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French JN, Pua VB, Laboulaye R, Leal TP, Olivas MC, Lima-Costa MF, Horta BL, Barreto ML, Tarazona-Santos E, Mata I, O’Connor TD. Comparing the effect of imputation reference panel composition in four distinct Latin American cohorts. bioRxiv 2024:2024.04.11.589057. [PMID: 38659746 PMCID: PMC11042191 DOI: 10.1101/2024.04.11.589057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Genome-wide association studies have been useful in identifying genetic risk factors for various phenotypes. These studies rely on imputation and many existing panels are largely composed of individuals of European ancestry, resulting in lower levels of imputation quality in underrepresented populations. We aim to analyze how the composition of imputation reference panels affects imputation quality in four target Latin American cohorts. We compared imputation quality for chromosomes 7 and X when altering the imputation reference panel by: 1) increasing the number of Latin American individuals; 2) excluding either Latin American, African, or European individuals, or 3) increasing the Indigenous American (IA) admixture proportions of included Latin Americans. We found that increasing the number of Latin Americans in the reference panel improved imputation quality in the four populations; however, there were differences between chromosomes 7 and X in some cohorts. Excluding Latin Americans from analysis resulted in worse imputation quality in every cohort, while differential effects were seen when excluding Europeans and Africans between and within cohorts and between chromosomes 7 and X. Finally, increasing IA-like admixture proportions in the reference panel increased imputation quality at different levels in different populations. The difference in results between populations and chromosomes suggests that existing and future reference panels containing Latin American individuals are likely to perform differently in different Latin American populations.
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Affiliation(s)
- Jennifer N French
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Victor Borda Pua
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
- University of Maryland Institute for Health Computing, Rockville, MD
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | - Thiago Peixoto Leal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mario Cornejo Olivas
- Neurogenetics Working Group, Universidad Cientifica del Sur, Lima, Peru
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | | | - Bernardo L Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Mauricio L Barreto
- Center for Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute (IGM), Oswaldo Cruz Foundation (FIOCRUZ-BA), Salvador, Bahia, Brazil
- Collective Health Institute, Federal University of Bahia (UFBA), Salvador, Bahia, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Ignacio Mata
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD
- Program in Health Equity and Population Health, University of Maryland School of Medicine
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2
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Leal TP, Rao SC, French-Kwawu JN, Gouveia MH, Borda V, Bandres-Ciga S, Inca-Martinez M, Mason EA, Horimoto AR, Loesch DP, Sarihan EI, Cornejo-Olivas MR, Torres LE, Mazzetti-Soler PE, Cosentino C, Sarapura-Castro EH, Rivera-Valdivia A, Medina AC, Dieguez EM, Raggio VE, Lescano A, Tumas V, Borges V, Ferraz HB, Rieder CR, Schuh AS, Santos-Lobato BL, Velez-Pardo C, Jimenez-Del-Rio M, Lopera F, Moreno S, Chana-Cuevas P, Fernandez W, Arboleda G, Arboleda H, Bustos CEA, Yearout D, Lima-Costa MF, Tarazona-Santos E, Zabetian CP, Thornton TA, O’Connor TD, Mata IF. X-Chromosome Association Study in Latin American Cohorts Identifies New Loci in Parkinson's Disease. Mov Disord 2023; 38:1625-1635. [PMID: 37469269 PMCID: PMC10524402 DOI: 10.1002/mds.29508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Sex differences in Parkinson's disease (PD) risk are well-known. However, the role of sex chromosomes in the development and progression of PD is still unclear. OBJECTIVE The objective of this study was to perform the first X-chromosome-wide association study for PD risk in a Latin American cohort. METHODS We used data from three admixed cohorts: (1) Latin American Research consortium on the Genetics of Parkinson's Disease (n = 1504) as discover cohort, and (2) Latino cohort from International Parkinson Disease Genomics Consortium (n = 155) and (3) Bambui Aging cohort (n = 1442) as replication cohorts. We also developed an X-chromosome framework specifically designed for admixed populations. RESULTS We identified eight linkage disequilibrium regions associated with PD. We replicated one of these regions (top variant rs525496; discovery odds ratio [95% confidence interval]: 0.60 [0.478-0.77], P = 3.13 × 10-5 replication odds ratio: 0.60 [0.37-0.98], P = 0.04). rs5525496 is associated with multiple expression quantitative trait loci in brain and non-brain tissues, including RAB9B, H2BFM, TSMB15B, and GLRA4, but colocalization analysis suggests that rs5525496 may not mediate risk by expression of these genes. We also replicated a previous X-chromosome-wide association study finding (rs28602900), showing that this variant is associated with PD in non-European populations. CONCLUSIONS Our results reinforce the importance of including X-chromosome and diverse populations in genetic studies. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Thiago P. Leal
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Jennifer N. French-Kwawu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mateus H. Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sara Bandres-Ciga
- Center for Alzheimer’s and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Miguel Inca-Martinez
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Emily A. Mason
