145 different genes. Seventeen of the 391 participating couples (4.34%) were identified as being at-risk couples. The most prevalent alleles found were associated with alpha thalassemia, cystic fibrosis, GJB2 nonsyndromic hearing loss, biotinidase deficiency, and familial Mediterranean fever. CONCLUSION Based on the prevalence and severity of Mendelian disorders, we recommend that couples who wish to conceive regardless of their ethnicity background explore carrier screening and genetic counseling prior to reproductive medical treatment.
Collapse
Affiliation(s)
- Carlos Hernandez-Nieto
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Tamar Alkon-Meadows
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Joseph Lee
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA
| | - Teresa Cacchione
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA
| | - Esther Iyune-Cojab
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Maria Garza-Galvan
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Martha Luna-Rojas
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| | - Alan B Copperman
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, A Mount Sinai Venture, Stamford CT, USA
| | - Benjamin Sandler
- Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York, New York, USA.,Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Reproductive Endocrinology and Infertility, Reproductive Medicine associates of New York-Mexico, Mexico City, Mexico
| |
Collapse
|
17
|
Damrauer SM, Chaudhary K, Cho JH, Liang LW, Argulian E, Chan L, Dobbyn A, Guerraty MA, Judy R, Kay J, Kember RL, Levin MG, Saha A, Van Vleck T, Verma SS, Weaver J, Abul-Husn NS, Baras A, Chirinos JA, Drachman B, Kenny EE, Loos RJF, Narula J, Overton J, Reid J, Ritchie M, Sirugo G, Nadkarni G, Rader DJ, Do R. Association of the V122I Hereditary Transthyretin Amyloidosis Genetic Variant With Heart Failure Among Individuals of African or Hispanic/Latino Ancestry. JAMA 2019; 322:2191-2202. [PMID: 31821430 PMCID: PMC7081752 DOI: 10.1001/jama.2019.17935] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
Importance Hereditary transthyretin (TTR) amyloid cardiomyopathy (hATTR-CM) due to the TTR V122I variant is an autosomal-dominant disorder that causes heart failure in elderly individuals of African ancestry. The clinical associations of carrying the variant, its effect in other African ancestry populations including Hispanic/Latino individuals, and the rates of achieving a clinical diagnosis in carriers are unknown. Objective To assess the association between the TTR V122I variant and heart failure and identify rates of hATTR-CM diagnosis among carriers with heart failure. Design, Setting, and Participants Cross-sectional analysis of carriers and noncarriers of TTR V122I of African ancestry aged 50 years or older enrolled in the Penn Medicine Biobank between 2008 and 2017 using electronic health record data from 1996 to 2017. Case-control study in participants of African and Hispanic/Latino ancestry with and without heart failure in the Mount Sinai BioMe Biobank enrolled between 2007 and 2015 using electronic health record data from 2007 to 2018. Exposures TTR V122I carrier status. Main Outcomes and Measures The primary outcome was prevalent heart failure. The rate of diagnosis with hATTR-CM among TTR V122I carriers with heart failure was measured. Results The cross-sectional cohort included 3724 individuals of African ancestry with a median age of 64 years (interquartile range, 57-71); 1755 (47%) were male, 2896 (78%) had a diagnosis of hypertension, and 753 (20%) had a history of myocardial infarction or coronary revascularization. There were 116 TTR V122I carriers (3.1%); 1121 participants (30%) had heart failure. The case-control study consisted of 2307 individuals of African ancestry and 3663 Hispanic/Latino individuals; the median age was 73 years (interquartile range, 68-80), 2271 (38%) were male, 4709 (79%) had a diagnosis of hypertension, and 1008 (17%) had a history of myocardial infarction or coronary revascularization. There were 1376 cases of heart failure. TTR V122I was associated with higher rates of heart failure (cross-sectional cohort: n = 51/116 TTR V122I carriers [44%], n = 1070/3608 noncarriers [30%], adjusted odds ratio, 1.7 [95% CI, 1.2-2.4], P = .006; case-control study: n = 36/1376 heart failure cases [2.6%], n = 82/4594 controls [1.8%], adjusted odds ratio, 1.8 [95% CI, 1.2-2.7], P = .008). Ten of 92 TTR V122I carriers with heart failure (11%) were diagnosed as having hATTR-CM; the median time from onset of symptoms to clinical diagnosis was 3 years. Conclusions and Relevance Among individuals of African or Hispanic/Latino ancestry enrolled in 2 academic medical center-based biobanks, the TTR V122I genetic variant was significantly associated with heart failure.
Collapse
Affiliation(s)
- Scott M. Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Surgery, Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania
| | - Kumardeep Chaudhary
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy H. Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lusha W. Liang
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Edgar Argulian
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lili Chan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amanda Dobbyn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marie A. Guerraty
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Renae Judy
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Jenna Kay
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Rachel L. Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- MIRECC, Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania
| | - Michael G. Levin
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Aparna Saha
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Shefali S. Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - JoEllen Weaver
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Noura S. Abul-Husn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York
| | - Julio A. Chirinos
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Brian Drachman
- Division of Cardiovascular Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Eimear E. Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- The Center for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jagat Narula
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Marylyn Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Giorgio Sirugo
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Daniel J. Rader
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Pennsylvania
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
18
|
Saccone NL, Emery LS, Sofer T, Gogarten SM, Becker DM, Bottinger EP, Chen LS, Culverhouse RC, Duan W, Hancock DB, Hosgood HD, Johnson EO, Loos RJF, Louie T, Papanicolaou G, Perreira KM, Rodriquez EJ, Schurmann C, Stilp AM, Szpiro AA, Talavera GA, Taylor KD, Thrasher JF, Yanek LR, Laurie CC, Pérez-Stable EJ, Bierut LJ, Kaplan RC. Genome-Wide Association Study of Heavy Smoking and Daily/Nondaily Smoking in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Nicotine Tob Res 2019; 20:448-457. [PMID: 28520984 DOI: 10.1093/ntr/ntx107] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/11/2017] [Indexed: 02/07/2023]
Abstract
Introduction Genetic variants associated with nicotine dependence have previously been identified, primarily in European-ancestry populations. No genome-wide association studies (GWAS) have been reported for smoking behaviors in Hispanics/Latinos in the United States and Latin America, who are of mixed ancestry with European, African, and American Indigenous components. Methods We examined genetic associations with smoking behaviors in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) (N = 12 741 with smoking data, 5119 ever-smokers), using ~2.3 million genotyped variants imputed to the 1000 Genomes Project phase 3. Mixed logistic regression models accounted for population structure, sampling, relatedness, sex, and age. Results The known region of CHRNA5, which encodes the α5 cholinergic nicotinic receptor subunit, was associated with heavy smoking at genome-wide significance (p ≤ 5 × 10-8) in a comparison of 1929 ever-smokers reporting cigarettes per day (CPD) > 10 versus 3156 reporting CPD ≤ 10. The functional variant rs16969968 in CHRNA5 had a p value of 2.20 × 10-7 and odds ratio (OR) of 1.32 for the minor allele (A); its minor allele frequency was 0.22 overall and similar across Hispanic/Latino background groups (Central American = 0.17; South American = 0.19; Mexican = 0.18; Puerto Rican = 0.22; Cuban = 0.29; Dominican = 0.19). CHRNA4 on chromosome 20 attained p < 10-4, supporting prior findings in non-Hispanics. For nondaily smoking, which is prevalent in Hispanic/Latino smokers, compared to daily smoking, loci on chromosomes 2 and 4 achieved genome-wide significance; replication attempts were limited by small Hispanic/Latino sample sizes. Conclusions Associations of nicotinic receptor gene variants with smoking, first reported in non-Hispanic European-ancestry populations, generalized to Hispanics/Latinos despite different patterns of smoking behavior. Implications We conducted the first large-scale genome-wide association study (GWAS) of smoking behavior in a US Hispanic/Latino cohort, and the first GWAS of daily/nondaily smoking in any population. Results show that the region of the nicotinic receptor subunit gene CHRNA5, which in non-Hispanic European-ancestry smokers has been associated with heavy smoking as well as cessation and treatment efficacy, is also significantly associated with heavy smoking in this Hispanic/Latino cohort. The results are an important addition to understanding the impact of genetic variants in understudied Hispanic/Latino smokers.
