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Guaragna MS, de Brito Lutaif ACG, de Souza ML, Maciel-Guerra AT, Belangero VMS, Guerra-Júnior G, de Mello MP. Promises and pitfalls of whole-exome sequencing exemplified by a nephrotic syndrome family. Mol Genet Genomics 2019; 295:135-142. [PMID: 31520189 DOI: 10.1007/s00438-019-01609-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/05/2019] [Indexed: 01/12/2023]
Abstract
High-throughput techniques such as whole-exome sequencing (WES) show promise for the identification of candidate genes that underlie Mendelian diseases such as nephrotic syndrome (NS). These techniques have enabled the identification of a proportion of the approximately 54 genes associated with NS. However, the main pitfall of using WES in clinical and research practice is the identification of multiple variants, which hampers interpretation during downstream analysis. One useful strategy is to evaluate the co-inheritance of rare variants in affected family members. Here, we performed WES of a patient with steroid-resistant NS (SRNS) and intermittent microhematuria. Currently, 15 years after kidney transplantation, this patient presents normal kidney function. The patient was found to be homozygous for a rare MYO1E stop-gain variant, and was heterozygous for rare variants in NS-associated genes, COL4A4, KANK1, LAMB2, ANLN, E2F3, and APOL1. We evaluated the presence or absence of these variants in both parents and 11 siblings, three of whom exhibited a milder phenotype of the kidney disease. Analysis of variant segregation in the family, indicated the MYO1E stop-gain variant as the putative causal variant underlying the kidney disease in the patient and two of her affected sisters. Two secondary variants in COL4A4-identified in some other affected family members-require further functional studies to determine whether they play a role in the development of microhematuria in affected family members. Our data illustrate the difficulties in distinguishing the causal pathogenic variants from incidental findings after WES-based variant analysis, especially in heterogenous genetic conditions, such as NS.
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Affiliation(s)
- Mara Sanches Guaragna
- Laboratory of Human Molecular Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas, UNICAMP, Caixa Postal 6010, 13083-875, Campinas, SP, Brazil.
| | - Anna Cristina Gervásio de Brito Lutaif
- Integrated Center of Pediatric Nephrology (CIN), Department of Pediatrics, School of Medical Sciences (FCM), State University of Campinas, UNICAMP, Campinas, Brazil
| | - Marcela Lopes de Souza
- Laboratory of Human Molecular Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas, UNICAMP, Caixa Postal 6010, 13083-875, Campinas, SP, Brazil
| | | | - Vera Maria Santoro Belangero
- Integrated Center of Pediatric Nephrology (CIN), Department of Pediatrics, School of Medical Sciences (FCM), State University of Campinas, UNICAMP, Campinas, Brazil.,Department of Pediatrics, School of Medical Sciences (FCM), UNICAMP, Campinas, SP, Brazil
| | - Gil Guerra-Júnior
- Department of Pediatrics, School of Medical Sciences (FCM), UNICAMP, Campinas, SP, Brazil.,Growth and Development Laboratory, Center for Investigation in Pediatrics (CIPED), School of Medical Sciences (FCM), UNICAMP, Campinas, SP, Brazil
| | - Maricilda Palandi de Mello
- Laboratory of Human Molecular Genetics, Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas, UNICAMP, Caixa Postal 6010, 13083-875, Campinas, SP, Brazil
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TSOKOS GEORGEC, TSOKOS MARIAG. TARGETING TARGETED TREATMENT FOR IMMUNE AND NON-IMMUNE KIDNEY DISEASES. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2019; 130:88-99. [PMID: 31516171 PMCID: PMC6735968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have found that calcium calmodulin kinase IV is increased in T cells, podocytes, and mesangial cells from patients with systemic lupus erythematosus, as well as in lupus-prone mice, podocytes of patients with focal segmental glomerulosclerosis, and in mice injected with doxorubicin. We showed that this accounts for aberrant T cell function and glomerular damage. Using nanoparticles (nlg) loaded with a small drug inhibitor of calcium calmodulin kinase IV and tagged with antibodies directed to CD4 we have been able to show inhibition of autoimmunity and lupus nephritis. Also, using nlg tagged with antibodies to nephrin, we showed suppression of nephritis in lupus-prone mice and of glomerular damage in mice exposed to doxorubicin. We propose the development of approaches to deliver drugs to cells in a targeted and precise manner.