- University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | | | - Douglas P. Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elif I. Sarihan
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mario R. Cornejo-Olivas
- Neurogenetics Working Group, Universidad Científica del Sur, Lima, Peru
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | - Luis E. Torres
- Movement Disorders Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | - Pilar E. Mazzetti-Soler
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- Departamento de Medicina Humana, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carlos Cosentino
- Movement Disorders Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
| | | | | | | | - Elena M. Dieguez
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Víctor E. Raggio
- Department of Genetics, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Andrés Lescano
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Vitor Tumas
- Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanderci Borges
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Henrique B. Ferraz
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos R. Rieder
- Departamento de Neurologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Artur Schumacher Schuh
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Farmacologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Carlos Velez-Pardo
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Marlene Jimenez-Del-Rio
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Francisco Lopera
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Sonia Moreno
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia, Medellín, Colombia
| | - Pedro Chana-Cuevas
- CETRAM, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - William Fernandez
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Humberto Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos E. Arboleda Bustos
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Dora Yearout
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
| | | | - Eduardo Tarazona-Santos
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cyrus P. Zabetian
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
| | | | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Program in Health Equity and Population Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ignacio F. Mata
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
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Kucera CW, Tian C, Tarney CM, Presti C, Jokajtys S, Winkler SS, Casablanca Y, Bateman NW, Mhawech-Fauceglia P, Wenzel L, Hamilton CA, Chan JK, Jones NL, Rocconi RP, O’Connor TD, Farley JH, Shriver CD, Conrads TP, Phippen NT, Maxwell GL, Darcy KM. Factors Associated With Survival Disparities Between Non-Hispanic Black and White Patients With Uterine Cancer. JAMA Netw Open 2023; 6:e238437. [PMID: 37067801 PMCID: PMC10111180 DOI: 10.1001/jamanetworkopen.2023.8437] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/02/2023] [Indexed: 04/18/2023] Open
Abstract
Importance Disparities in survival exist between non-Hispanic Black (hereafter, Black) and non-Hispanic White (hereafter, White) patients with uterine cancer. Objective To investigate factors associated with racial disparities in survival between Black and White patients with uterine cancer. Design, Setting, and Patients This cohort study used data from the National Cancer Database on 274 838 Black and White patients who received a diagnosis of uterine cancer from January 1, 2004, to December 31, 2017, with follow-up through December 2020. Statistical analysis was performed in July 2022. Main Outcomes and Measures Overall survival by self-reported race and evaluation of explanatory study factors associated with hazard ratio (HR) reduction for Black vs White patients. A propensity scoring approach was applied sequentially to balance racial differences in demographic characteristics, comorbidity score, neighborhood income, insurance status, histologic subtype, disease stage, and treatment. Results The study included 32 230 Black female patients (mean [SD] age at diagnosis, 63.8 [10.0] years) and 242 608 White female patients (mean [SD] age at diagnosis, 63.5 [10.5] years) and had a median follow-up of 74.0 months (range, 43.5-113.8 months). Black patients were more likely than White patients to have low income (44.1% vs 14.0%), be uninsured (5.7% vs 2.6%), present with nonendometrioid histologic characteristics (46.1% vs 21.6%), have an advanced disease stage (34.1% vs 19.8%), receive first-line chemotherapy (33.8% vs 18.2%), and have worse 5-year survival (58.6% vs 78.5%). Among patients who received a diagnosis at younger than 65 years of age, the HR for death for Black vs White patients was 2.43 (95% CI, 2.34-2.52) in a baseline demographic-adjusted model and 1.29 (95% CI, 1.23-1.35) after balancing other factors. Comorbidity score, neighborhood income, insurance status, histologic subtype, disease stage, treatment, and unexplained factors accounted for 0.8%, 7.2%, 11.5%, 53.1%, 5.8%, 1.2%, and 20.4%, respectively, of the excess relative risk (ERR) among the younger Black vs White patients. Among patients 65 years or older, the HR for death for Black vs White patients was 1.87 (95% CI, 1.81-1.93) in the baseline model and 1.14 (95% CI, 1.09-1.19) after balancing other factors. Comorbidity score, neighborhood income, insurance status, histologic subtype, disease stage, treatment, and unexplained factors accounted for 3.0%, 7.5%, 0.0%, 56.2%, 10.6%, 6.9%, and 15.8%, respectively, of the ERR among Black vs White patients aged 65 years or older. Conclusions and Relevance This study suggests that histologic subtype was the dominant factor associated with racial survival disparity among patients with uterine cancer, while insurance status represented the main modifiable factor for women younger than 65 years. Additional studies of interactions between biology and social determinants of health are merited.