Collapse
Affiliation(s)
- Nancy L Saccone
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Leslie S Emery
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA
| | | | - Diane M Becker
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | | | - Weimin Duan
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC
| | - H Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| | - Eric O Johnson
- Fellow Program and Behavioral Health and Criminal Justice Division, RTI International, Research Triangle Park, NC
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Krista M Perreira
- Department of Public Policy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Erik J Rodriquez
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.,Division of General Internal Medicine, University of California, San Francisco, San Francisco, CA
| | - Claudia Schurmann
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Adrienne M Stilp
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Adam A Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Gregory A Talavera
- Graduate School of Public Health, San Diego State University, San Diego, CA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - James F Thrasher
- Department of Health Promotion, Education and Behavior, University of South Carolina, Columbia, SC
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Eliseo J Pérez-Stable
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD
| | - Laura J Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY
| |
Collapse
|
19
|
Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans. BMC Genet 2019; 20:52. [PMID: 31266448 PMCID: PMC6604157 DOI: 10.1186/s12863-019-0758-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/20/2019] [Indexed: 11/25/2022] Open
Abstract
Background Genetic diversity is known to confer survival advantage in many species across the tree of life. Here, we hypothesize that such pattern applies to humans as well and could be a result of higher fitness in individuals with higher genomic heterozygosity. Results We use healthy aging as a proxy for better health and fitness, and observe greater heterozygosity in healthy-aged individuals. Specifically, we find that only common genetic variants show significantly higher excess of heterozygosity in the healthy-aged cohort. Lack of difference in heterozygosity for low-frequency variants or disease-associated variants excludes the possibility of compensation for deleterious recessive alleles as a mechanism. In addition, coding SNPs with the highest excess of heterozygosity in the healthy-aged cohort are enriched in genes involved in extracellular matrix and glycoproteins, a group of genes known to be under long-term balancing selection. We also find that individual heterozygosity rate is a significant predictor of electronic health record (EHR)-based estimates of 10-year survival probability in men but not in women, accounting for several factors including age and ethnicity. Conclusions Our results demonstrate that the genomic heterozygosity is associated with human healthspan, and that the relationship between higher heterozygosity and healthy aging could be explained by heterozygote advantage. Further characterization of this relationship will have important implications in aging-associated disease risk prediction. Electronic supplementary material The online version of this article (10.1186/s12863-019-0758-4) contains supplementary material, which is available to authorized users.
Collapse
|
20
|
Thompson J, Vogel Postula K, Wong K, Spencer S. Prenatal genetic counselors' practices and confidence level when counseling on cancer risk identified on expanded carrier screening. J Genet Couns 2019; 28:908-914. [PMID: 30888734 DOI: 10.1002/jgc4.1118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jennifer Thompson
- Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, Illinois
| | | | - Kenny Wong
- Counsyl Inc., South San Francisco, California
| | - Sara Spencer
- Department of Obstetrics and Gynecology, Northwestern Medicine, Chicago, Illinois
| |
Collapse
|
21
|
Hong Q, Zhang L, Fu J, Verghese DA, Chauhan K, Nadkarni GN, Li Z, Ju W, Kretzler M, Cai GY, Chen XM, D'Agati VD, Coca SG, Schlondorff D, He JC, Lee K. LRG1 Promotes Diabetic Kidney Disease Progression by Enhancing TGF- β-Induced Angiogenesis. J Am Soc Nephrol 2019; 30:546-562. [PMID: 30858225 DOI: 10.1681/asn.2018060599] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Glomerular endothelial dysfunction and neoangiogenesis have long been implicated in the pathogenesis of diabetic kidney disease (DKD). However, the specific molecular pathways contributing to these processes in the early stages of DKD are not well understood. Our recent transcriptomic profiling of glomerular endothelial cells identified a number of proangiogenic genes that were upregulated in diabetic mice, including leucine-rich α-2-glycoprotein 1 (LRG1). LRG1 was previously shown to promote neovascularization in mouse models of ocular disease by potentiating endothelial TGF-β/activin receptor-like kinase 1 (ALK1) signaling. However, LRG1's role in the kidney, particularly in the setting of DKD, has been unclear. METHODS We analyzed expression of LRG1 mRNA in glomeruli of diabetic kidneys and assessed its localization by RNA in situ hybridization. We examined the effects of genetic ablation of Lrg1 on DKD progression in unilaterally nephrectomized, streptozotocin-induced diabetic mice at 12 and 20 weeks after diabetes induction. We also assessed whether plasma LRG1 was associated with renal outcome in patients with type 2 diabetes. RESULTS LRG1 localized predominantly to glomerular endothelial cells, and its expression was elevated in the diabetic kidneys. LRG1 ablation markedly attenuated diabetes-induced glomerular angiogenesis, podocyte loss, and the development of diabetic glomerulopathy. These improvements were associated with reduced ALK1-Smad1/5/8 activation in glomeruli of diabetic mice. Moreover, increased plasma LRG1 was associated with worse renal outcome in patients with type 2 diabetes. CONCLUSIONS These findings identify LRG1 as a potential novel pathogenic mediator of diabetic glomerular neoangiogenesis and a risk factor in DKD progression.
Collapse
Affiliation(s)
- Quan Hong
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing, China
| | - Lu Zhang
- Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen, China.,Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jia Fu
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Divya A Verghese
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kinsuk Chauhan
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Girish N Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zhengzhe Li
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Wenjun Ju
- Division of Nephrology, University of Michigan, Ann Arbor, Michigan
| | | | - Guang-Yan Cai
- Department of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing, China
| | - Xiang-Mei Chen
- Department of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center of Kidney Diseases, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, Beijing, China
| | - Vivette D D'Agati
- Department of Pathology, Columbia University Medical Center, New York, New York; and
| | - Steven G Coca
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Detlef Schlondorff
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John C He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; .,Renal Section, James J. Peters Veterans Affair Medical Center, Bronx, New York
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York;
| |
Collapse
|
22
|
Chauhan K, Verghese DA, Rao V, Chan L, Parikh CR, Coca SG, Nadkarni GN. Plasma endostatin predicts kidney outcomes in patients with type 2 diabetes. Kidney Int 2019; 95:439-446. [PMID: 30591223 PMCID: PMC6342645 DOI: 10.1016/j.kint.2018.09.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/23/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023]
Abstract
Novel biomarkers are needed to predict kidney function decline in patients with type 2 diabetes, especially those with preserved glomerular filtration rate (GFR). There are limited data on the association of markers of endothelial dysfunction with longitudinal GFR decline. We used banked specimens from a nested case-control study in the Action to Control Cardiovascular Disease (ACCORD) trial (n=187 cases: 187 controls) and from a diverse contemporary cohort of type 2 diabetic patients from the Mount Sinai BioMe Biobank (n=871) to assess the association of plasma endostatin and kidney outcomes. We measured plasma endostatin at enrollment and examined its association with a composite kidney outcome of sustained 40% decline in estimated GFR or end-stage renal disease. Baseline plasma endostatin levels were higher in participants with the composite outcome. Each log2 increment in plasma endostatin was associated with approximately 2.5-fold higher risk of the kidney outcome (adjusted odds ratio [OR] 2.5; 95% confidence interval [CI] 1.5-4.3 in ACCORD and adjusted hazard ratio [HR] 2.6; 95% CI 1.8-3.8 in BioMe). Participants in the highest vs. lowest quartile of plasma endostatin had approximately four-fold higher risk for the kidney outcome (adjusted OR 3.6; 95% CI 1.8-7.3 in ACCORD and adjusted HR 4.4; 95% CI 2.3-8.5 in BioMe). The AUC for the kidney outcome improved from 0.74 to 0.77 in BioMe with the addition of endostatin to a base clinical model. Plasma endostatin was strongly associated with kidney outcomes in type 2 diabetics with preserved eGFR and improved risk discrimination over traditional predictors.