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Affiliation(s)
- GEORGE C. TSOKOS
- Correspondence and reprint requests: George C. Tsokos, MD, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School,
330 Brookline Ave., CLS 937, Boston, Massachusetts 02215617-735-4161
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3
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Ferretti AP, Bhargava R, Dahan S, Tsokos MG, Tsokos GC. Calcium/Calmodulin Kinase IV Controls the Function of Both T Cells and Kidney Resident Cells. Front Immunol 2018; 9:2113. [PMID: 30333818 PMCID: PMC6176098 DOI: 10.3389/fimmu.2018.02113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/28/2018] [Indexed: 12/12/2022] Open
Abstract
Calcium calmodulin kinase IV (CaMK4) regulates multiple processes that significantly contribute to the lupus-related pathology by controlling the production of IL-2 and IL-17 by T cells, the proliferation of mesangial cells, and the function and structure of podocytes. CaMK4 is also upregulated in podocytes from patients with focal segmental glomerulosclerosis (FSGS). In both immune and non-immune podocytopathies, CaMK4 disrupts the structure and function of podocytes. In lupus-prone mice, targeted delivery of a CaMK4 inhibitor to CD4+ T cells suppresses both autoimmunity and the development of nephritis. Targeted delivery though to podocytes averts the deposition of immune complexes without affecting autoimmunity in lupus-prone mice and averts pathology induced by adriamycin in normal mice. Therefore, targeted delivery of a CaMK4 inhibitor to podocytes holds high therapeutic promise for both immune (lupus nephritis) and non-immune (FSGS) podocytopathies.
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Affiliation(s)
- Andrew P Ferretti
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Rhea Bhargava
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Shani Dahan
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Maria G Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - George C Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
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Gillies CE, Putler R, Menon R, Otto E, Yasutake K, Nair V, Hoover P, Lieb D, Li S, Eddy S, Fermin D, McNulty MT, Hacohen N, Kiryluk K, Kretzler M, Wen X, Sampson MG. An eQTL Landscape of Kidney Tissue in Human Nephrotic Syndrome. Am J Hum Genet 2018; 103:232-244. [PMID: 30057032 PMCID: PMC6081280 DOI: 10.1016/j.ajhg.2018.07.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/29/2018] [Indexed: 01/14/2023] Open
Abstract
Expression quantitative trait loci (eQTL) studies illuminate the genetics of gene expression and, in disease research, can be particularly illuminating when using the tissues directly impacted by the condition. In nephrology, there is a paucity of eQTL studies of human kidney. Here, we used whole-genome sequencing (WGS) and microdissected glomerular (GLOM) and tubulointerstitial (TI) transcriptomes from 187 individuals with nephrotic syndrome (NS) to describe the eQTL landscape in these functionally distinct kidney structures. Using MatrixEQTL, we performed cis-eQTL analysis on GLOM (n = 136) and TI (n = 166). We used the Bayesian "Deterministic Approximation of Posteriors" (DAP) to fine-map these signals, eQTLBMA to discover GLOM- or TI-specific eQTLs, and single-cell RNA-seq data of control kidney tissue to identify the cell type specificity of significant eQTLs. We integrated eQTL data with an IgA Nephropathy (IgAN) GWAS to perform a transcriptome-wide association study (TWAS). We discovered 894 GLOM eQTLs and 1,767 TI eQTLs at FDR < 0.05. 14% and 19% of GLOM and TI eQTLs, respectively, had >1 independent signal associated with its expression. 12% and 26% of eQTLs were GLOM specific and TI specific, respectively. GLOM eQTLs were most significantly enriched in podocyte transcripts and TI eQTLs in proximal tubules. The IgAN TWAS identified significant GLOM and TI genes, primarily at the HLA region. In this study, we discovered GLOM and TI eQTLs, identified those that were tissue specific, deconvoluted them into cell-specific signals, and used them to characterize known GWAS alleles. These data are available for browsing and download via our eQTL browser, "nephQTL."