Collapse
Affiliation(s)
- Kinsuk Chauhan
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Veena Rao
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lili Chan
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chirag R Parikh
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Steven G Coca
- Icahn School of Medicine at Mount Sinai, New York, New York, USA.
| | | |
Collapse
|
23
|
Capalbo A, Chokoshvili D, Dugoff L, Franasiak J, Gleicher N, Pennings G, Simon C. Should the reproductive risk of a couple aiming to conceive be tested in the contemporary clinical context? Fertil Steril 2019; 111:229-238. [PMID: 30642571 DOI: 10.1016/j.fertnstert.2018.11.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Davit Chokoshvili
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Lorraine Dugoff
- Maternal Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Jason Franasiak
- IVI-RMA America, Reproductive Medicine Associates of New Jersey, Basking Ridge, New Jersey; Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Norbert Gleicher
- Center for Human Reproduction, New York, New York; Foundation for Reproductive Medicine, New York, New York; Stem Cell Biology and Molecular Embryology Laboratory, Rockefeller University, New York, New York; Department of Obstetrics and Gynecology, Vienna University of Medicine, Vienna, Austria
| | - Guido Pennings
- Bioethics Institute Ghent (BIG), Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University, and INCLIVA, Valencia, Spain; Department of Obstetrics and Gynecology, Stanford University, Stanford, California; Igenomix, Valencia, Spain.
| |
Collapse
|
24
|
Pharmacogenomics in Psychiatric Disorders. Pharmacogenomics 2019. [DOI: 10.1016/b978-0-12-812626-4.00007-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
25
|
Physician Knowledge of Human Genetic Variation, Beliefs About Race and Genetics, and Use of Race in Clinical Decision-making. J Racial Ethn Health Disparities 2018; 6:110-116. [PMID: 29926440 DOI: 10.1007/s40615-018-0505-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND Race in the USA has an enduring connection to health and well-being. It is often used as a proxy for ancestry and genetic variation, although self-identified race does not establish genetic risk of disease for an individual patient. How physicians reconcile these seemingly paradoxical facts as they make clinical decisions is unknown. OBJECTIVE To examine physicians' genetic knowledge and beliefs about race with their use of race in clinical decision-making DESIGN: Cross-sectional survey of a national sample of clinically active general internists RESULTS: Seven hundred eighty-seven physicians completed the survey. Regression models indicate that genetic knowledge was not significantly associated with use of race. However, physicians who agreed with notions of race as a biological phenomenon and those who agreed that race has clinical importance were more likely to report using race in their decision-making. CONCLUSIONS Genomic and precision medicine holds considerable promise for narrowing the gap in health among racial groups in the USA. For this promise to be realized, our findings suggest that future research and education efforts related to race, genomics, and health must go beyond educating health care providers about common genetic conditions to delving into assumptions about race and genetics.
Collapse
|
26
|
Nadkarni GN, Chauhan K, Verghese DA, Parikh CR, Do R, Horowitz CR, Bottinger EP, Coca SG. Plasma biomarkers are associated with renal outcomes in individuals with APOL1 risk variants. Kidney Int 2018; 93:1409-1416. [PMID: 29685497 PMCID: PMC5918426 DOI: 10.1016/j.kint.2018.01.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/10/2018] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
Abstract
G1/G2 variants in the Apolipoprotein L1 (APOL1) gene are associated with end-stage renal disease (ESRD) in people with African ancestry. Plasma biomarkers may have utility for risk stratification in APOL1 high-risk individuals of African ancestry. To evaluate this, we measured tumor necrosis factor receptor 1/2 (TNFR1/2) and kidney injury molecule-1 (KIM1) in baseline plasma specimens from individuals of African ancestry with high-risk APOL1 genotype. Biomarker association with a composite renal outcome of ESRD or 40% sustained decline in estimated glomerular filtration rate (eGFR) was then determined and then assessed as improvement in area under curve. Among the 498 participants, the median age was 56 years, 67.7% were female, and the baseline eGFR was 83.3 ml/min/1.73 m2 with 80 reaching outcome over 5.9 years. TNFR1, TNFR2, and KIM1 at enrollment were independently associated with renal outcome continuously (adjusted hazard ratio 2.0 [95% confidence interval 1.3-3.1]; 1.5 [1.2-1.9]; and 1.6 [1.3-1.9] per doubling in levels, respectively) or by tertiles. The area under the curve significantly improved from 0.75 with the clinical model to 0.79 with the biomarker-enhanced model. The event rate was 40% with all 3 biomarkers elevated (adjusted odds ratio of 5.3 (2.3-12.0) vs. 17% (adjusted odds ratio 1.8 [0.9-3.6] with 1 or 2 elevated and 7% with no biomarkers elevated. Thus, plasma concentrations of TNFR1, TNFR2, and KIM1 are independently associated with renal outcome and improve discrimination or reclassification of African ancestry individuals with a high-risk APOL1 genotype and preserve renal function. Elevation of all markers had higher risk of outcome and can assist with better clinical prediction and improved clinical trial efficiency by enriching event rates.
Collapse
Affiliation(s)
- Girish N Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
| | - Kinsuk Chauhan
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Divya A Verghese
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chirag R Parikh
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ron Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Erwin P Bottinger
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Steven G Coca
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
| |
Collapse
|
27
|
Tin A, Nadkarni G, Evans AM, Winkler CA, Bottinger E, Rebholz CM, Sarnak MJ, Inker LA, Levey AS, Lipkowitz MS, Appel LJ, Arking DE, Coresh J, Grams ME. Serum 6-Bromotryptophan Levels Identified as a Risk Factor for CKD Progression. J Am Soc Nephrol 2018; 29:1939-1947. [PMID: 29777021 DOI: 10.1681/asn.2017101064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/18/2018] [Indexed: 12/13/2022] Open
Abstract
Background Metabolite levels reflect physiologic homeostasis and may serve as biomarkers of disease progression. Identifying metabolites associated with APOL1 risk alleles-genetic variants associated with CKD risk commonly present in persons of African descent-may reveal novel markers of CKD progression relevant to other populations.Methods We evaluated associations between the number of APOL1 risk alleles and 760 serum metabolites identified via untargeted profiling in participants of the African American Study of Kidney Disease and Hypertension (AASK) (n=588; Bonferroni significance threshold P<6.5×10-5) and replicated findings in 678 black participants with CKD in BioMe, an electronic medical record-linked biobank. We tested the metabolite association with CKD progression in AASK, BioMe, and the Modification of Diet in Renal Disease (MDRD) Study.Results One metabolite, 6-bromotryptophan, was significant in AASK (P=4.7×10-5) and replicated in BioMe (P=5.7×10-3) participants, with lower levels associated with more APOL1 risk alleles. Lower levels of 6-bromotryptophan were associated with CKD progression in AASK and BioMe participants and in white participants in the MDRD Study, independent of demographics and clinical characteristics, including baseline GFR (adjusted hazard ratio per two-fold higher 6-bromotryptophan level, AASK, 0.76; 95% confidence interval [95% CI], 0.64 to 0.91; BioMe, 0.61; 95% CI, 0.43 to 0.85; MDRD, 0.52; 95% CI, 0.34 to 0.79). The interaction between the APOL1 risk alleles and 6-bromotryptophan was not significant. The identity of 6-bromotryptophan was confirmed in experiments comparing its molecular signature with that of authentic standards of other bromotryptophan isomers.Conclusions Serum 6-bromotryptophan is a consistent and novel risk factor for CKD progression.
Collapse
Affiliation(s)
- Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; .,Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland
| | - Girish Nadkarni
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health and Leidos Biomedical Research, Frederick National Laboratory, Frederick, Maryland
| | - Erwin Bottinger
- Hasso Plattner Institute, Center of Digital Health, Potsdam, Germany
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland
| | - Mark J Sarnak
- William B. Schwartz Division of Nephrology, Department of Medicine, Tufts Medical Center, Boston, Maryland
| | - Lesley A Inker
- William B. Schwartz Division of Nephrology, Department of Medicine, Tufts Medical Center, Boston, Maryland
| | - Andrew S Levey
- William B. Schwartz Division of Nephrology, Department of Medicine, Tufts Medical Center, Boston, Maryland
| | - Michael S Lipkowitz
- Division of Nephrology, Department of Medicine, Georgetown University, Washington, DC; and
| | - Lawrence J Appel
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine and Department of Medicine, Division of Cardiology, and
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Welch Center for Prevention, Epidemiology, and Clinical Research, Baltimore, Maryland
| | - Morgan E Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; .,Division of Nephrology, Johns Hopkins School of Medicine, Baltimore, Maryland
| |
Collapse
|
28
|
Hu J, Iragavarapu S, Nadkarni GN, Huang R, Erazo M, Bao X, Verghese D, Coca S, Ahmed MK, Peter I. Location-Specific Oral Microbiome Possesses Features Associated With CKD. Kidney Int Rep 2018; 3:193-204. [PMID: 29340331 PMCID: PMC5762954 DOI: 10.1016/j.ekir.2017.08.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 08/29/2017] [Indexed: 01/01/2023] Open
Abstract
INTRODUCTION Chronic kidney disease (CKD), a progressive loss of renal function, can lead to serious complications if underdiagnosed. Many studies suggest that the oral microbiota plays important role in the health of the host; however, little is known about the association between the oral microbiota and CKD pathogenesis. METHODS In this study, we surveyed the oral microbiota in saliva, the left and right molars, and the anterior mandibular lingual area from 77 participants (18 with and 59 without CKD), and tested their association with CKD to identify microbial features that may be predictive of CKD status. RESULTS The overall oral microbiota composition significantly differed by oral locations and was associated with CKD status in saliva and anterior mandibular lingual samples. In CKD patients, we observed a significant enrichment of Neisseria and depletion of Veillonella in both sample types and a lower prevalence of Streptococcus in saliva after adjustment for other comorbidities. Furthermore, we detected a negative association of Neisseria and Streptococcus genera with the kidney function as measured by estimated glomerular filtration rate. Neisseria abundance also correlated with plasma interleukin-18 levels. CONCLUSION We demonstrate the association of the oral microbiome with CKD and inflammatory kidney biomarkers, highlighting a potential role of the commensal bacteria in CKD pathogenesis. A better understanding of the interplay between the oral microbiota and CKD may help in the development of new strategies to identify at-risk individuals or to serve as a novel target for therapeutic intervention.
Collapse
Affiliation(s)
- Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Girish N. Nadkarni
- Department of Medicine, Division of Nephrology and the Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ruiqi Huang
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Monica Erazo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Xiuliang Bao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Divya Verghese
- Department of Medicine, Division of Nephrology and the Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Steven Coca
- Department of Medicine, Division of Nephrology and the Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mairaj K. Ahmed
- Departments of Dentistry/Oral Maxillofacial Surgery, Otolaryngology and Plastic Surgery, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
29
|
Leveraging functional annotations in genetic risk prediction for human complex diseases. PLoS Comput Biol 2017; 13:e1005589. [PMID: 28594818 PMCID: PMC5481142 DOI: 10.1371/journal.pcbi.1005589] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 06/22/2017] [Accepted: 05/19/2017] [Indexed: 12/25/2022] Open
Abstract
Genetic risk prediction is an important goal in human genetics research and precision medicine. Accurate prediction models will have great impacts on both disease prevention and early treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome wide association studies (GWAS), genetic risk prediction accuracy remains moderate for most diseases, which is largely due to the challenges in both identifying all the functionally relevant variants and accurately estimating their effect sizes in the presence of linkage disequilibrium. In this paper, we introduce AnnoPred, a principled framework that leverages diverse types of genomic and epigenomic functional annotations in genetic risk prediction for complex diseases. AnnoPred is trained using GWAS summary statistics in a Bayesian framework in which we explicitly model various functional annotations and allow for linkage disequilibrium estimated from reference genotype data. Compared with state-of-the-art risk prediction methods, AnnoPred achieves consistently improved prediction accuracy in both extensive simulations and real data.
Collapse
|
30
|
Fernández-Rhodes L, Gong J, Haessler J, Franceschini N, Graff M, Nishimura KK, Wang Y, Highland HM, Yoneyama S, Bush WS, Goodloe R, Ritchie MD, Crawford D, Gross M, Fornage M, Buzkova P, Tao R, Isasi C, Avilés-Santa L, Daviglus M, Mackey RH, Houston D, Gu CC, Ehret G, Nguyen KDH, Lewis CE, Leppert M, Irvin MR, Lim U, Haiman CA, Le Marchand L, Schumacher F, Wilkens L, Lu Y, Bottinger EP, Loos RJL, Sheu WHH, Guo X, Lee WJ, Hai Y, Hung YJ, Absher D, Wu IC, Taylor KD, Lee IT, Liu Y, Wang TD, Quertermous T, Juang JMJ, Rotter JI, Assimes T, Hsiung CA, Chen YDI, Prentice R, Kuller LH, Manson JE, Kooperberg C, Smokowski P, Robinson WR, Gordon-Larsen P, Li R, Hindorff L, Buyske S, Matise TC, Peters U, North KE. Trans-ethnic fine-mapping of genetic loci for body mass index in the diverse ancestral populations of the Population Architecture using Genomics and Epidemiology (PAGE) Study reveals evidence for multiple signals at established loci. Hum Genet 2017; 136:771-800. [PMID: 28391526 PMCID: PMC5485655 DOI: 10.1007/s00439-017-1787-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/23/2017] [Indexed: 11/26/2022]
Abstract
Most body mass index (BMI) genetic loci have been identified in studies of primarily European ancestries. The effect of these loci in other racial/ethnic groups is less clear. Thus, we aimed to characterize the generalizability of 170 established BMI variants, or their proxies, to diverse US populations and trans-ethnically fine-map 36 BMI loci using a sample of >102,000 adults of African, Hispanic/Latino, Asian, European and American Indian/Alaskan Native descent from the Population Architecture using Genomics and Epidemiology Study. We performed linear regression of the natural log of BMI (18.5-70 kg/m2) on the additive single nucleotide polymorphisms (SNPs) at BMI loci on the MetaboChip (Illumina, Inc.), adjusting for age, sex, population stratification, study site, or relatedness. We then performed fixed-effect meta-analyses and a Bayesian trans-ethnic meta-analysis to empirically cluster by allele frequency differences. Finally, we approximated conditional and joint associations to test for the presence of secondary signals. We noted directional consistency with the previously reported risk alleles beyond what would have been expected by chance (binomial p < 0.05). Nearly, a quarter of the previously described BMI index SNPs and 29 of 36 densely-genotyped BMI loci on the MetaboChip replicated/generalized in trans-ethnic analyses. We observed multiple signals at nine loci, including the description of seven loci with novel multiple signals. This study supports the generalization of most common genetic loci to diverse ancestral populations and emphasizes the importance of dense multiethnic genomic data in refining the functional variation at genetic loci of interest and describing several loci with multiple underlying genetic variants.