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Affiliation(s)
- Christopher E Gillies
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Rosemary Putler
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Edgar Otto
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Kalyn Yasutake
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Viji Nair
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Paul Hoover
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - David Lieb
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Shuqiang Li
- Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Sean Eddy
- Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Damian Fermin
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Michelle T McNulty
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Nir Hacohen
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Matthias Kretzler
- Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA; Department of Medicine-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
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Jin YY, Feng BY, Mao JH. The status quo and challenges of genetic diagnosis in children with steroid-resistant nephrotic syndrome. World J Pediatr 2018; 14:105-109. [PMID: 29644498 DOI: 10.1007/s12519-018-0156-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/28/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Yan-Yan Jin
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, 310003, China
| | - Bing-Yu Feng
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, 310003, China.,Department of Paediatrics, The First People's Hospital of Huzhou, Huzhou, 313000, China
| | - Jian-Hua Mao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, #57 Zhugan Lane, Hangzhou, 310003, China.
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6
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The Democratization of Genomic Inquiry Empowers Our Understanding of Nephrotic Syndrome. Transplantation 2018; 101:2814-2815. [PMID: 28737604 DOI: 10.1097/tp.0000000000001897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Kim Y, Park SJ, Manson SR, Molina CA, Kidd K, Thiessen-Philbrook H, Perry RJ, Liapis H, Kmoch S, Parikh CR, Bleyer AJ, Chen YM. Elevated urinary CRELD2 is associated with endoplasmic reticulum stress-mediated kidney disease. JCI Insight 2017; 2:92896. [PMID: 29212948 DOI: 10.1172/jci.insight.92896] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 11/01/2017] [Indexed: 02/06/2023] Open
Abstract
ER stress has emerged as a signaling platform underlying the pathogenesis of various kidney diseases. Thus, there is an urgent need to develop ER stress biomarkers in the incipient stages of ER stress-mediated kidney disease, when a kidney biopsy is not yet clinically indicated, for early therapeutic intervention. Cysteine-rich with EGF-like domains 2 (CRELD2) is a newly identified protein that is induced and secreted under ER stress. For the first time to our knowledge, we demonstrate that CRELD2 can serve as a sensitive urinary biomarker for detecting ER stress in podocytes or renal tubular cells in murine models of podocyte ER stress-induced nephrotic syndrome and tunicamycin- or ischemia-reperfusion-induced acute kidney injury (AKI), respectively. Most importantly, urinary CRELD2 elevation occurs in patients with autosomal dominant tubulointerstitial kidney disease caused by UMOD mutations, a prototypical tubular ER stress disease. In addition, in pediatric patients undergoing cardiac surgery, detectable urine levels of CRELD2 within postoperative 6 hours strongly associate with severe AKI after surgery. In conclusion, our study has identified CRELD2 as a potentially novel urinary ER stress biomarker with potential utility in early diagnosis, risk stratification, treatment response monitoring, and directing of ER-targeted therapies in selected patient subgroups in the emerging era of precision nephrology.
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Affiliation(s)
- Yeawon Kim
- Division of Nephrology, Department of Internal Medicine
| | - Sun-Ji Park
- Division of Nephrology, Department of Internal Medicine
| | - Scott R Manson
- Division of Urology, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carlos Af Molina
- Division of Urology, Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, USA.,Division of Urology, Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Kendrah Kidd
- Section of Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | | | - Rebecca J Perry
- Section of Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Helen Liapis
- RTE Professor of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, USA.,Arkana Laboratories, Little Rock, Arkansas, USA
| | - Stanislav Kmoch
- Section of Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Institute for Inherited Metabolic Disorders, Charles University in Prague, Prague, Czech Republic
| | - Chirag R Parikh
- Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut.,Clinical Epidemiology Research Center, Veterans Affairs Medical Center, West Haven, Connecticut, USA
| | - Anthony J Bleyer
- Section of Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Ha TS. Genetics of hereditary nephrotic syndrome: a clinical review. KOREAN JOURNAL OF PEDIATRICS 2017; 60:55-63. [PMID: 28392820 PMCID: PMC5383633 DOI: 10.3345/kjp.2017.60.3.55] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 01/01/2023]
Abstract
Advances in podocytology and genetic techniques have expanded our understanding of the pathogenesis of hereditary steroid-resistant nephrotic syndrome (SRNS). In the past 20 years, over 45 genetic mutations have been identified in patients with hereditary SRNS. Genetic mutations on structural and functional molecules in podocytes can lead to serious injury in the podocytes themselves and in adjacent structures, causing sclerotic lesions such as focal segmental glomerulosclerosis or diffuse mesangial sclerosis. This paper provides an update on the current knowledge of podocyte genes involved in the development of hereditary nephrotic syndrome and, thereby, reviews genotype-phenotype correlations to propose an approach for appropriate mutational screening based on clinical aspects.