Collapse
Affiliation(s)
- Lindsay Fernández-Rhodes
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jian Gong
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nora Franceschini
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mariaelisa Graff
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katherine K Nishimura
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yujie Wang
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heather M Highland
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sachiko Yoneyama
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William S Bush
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Goodloe
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
| | - Marylyn D Ritchie
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Dana Crawford
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Myriam Fornage
- Center for Human Genetics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Petra Buzkova
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Ran Tao
- Department of Biostatistics, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carmen Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Martha Daviglus
- Insitute of Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Rachel H Mackey
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Denise Houston
- Geriatrics and Gerontology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - C Charles Gu
- Division of Biostatistics, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Georg Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Division of Cardiology, Geneva University Hospital, Geneva, OH, Switzerland
| | - Khanh-Dung H Nguyen
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Cora E Lewis
- Department of Medicine, University of Alabama, Birmingham, AL, USA
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lynne Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yingchang Lu
- Charles R. Bronfman Instituted for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erwin P Bottinger
- Charles R. Bronfman Instituted for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruth J L Loos
- Charles R. Bronfman Instituted for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wayne H-H Sheu
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, National Yang-Ming University, Taipei, Taiwan
| | - Xiuqing Guo
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yang Hai
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yi-Jen Hung
- Division of Endocrinology and Metabolism, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - I-Chien Wu
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - I-Te Lee
- Division of Endocrine and Metabolism, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Defense Medical Center, National Yang-Ming University, Taipei, Taiwan
| | - Yeheng Liu
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Tzung-Dau Wang
- Division of Cardiology, Department of Internal Medicine, Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jyh-Ming J Juang
- Division of Cardiology, Department of Internal Medicine, Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Themistocles Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Chao A Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Taiwan
| | - Yii-Der Ida Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, LABioMed at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ross Prentice
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lewis H Kuller
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - JoAnn E Manson
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul Smokowski
- School of Social Welfare, The University of Kansas, Lawrence, KS, USA
| | - Whitney R Robinson
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rongling Li
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven Buyske
- Department of Statistics and Biostatistics, Rutgers University, Piscataway, NJ, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kari E North
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
31
|
Jain D, Hodonsky CJ, Schick UM, Morrison JV, Minnerath S, Brown L, Schurmann C, Liu Y, Auer PL, Laurie CA, Taylor KD, Browning BL, Papanicolaou G, Browning SR, Loos RJF, North KE, Thyagarajan B, Laurie CC, Thornton TA, Sofer T, Reiner AP. Genome-wide association of white blood cell counts in Hispanic/Latino Americans: the Hispanic Community Health Study/Study of Latinos. Hum Mol Genet 2017; 26:1193-1204. [PMID: 28158719 DOI: 10.1093/hmg/ddx024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/11/2017] [Indexed: 12/13/2022] Open
Abstract
Circulating white blood cell (WBC) counts (neutrophils, monocytes, lymphocytes, eosinophils, basophils) differ by ethnicity. The genetic factors underlying basal WBC traits in Hispanics/Latinos are unknown. We performed a genome-wide association study of total WBC and differential counts in a large, ethnically diverse US population sample of Hispanics/Latinos ascertained by the Hispanic Community Health Study and Study of Latinos (HCHS/SOL). We demonstrate that several previously known WBC-associated genetic loci (e.g. the African Duffy antigen receptor for chemokines null variant for neutrophil count) are generalizable to WBC traits in Hispanics/Latinos. We identified and replicated common and rare germ-line variants at FLT3 (a gene often somatically mutated in leukemia) associated with monocyte count. The common FLT3 variant rs76428106 has a large allele frequency differential between African and non-African populations. We also identified several novel genetic loci involving or regulating hematopoietic transcription factors (CEBPE-SLC7A7, CEBPA and CRBN-TRNT1) associated with basophil count. The minor allele of the CEBPE variant associated with lower basophil count has been previously associated with Amerindian ancestry and higher risk of acute lymphoblastic leukemia in Hispanics. Together, these data suggest that germline genetic variation affecting transcriptional and signaling pathways that underlie WBC development and lineage specification can contribute to inter-individual as well as ethnic differences in peripheral blood cell counts (normal hematopoiesis) in addition to susceptibility to leukemia (malignant hematopoiesis).
Collapse
Affiliation(s)
- Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC 27514, USA
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | - Jean V Morrison
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sharon Minnerath
- Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lisa Brown
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, School of Medicine, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Paul L Auer
- Department of Biostatistics, Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53201, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.,Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Brian L Browning
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung and Blood Institute, Bethesda, MD 20824, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina Gillings School of Public Health, Chapel Hill, NC 27514, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Bharat Thyagarajan
- Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| |
Collapse
|
32
|
Cook JP, Mahajan A, Morris AP. Guidance for the utility of linear models in meta-analysis of genetic association studies of binary phenotypes. Eur J Hum Genet 2016; 25:240-245. [PMID: 27848946 PMCID: PMC5237383 DOI: 10.1038/ejhg.2016.150] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/13/2016] [Accepted: 09/27/2016] [Indexed: 12/12/2022] Open
Abstract
Linear mixed models are increasingly used for the analysis of genome-wide association studies (GWAS) of binary phenotypes because they can efficiently and robustly account for population stratification and relatedness through inclusion of random effects for a genetic relationship matrix. However, the utility of linear (mixed) models in the context of meta-analysis of GWAS of binary phenotypes has not been previously explored. In this investigation, we present simulations to compare the performance of linear and logistic regression models under alternative weighting schemes in a fixed-effects meta-analysis framework, considering designs that incorporate variable case–control imbalance, confounding factors and population stratification. Our results demonstrate that linear models can be used for meta-analysis of GWAS of binary phenotypes, without loss of power, even in the presence of extreme case–control imbalance, provided that one of the following schemes is used: (i) effective sample size weighting of Z-scores or (ii) inverse-variance weighting of allelic effect sizes after conversion onto the log-odds scale. Our conclusions thus provide essential recommendations for the development of robust protocols for meta-analysis of binary phenotypes with linear models.
Collapse
Affiliation(s)
- James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| |
Collapse
|
33
|
Expanded carrier screening in an infertile population: how often is clinical decision making affected? Genet Med 2016; 18:1097-1101. [PMID: 26938781 DOI: 10.1038/gim.2016.8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/06/2016] [Indexed: 12/28/2022] Open
Abstract
PURPOSE Options for preconception genetic screening have grown dramatically. Expanded carrier screening (ECS) now allows for determining carrier status for hundreds of genetic mutations by using a single sample, and some recommend ECS prior to in vitro fertilization. This study seeks to evaluate how often ECS alters clinical management when patients present for infertility care. METHODS All patients tested with ECS at a single infertility care center from 2011 to 2014 were evaluated. The overall rate of positive ECS results and the number of couples who were carriers of the same genetic disorder were evaluated. RESULTS A total of 6,643 individuals were tested, representing 3,738 couples; 1,666 (25.1%) of the individuals had a positive test result for at least one disorder. In 8 of the 3,738 couples, both members of the couple were positive for the same genetic disorder or had a test result that placed them at risk of having an affected child. Three of eight cases were cystic fibrosis. In this cohort, ECS affected clinical care eight times after 6,643 tests (0.12%, confidence interval: 0.05-0.24%) in 3,738 couples (0.21%, confidence interval: 0.09-0.42%). CONCLUSIONS ECS is becoming more widespread. In a large case series, ECS affected clinical decision making for patients presenting for infertility care in 0.21% of cases. This information must be weighed when utilizing these tests and may be a helpful part of patient counseling.Genet Med 18 11, 1097-1101.
Collapse
|
34
|
Zhang J, Fedick A, Wasserman S, Zhao G, Edelmann L, Bottinger EP, Kornreich R, Scott SA. Analytical Validation of a Personalized Medicine APOL1 Genotyping Assay for Nondiabetic Chronic Kidney Disease Risk Assessment. J Mol Diagn 2016; 18:260-6. [PMID: 26773863 PMCID: PMC4816711 DOI: 10.1016/j.jmoldx.2015.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 01/13/2023] Open
Abstract
The incidence of chronic kidney disease (CKD) varies by ancestry, with African Americans (AA) having a threefold to fourfold higher rate than whites. Notably, two APOL1 alleles, termed G1 [c.(1072A>G; 1200T>G)] and G2 (c.1212_1217del6), are strongly associated with higher rates of nondiabetic CKD and an increased risk for hypertensive end-stage renal disease. This has prompted the opportunity to implement APOL1 testing to identify at-risk patients and modify other risk factors to reduce the progression of CKD to end-stage renal disease. We developed an APOL1 genotyping assay using multiplex allele-specific primer extension, and validated using 58 positive and negative controls. Genotyping results were completely concordant with Sanger sequencing, and both triplicate interrun and intrarun genotyping results were completely concordant. Multiethnic APOL1 allele frequencies were also determined by genotyping 7059 AA, Hispanic, and Asian individuals from the New York City metropolitan area. The AA, Hispanic, and Asian APOL1 G1 and G2 allele frequencies were 0.22 and 0.13, 0.037 and 0.025, and 0.013 and 0.004, respectively. Notably, approximately 14% of the AA population carried two risk alleles and are at increased risk for CKD, compared with <1% of the Hispanic and Asian populations. This novel APOL1 genotyping assay is robust and highly accurate, and represents one of the first personalized medicine clinical genetic tests for disease risk prediction.
Collapse
Affiliation(s)
- Jinglan Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Anastasia Fedick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stephanie Wasserman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Geping Zhao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Erwin P Bottinger
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruth Kornreich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| |
Collapse
|
35
|
Claudio-Campos K, Duconge J, Cadilla CL, Ruaño G. Pharmacogenetics of drug-metabolizing enzymes in US Hispanics. Drug Metab Pers Ther 2016; 30:87-105. [PMID: 25431893 DOI: 10.1515/dmdi-2014-0023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/02/2014] [Indexed: 12/19/2022]
Abstract
Although the Hispanic population is continuously growing in the United States, they are underrepresented in pharmacogenetic studies. This review addresses the need for compiling available pharmacogenetic data in US Hispanics, discussing the prevalence of clinically relevant polymorphisms in pharmacogenes encoding for drug-metabolizing enzymes. CYP3A5*3 (0.245-0.867) showed the largest frequency in a US Hispanic population. A higher prevalence of CYP2C9*3, CYP2C19*4, and UGT2B7 IVS1+985 A>G was observed in US Hispanic vs. non-Hispanic populations. We found interethnic and intraethnic variability in frequencies of genetic polymorphisms for metabolizing enzymes, which highlights the need to define the ancestries of participants in pharmacogenetic studies. New approaches should be integrated in experimental designs to gain knowledge about the clinical relevance of the unique combination of genetic variants occurring in this admixed population. Ethnic subgroups in the US Hispanic population may harbor variants that might be part of multiple causative loci or in linkage-disequilibrium with functional variants. Pharmacogenetic studies in Hispanics should not be limited to ascertain commonly studied polymorphisms that were originally identified in their parental populations. The success of the Personalized Medicine paradigm will depend on recognizing genetic diversity between and within US Hispanics and the uniqueness of their genetic backgrounds.
Collapse
|
36
|
Schick UM, Jain D, Hodonsky CJ, Morrison JV, Davis JP, Brown L, Sofer T, Conomos MP, Schurmann C, McHugh CP, Nelson SC, Vadlamudi S, Stilp A, Plantinga A, Baier L, Bien SA, Gogarten SM, Laurie CA, Taylor KD, Liu Y, Auer PL, Franceschini N, Szpiro A, Rice K, Kerr KF, Rotter JI, Hanson RL, Papanicolaou G, Rich SS, Loos RJF, Browning BL, Browning SR, Weir BS, Laurie CC, Mohlke KL, North KE, Thornton TA, Reiner AP. Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans. Am J Hum Genet 2016; 98:229-42. [PMID: 26805783 PMCID: PMC4746331 DOI: 10.1016/j.ajhg.2015.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/07/2015] [Indexed: 12/23/2022] Open
Abstract
Platelets play an essential role in hemostasis and thrombosis. We performed a genome-wide association study of platelet count in 12,491 participants of the Hispanic Community Health Study/Study of Latinos by using a mixed-model method that accounts for admixture and family relationships. We discovered and replicated associations with five genes (ACTN1, ETV7, GABBR1-MOG, MEF2C, and ZBTB9-BAK1). Our strongest association was with Amerindian-specific variant rs117672662 (p value = 1.16 × 10(-28)) in ACTN1, a gene implicated in congenital macrothrombocytopenia. rs117672662 exhibited allelic differences in transcriptional activity and protein binding in hematopoietic cells. Our results underscore the value of diverse populations to extend insights into the allelic architecture of complex traits.
Collapse
Affiliation(s)
- Ursula M Schick
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jean V Morrison
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - James P Davis
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lisa Brown
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Claudia Schurmann
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caitlin P McHugh
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Anna Plantinga
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Leslie Baier
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, NIH, 445 North 5(th) Street, Phoenix, AZ 85004, USA
| | - Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
| | | | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yongmei Liu
- School of Medicine, Wake Forest University, Winston-Salem, NC 27157, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53201, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Adam Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kathleen F Kerr
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, NIH, 445 North 5(th) Street, Phoenix, AZ 85004, USA
| | - George Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA; Division of Endocrinology, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian L Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA.
| |
Collapse
|
37
|
A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set. Eur J Hum Genet 2015; 24:725-31. [PMID: 26395555 DOI: 10.1038/ejhg.2015.187] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 07/12/2015] [Indexed: 11/08/2022] Open
Abstract
The Brazilian population is considered to be highly admixed. The main contributing ancestral populations were European and African, with Amerindians contributing to a lesser extent. The aims of this study were to provide a resource for determining and quantifying individual continental ancestry using the smallest number of SNPs possible, thus allowing for a cost- and time-efficient strategy for genomic ancestry determination. We identified and validated a minimum set of 192 ancestry informative markers (AIMs) for the genetic ancestry determination of Brazilian populations. These markers were selected on the basis of their distribution throughout the human genome, and their capacity of being genotyped on widely available commercial platforms. We analyzed genotyping data from 6487 individuals belonging to three Brazilian cohorts. Estimates of individual admixture using this 192 AIM panels were highly correlated with estimates using ~370 000 genome-wide SNPs: 91%, 92%, and 74% of, respectively, African, European, and Native American ancestry components. Besides that, 192 AIMs are well distributed among populations from these ancestral continents, allowing greater freedom in future studies with this panel regarding the choice of reference populations. We also observed that genetic ancestry inferred by AIMs provides similar association results to the one obtained using ancestry inferred by genomic data (370 K SNPs) in a simple regression model with rs1426654, related to skin pigmentation, genotypes as dependent variable. In conclusion, these markers can be used to identify and accurately quantify ancestry of Latin Americans or US Hispanics/Latino individuals, in particular in the context of fine-mapping strategies that require the quantification of continental ancestry in thousands of individuals.
Collapse
|
38
|
Rivera-Garcia C, Bristow SL, Yarnall S, Kumar N, Rodriguez S, De Veaux N, Bisignano A, Chu B, Prates R, Munne S. Retracted: Validation of a multiplex genotyping platform using a novel genomic database approach. Genet Med 2015. [DOI: 10.1038/gim.2015.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
39
|
Abstract
Personalized medicine has seen a recent increase in popularity amongst medical researchers and policymakers. Nevertheless, there are persistent legal, ethical, and social questions that need to be explored, particularly related to the criticism that personalized medicine constitutes an elitist model of healthcare. Investigating this critique the current manuscript argues that personalized medicine has the potential to become a positive force for equitable access to better healthcare at a national and international level.
Collapse
Affiliation(s)
- Yann Joly
- Centre de génomique et politique, université McGill, 740 avenue du Dr Penfield, Montréal, Québec H3A 0G1, Canada
| | - Bartha M Knoppers
- Centre de génomique et politique, université McGill, 740 avenue du Dr Penfield, Montréal, Québec H3A 0G1, Canada
| |
Collapse
|
40
|
Udler MS, Nadkarni GN, Belbin G, Lotay V, Wyatt C, Gottesman O, Bottinger EP, Kenny EE, Peter I. Effect of Genetic African Ancestry on eGFR and Kidney Disease. J Am Soc Nephrol 2014; 26:1682-92. [PMID: 25349204 DOI: 10.1681/asn.2014050474] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/02/2014] [Indexed: 01/08/2023] Open
Abstract
Self-reported ancestry, genetically determined ancestry, and APOL1 polymorphisms are associated with variation in kidney function and related disease risk, but the relative importance of these factors remains unclear. We estimated the global proportion of African ancestry for 9048 individuals at Mount Sinai Medical Center in Manhattan (3189 African Americans, 1721 European Americans, and 4138 Hispanic/Latino Americans by self-report) using genome-wide genotype data. CKD-EPI eGFR and genotypes of three APOL1 coding variants were available. In admixed African Americans and Hispanic/Latino Americans, serum creatinine values increased as African ancestry increased (per 10% increase in African ancestry, creatinine values increased 1% in African Americans and 0.9% in Hispanic/Latino Americans; P≤1x10(-7)). eGFR was likewise significantly associated with African genetic ancestry in both populations. In contrast, APOL1 risk haplotypes were significantly associated with CKD, eGFR<45 ml/min per 1.73 m(2), and ESRD, with effects increasing with worsening disease states and the contribution of genetic African ancestry decreasing in parallel. Using genetic ancestry in the eGFR equation to reclassify patients as black on the basis of ≥50% African ancestry resulted in higher eGFR for 14.7% of Hispanic/Latino Americans and lower eGFR for 4.1% of African Americans, affecting CKD staging in 4.3% and 1% of participants, respectively. Reclassified individuals had electrolyte values consistent with their newly assigned CKD stage. In summary, proportion of African ancestry was significantly associated with normal-range creatinine and eGFR, whereas APOL1 risk haplotypes drove the associations with CKD. Recalculation of eGFR on the basis of genetic ancestry affected CKD staging and warrants additional investigation.