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Affiliation(s)
- Tae-Sun Ha
- Department of Pediatrics, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
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9
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Abstract
Genetic studies of hereditary forms of nephrotic syndrome have identified several proteins that are involved in regulating the permselective properties of the glomerular filtration system. Further extensive research has elucidated the complex molecular basis of the glomerular filtration barrier and clearly established the pivotal role of podocytes in the pathophysiology of glomerular diseases. Podocyte architecture is centred on focal adhesions and slit diaphragms - multiprotein signalling hubs that regulate cell morphology and function. A highly interconnected actin cytoskeleton enables podocytes to adapt in order to accommodate environmental changes and maintain an intact glomerular filtration barrier. Actin-based endocytosis has now emerged as a regulator of podocyte integrity, providing an impetus for understanding the precise mechanisms that underlie the steady-state control of focal adhesion and slit diaphragm components. This Review outlines the role of actin dynamics and endocytosis in podocyte biology, and discusses how molecular heterogeneity in glomerular disorders could be exploited to deliver more rational therapeutic interventions, paving the way for targeted medicine in nephrology.
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Sampson MG, Gillies CE, Robertson CC, Crawford B, Vega-Warner V, Otto EA, Kretzler M, Kang HM. Using Population Genetics to Interrogate the Monogenic Nephrotic Syndrome Diagnosis in a Case Cohort. J Am Soc Nephrol 2016; 27:1970-83. [PMID: 26534921 PMCID: PMC4926977 DOI: 10.1681/asn.2015050504] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/06/2015] [Indexed: 01/02/2023] Open
Abstract
To maximize clinical benefits of genetic screening of patients with nephrotic syndrome (NS) to diagnose monogenic causes, reliably distinguishing NS-causing variants from the background of rare, noncausal variants prevalent in all genomes is vital. To determine the prevalence of monogenic NS in a North American case cohort while accounting for background prevalence of genetic variation, we sequenced 21 implicated monogenic NS genes in 312 participants from the Nephrotic Syndrome Study Network and 61 putative controls from the 1000 Genomes Project (1000G). These analyses were extended to available sequence data from approximately 2500 subjects from the 1000G. A typical pathogenicity filter identified causal variants for NS in 4.2% of patients and 5.8% of subjects from the 1000G. We devised a more stringent pathogenicity filtering strategy, reducing background prevalence of causal variants to 1.5%. When applying this stringent filter to patients, prevalence of monogenic NS was 2.9%; of these patients, 67% were pediatric, and 44% had FSGS on biopsy. The rate of complete remission did not associate with monogenic classification. Thus, we identified factors contributing to inaccurate monogenic classification of NS and developed a more accurate variant filtering strategy. The prevalence and clinical correlates of monogenic NS in this sporadically affected cohort differ substantially from those reported for patients referred for genetic analysis. Particularly in unselected, population-based cases, considering putative causal variants in known NS genes from a probabilistic rather than a deterministic perspective may be more precise. We also introduce GeneVetter, a web tool for monogenic assessment of rare disease.
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Affiliation(s)
| | | | | | | | | | - Edgar A Otto
- Departments of Pediatrics and Communicable Diseases, and
| | - Matthias Kretzler
- Internal Medicine, Division of Nephrology and Department of Computational Medicine and Bioinformatics, University of Michigan School of Medicine, Ann Arbor, Michigan; and
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
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