Collapse
Affiliation(s)
- Miriam S Udler
- Departments of Medicine and Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine,
| | - Girish N Nadkarni
- Departments of Medicine and The Charles Bronfman Institute for Personalized Medicine, Division of Nephrology
| | - Gillian Belbin
- Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine
| | - Vaneet Lotay
- The Charles Bronfman Institute for Personalized Medicine
| | | | - Omri Gottesman
- Departments of Medicine and The Charles Bronfman Institute for Personalized Medicine
| | - Erwin P Bottinger
- Departments of Medicine and The Charles Bronfman Institute for Personalized Medicine, Division of Nephrology
| | - Eimear E Kenny
- Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, The Center for Statistical Genetics, and The Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Inga Peter
- Genetics and Genomic Sciences, The Charles Bronfman Institute for Personalized Medicine, The Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
41
|
Wang YJ, Tayo BO, Bandyopadhyay A, Wang H, Feng T, Franceschini N, Tang H, Gao J, Sung YJ, Elston RC, Williams SM, Cooper RS, Mu TW, Zhu X. The association of the vanin-1 N131S variant with blood pressure is mediated by endoplasmic reticulum-associated degradation and loss of function. PLoS Genet 2014; 10:e1004641. [PMID: 25233454 PMCID: PMC4169380 DOI: 10.1371/journal.pgen.1004641] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/30/2014] [Indexed: 02/07/2023] Open
Abstract
High blood pressure (BP) is the most common cardiovascular risk factor worldwide and a major contributor to heart disease and stroke. We previously discovered a BP-associated missense SNP (single nucleotide polymorphism)–rs2272996–in the gene encoding vanin-1, a glycosylphosphatidylinositol (GPI)-anchored membrane pantetheinase. In the present study, we first replicated the association of rs2272996 and BP traits with a total sample size of nearly 30,000 individuals from the Continental Origins and Genetic Epidemiology Network (COGENT) of African Americans (P = 0.01). This association was further validated using patient plasma samples; we observed that the N131S mutation is associated with significantly lower plasma vanin-1 protein levels. We observed that the N131S vanin-1 is subjected to rapid endoplasmic reticulum-associated degradation (ERAD) as the underlying mechanism for its reduction. Using HEK293 cells stably expressing vanin-1 variants, we showed that N131S vanin-1 was degraded significantly faster than wild type (WT) vanin-1. Consequently, there were only minimal quantities of variant vanin-1 present on the plasma membrane and greatly reduced pantetheinase activity. Application of MG-132, a proteasome inhibitor, resulted in accumulation of ubiquitinated variant protein. A further experiment demonstrated that atenolol and diltiazem, two current drugs for treating hypertension, reduce the vanin-1 protein level. Our study provides strong biological evidence for the association of the identified SNP with BP and suggests that vanin-1 misfolding and degradation are the underlying molecular mechanism. Hypertension (HTN) or high blood pressure (BP) is common worldwide and a major risk factor for cardiovascular disease and all-cause mortality. Identification of genetic variants of consequence for HTN serves as the molecular basis for its treatment. Using admixture mapping analysis of the Family Blood Pressure Program data, we recently identified that the VNN1 gene (encoding the protein vanin-1), in particular SNP rs2272996 (N131S), was associated with BP in both African Americans and Mexican Americans. Vanin-1 was reported to act as an oxidative stress sensor using its pantetheinase enzyme activity. Because a linkage between oxidative stress and HTN has been hypothesized for many years, vanin-1's pantetheinase activity offers a physiologic rationale for BP regulation. Here, we first replicated the association of rs2272996 with BP in the Continental Origins and Genetic Epidemiology Network (COGENT), which included nearly 30,000 African Americans. We further demonstrated that the N131S mutation in vanin-1 leads to its rapid degradation in cells, resulting in loss of function on the plasma membrane. The loss of function of vanin-1 is associated with reduced BP. Therefore, our results indicate that vanin-1 is a new candidate to be manipulated to ameliorate HTN.
Collapse
Affiliation(s)
- Ya-Juan Wang
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (YJW); (XZ)
| | - Bamidele O. Tayo
- Department of Public Health Sciences, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Anupam Bandyopadhyay
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Heming Wang
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Tao Feng
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jianmin Gao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St Louis, Missouri, United States of America
| | | | - Robert C. Elston
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Scott M. Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Richard S. Cooper
- Department of Public Health Sciences, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, United States of America
| | - Ting-Wei Mu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (YJW); (XZ)
| |
Collapse
|
42
|
Duster T. Social diversity in humans: implications and hidden consequences for biological research. Cold Spring Harb Perspect Biol 2014; 6:a008482. [PMID: 24789817 DOI: 10.1101/cshperspect.a008482] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Humans are both similar and diverse in such a vast number of dimensions that for human geneticists and social scientists to decide which of these dimensions is a worthy focus of empirical investigation is a formidable challenge. For geneticists, one vital question, of course, revolves around hypothesizing which kind of social diversity might illuminate genetic variation-and vice versa (i.e., what genetic variation illuminates human social diversity). For example, are there health outcomes that can be best explained by genetic variation-or for social scientists, are health outcomes mainly a function of the social diversity of lifestyles and social circumstances of a given population? Indeed, what is a "population," how is it bounded, and are those boundaries most appropriate or relevant for human genetic research, be they national borders, religious affiliation, ethnic or racial identification, or language group, to name but a few? For social scientists, the matter of what constitutes the relevant borders of a population is equally complex, and the answer is demarcated by the goal of the research project. Although race and caste are categories deployed in both human genetics and social science, the social meaning of race and caste as pathways to employment, health, or education demonstrably overwhelms the analytic and explanatory power of genetic markers of difference between human aggregates.
Collapse
Affiliation(s)
- Troy Duster
- Chancellor's Professor & Senior Fellow, Warren Institute on Law and Social Policy, Boalt School of Law, University of California Berkeley, Berkeley, California 94720
| |
Collapse
|
43
|
Abstract
The concept of race has had a significant influence on research in human biology since the early 19th century. But race was given its meaning and social impact in the political sphere and subsequently intervened in science as a foreign concept, not grounded in the dominant empiricism of modern biology. The uses of race in science were therefore often disruptive and controversial; at times, science had to be retrofitted to accommodate race, and science in turn was often used to explain and justify race. This relationship was unstable in large part because race was about a phenomenon that could not be observed directly, being based on claims about the structure and function of genomic DNA. Over time, this relationship has been characterized by distinct phases, evolving from the inference of genetic effects based on the observed phenotype to the measurement of base-pair variation in DNA. Despite this fundamental advance in methodology, liabilities imposed by the dual political-empirical origins of race persist. On the one hand, an optimistic prediction can be made that just as geology made it possible to overturn the myth of the recent creation of the earth and evolution told us where the living world came from, molecular genetics will end the use of race in biology. At the same time, because race is fundamentally a political and not a scientific idea, it is possible that only a political intervention will relieve us of the burden of race.
Collapse
Affiliation(s)
- Richard S Cooper
- Department of Public Health Sciences, Loyola University Medical School, Maywood, Illinois 60153
| |
Collapse
|
44
|
Cicogna F, Pinzino C, Castellano S, Porta A, Forte C, Calucci L. Interaction of Azole Compounds with DOPC and DOPC/Ergosterol Bilayers by Spin Probe EPR Spectroscopy: Implications for Antifungal Activity. J Phys Chem B 2013; 117:11978-87. [DOI: 10.1021/jp406776x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francesca Cicogna
- Istituto di Chimica
dei Composti OrganoMetallici, Consiglio Nazionale delle Ricerche −
CNR, Area della Ricerca di Pisa, via
G. Moruzzi 1, 56124, Pisa, Italy
| | - Calogero Pinzino
- Istituto di Chimica
dei Composti OrganoMetallici, Consiglio Nazionale delle Ricerche −
CNR, Area della Ricerca di Pisa, via
G. Moruzzi 1, 56124, Pisa, Italy
| | - Sabrina Castellano
- Dipartimento
di Farmacia, Università di Salerno, via Giovanni Paolo II, 84084 Fisciano, Salerno, Italy
| | - Amalia Porta
- Dipartimento
di Farmacia, Università di Salerno, via Giovanni Paolo II, 84084 Fisciano, Salerno, Italy
| | - Claudia Forte
- Istituto di Chimica
dei Composti OrganoMetallici, Consiglio Nazionale delle Ricerche −
CNR, Area della Ricerca di Pisa, via
G. Moruzzi 1, 56124, Pisa, Italy
| | - Lucia Calucci
- Istituto di Chimica
dei Composti OrganoMetallici, Consiglio Nazionale delle Ricerche −
CNR, Area della Ricerca di Pisa, via
G. Moruzzi 1, 56124, Pisa, Italy
| |
Collapse
|
45
|
Hertz DL, Roy S, Motsinger-Reif AA, Drobish A, Clark LS, McLeod HL, Carey LA, Dees EC. CYP2C8*3 increases risk of neuropathy in breast cancer patients treated with paclitaxel. Ann Oncol 2013; 24:1472-8. [PMID: 23413280 DOI: 10.1093/annonc/mdt018] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Paclitaxel-induced neuropathy is an adverse event that often leads to therapeutic disruption and patient discomfort. We attempted to replicate a previously reported association between increased neuropathy risk and CYP2C8*3 genotype. PATIENTS AND METHODS Demographic, treatment, and toxicity data were collected for paclitaxel-treated breast cancer patients who were genotyped for the CYP2C8*3 K399R (rs10509681) variant. A log-rank test was used in the primary analysis of European-American patients. An additional independent replication was then attempted in a cohort of African-American patients, followed by modeling of the entire patient cohort with relevant covariates. RESULTS In the primary analysis of 209 European patients, there was an increased risk of paclitaxel-induced neuropathy related to CYP2C8*3 status [HR (per allele) = 1.93 (95% CI: 1.05-3.55), overall log-rank P = 0.006]. The association was replicated in direction and magnitude of effect in 107 African-American patients (P = 0.043). In the Cox model using the entire mixed-race cohort (n = 411), each CYP2C8*3 allele approximately doubled the patient's risk of grade 2+ neuropathy (P = 0.004), and non-Europeans were at higher neuropathy risk than Europeans of similar genotype (P = 0.030). CONCLUSIONS The increased risk of paclitaxel-induced neuropathy in patients who carry the CYP2C8*3 variant was replicated in two racially distinct patient cohorts.
Collapse
Affiliation(s)
- D L Hertz
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, UNC Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Libiger O, Schork NJ. A Method for Inferring an Individual's Genetic Ancestry and Degree of Admixture Associated with Six Major Continental Populations. Front Genet 2013; 3:322. [PMID: 23335941 PMCID: PMC3543981 DOI: 10.3389/fgene.2012.00322] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/24/2012] [Indexed: 01/27/2023] Open
Abstract
The determination of the ancestry and genetic backgrounds of the subjects in genetic and general epidemiology studies is a crucial component in the analysis of relevant outcomes or associations. Although there are many methods for differentiating ancestral subgroups among individuals based on genetic markers only a few of these methods provide actual estimates of the fraction of an individual’s genome that is likely to be associated with different ancestral populations. We propose a method for assigning ancestry that works in stages to refine estimates of ancestral population contributions to individual genomes. The method leverages genotype data in the public domain obtained from individuals with known ancestries. Although we showcase the method in the assessment of ancestral genome proportions leveraging largely continental populations, the strategy can be used for assessing within-continent or more subtle ancestral origins with the appropriate data.
Collapse
Affiliation(s)
- Ondrej Libiger
- Department of Molecular and Experimental Medicine, The Scripps Research Institute and the Scripps Translational Science Institute La Jolla, CA, USA
| | | |
Collapse
|
47
|
Tayo BO. Book review: Fatal invention: How science, politics, and big business re-create race in the twenty-first century. Am J Hum Biol 2012. [DOI: 10.1002/ajhb.22290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
48
|
Juengst ET, Settersten RA, Fishman JR, McGowan ML. After the revolution? Ethical and social challenges in 'personalized genomic medicine'. Per Med 2012; 9:429-439. [PMID: 23662108 PMCID: PMC3646379 DOI: 10.2217/pme.12.37] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Personalized genomic medicine (PGM) is a goal that currently unites a wide array of biomedical initiatives, and is promoted as a 'new paradigm for healthcare' by its champions. Its promissory virtues include individualized diagnosis and risk prediction, more effective prevention and health promotion, and patient empowerment. Beyond overcoming scientific and technological hurdles to realizing PGM, proponents may interpret and rank these promises differently, which carries ethical and social implications for the realization of PGM as an approach to healthcare. We examine competing visions of PGM's virtues and the directions in which they could take the field, in order to anticipate policy choices that may lie ahead for researchers, healthcare providers and the public.
Collapse
Affiliation(s)
- Eric T Juengst
- University of North Carolina – Chapel Hill, Center for Bioethics, 333 MacNider Hall, Chapel Hill, NC 27599–7240, USA
| | - Richard A Settersten
- Oregon State University, College of Public Health & Human Sciences, 2631 SW Campus Way (HFC), Corvallis, OR 97331–5102, USA
| | - Jennifer R Fishman
- McGill University, Social Studies of Medicine Department, Biomedical Ethics Unit, 3647 Peel Street, 307, Montreal, QC H3A 1X1, Canada
| | - Michelle L McGowan
- Case Western Reserve University, School of Medicine, Department of Bioethics, 10900 Euclid Avenue, Cleveland, OH 44106–4976, USA
| |
Collapse
|
49
|
Abstract
Clinical genetic testing has grown substantially over the past 30 years as the causative mutations for Mendelian diseases have been identified, particularly aided in part by the recent advances in molecular-based technologies. Importantly, the adoption of new tests and testing strategies (e.g., diagnostic confirmation, prenatal testing, and population-based carrier screening) has often been met with caution and careful consideration before clinical implementation, which facilitates the appropriate use of new genetic tests. Although the field of pharmacogenetics was established in the 1950s, clinical testing for constitutional pharmacogenetic variants implicated in interindividual drug response variability has only recently become available to help clinicians guide pharmacotherapy, in part due to US Food and Drug Administration-mediated product insert revisions that include pharmacogenetic information for selected drugs. However, despite pharmacogenetic associations with adverse outcomes, physician uptake of clinical pharmacogenetic testing has been slow. Compared with testing for Mendelian diseases, pharmacogenetic testing for certain indications can have a lower positive predictive value, which is one reason for underutilization. A number of other barriers remain with implementing clinical pharmacogenetics, including clinical utility, professional education, and regulatory and reimbursement issues, among others. This review presents some of the current opportunities and challenges with implementing clinical pharmacogenetic testing.
Collapse
|
50
|
Abstract
Scientific and policy interest in health disparities, defined as systematic, plausibly avoidable health differences adversely affecting socially disadvantaged groups, has increased markedly over the past few decades. Like other research, research in health disparities is strongly influenced by the underlying conceptual model of the hypothetical causes of disparities. Conceptual models are important and a major source of debate because multiple types of factors and processes may be involved in generating disparities, because different disciplines emphasize different types of factors, and because the conceptual model often drives what is studied, how results are interpreted, and which interventions are identified as most promising. This article reviews common conceptual approaches to health disparities including the genetic model, the fundamental cause model, the pathways model, and the interaction model. Strengths and limitations of the approaches are highlighted. The article concludes by outlining key elements and implications of an integrative systems-based conceptual model.
Collapse
Affiliation(s)
- Ana V Diez Roux
- Center for Social Epidemiology and Population Health, Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48109, USA.
| |
Collapse
|