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Affiliation(s)
- Calen W. Kucera
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland
| | - Christopher M. Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Cassandra Presti
- Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, Virginia
| | - Suzanne Jokajtys
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Stuart S. Winkler
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland
| | - Paulette Mhawech-Fauceglia
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Aurora Diagnostics, LMC Pathology Services, Las Vegas, Nevada
| | - Lari Wenzel
- Department of Medicine, School of Medicine, University of California, Irvine
- Department of Public Health, School of Medicine, University of California, Irvine
| | - Chad A. Hamilton
- Gynecologic Oncology Section, Women’s Services and The Ochsner Cancer Institute, Ochsner Health, New Orleans, Louisiana
| | - John K. Chan
- Gynecologic Oncology Division, Palo Alto Medical Foundation/California Pacific Medical Center/Sutter Health, San Francisco
| | - Nathaniel L. Jones
- Division of Gynecologic Oncology, the Mitchell Cancer Institute, University of South Alabama, Mobile
| | - Rodney P. Rocconi
- Division of Gynecologic Oncology, the University of Alabama at Birmingham, Infirmary Cancer Care, Infirmary Health, Mobile
| | - Timothy D. O’Connor
- Institute for Genome Sciences, Department of Medicine, Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore
- Program in Health Equity and Population Health, University of Maryland School of Medicine, Baltimore
- The University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore
| | - John H. Farley
- Division of Gynecologic Oncology, Dignity Health Cancer Institute, Dignity Health St Joseph’s Hospital and Medical Center, Phoenix, Arizona
| | - Craig D. Shriver
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Women’s Health Integrated Research Center, Inova Women’s Service Line, Inova Health System, Falls Church, Virginia
| | - Neil T. Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - G. Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Women’s Health Integrated Research Center, Inova Women’s Service Line, Inova Health System, Falls Church, Virginia
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland
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Leal TP, French-Kwawu JN, Gouveia MH, Borda V, Inca-Martinez M, Mason EA, Horimoto ARVR, Loesch DP, Sarihan EI, Cornejo-Olivas MR, Torres LE, Mazzetti-Soler PE, Cosentino C, Sarapura-Castro EH, Rivera-Valdivia A, Medina AC, Dieguez EM, Raggio VE, Lescano A, Tumas V, Borges V, Ferraz HB, Rieder CR, Schumacher-Schuh A, Santos-Lobato BL, Velez-Pardo C, Jimenez-Del-Rio M, Lopera F, Moreno S, Chana-Cuevas P, Fernandez W, Arboleda G, Arboleda H, Arboleda Bustos CE, Yearout D, Lima-Costa MF, Tarazona E, Zabetian C, Thornton TA, O’Connor TD, Mata IF. X-Chromosome Association Study in Latin American Cohorts Identifies New Loci in Parkinson Disease. medRxiv 2023:2023.01.31.23285199. [PMID: 36778409 PMCID: PMC9915833 DOI: 10.1101/2023.01.31.23285199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Sex differences in Parkinson Disease (PD) risk are well-known. However, it is still unclear the role of sex chromosomes in the development and progression of PD. We performed the first X-chromosome Wide Association Study (XWAS) for PD risk in Latin American individuals. We used data from three admixed cohorts: (i) Latin American Research consortium on the GEnetics of Parkinson's Disease (n=1,504) as discover cohort and (ii) Latino cohort from International Parkinson Disease Genomics Consortium (n = 155) and (iii) Bambui Aging cohort (n= 1,442) as replication cohorts. After developing a X-chromosome framework specifically designed for admixed populations, we identified eight linkage disequilibrium regions associated with PD. We fully replicated one of these regions (top variant rs525496; discovery OR [95%CI]: 0.60 [0.478 - 0.77], p = 3.13 × 10 -5 ; replication OR: 0.60 [0.37-0.98], p = 0.04). rs525496 is an expression quantitative trait loci for several genes expressed in brain tissues, including RAB9B, H2BFM, TSMB15B and GLRA4 . We also replicated a previous XWAS finding (rs28602900), showing that this variant is associated with PD in non-European populations. Our results reinforce the importance of including X-chromosome and diverse populations in genetic studies.
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Xu H, Nguyen K, Gaynor BJ, Ling H, Zhao W, McArdle PF, O’Connor TD, Stine OC, Ryan KA, Lynch M, Smith JA, Faul JD, Hu Y, Haessler JW, Fornage M, Kooperberg C, Perry JA, Hong CC, Cole JW, Pugh E, Doheny K, Kardia SLR, Weir DR, Kittner SJ, Mitchell BD. Exome Array Analysis of 9721 Ischemic Stroke Cases from the SiGN Consortium. Genes (Basel) 2022; 14:61. [PMID: 36672803 PMCID: PMC9858999 DOI: 10.3390/genes14010061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Recent genome wide association studies have identified 89 common genetic variants robustly associated with ischemic stroke and primarily located in non-coding regions. To evaluate the contribution of coding variants, which are mostly rare, we performed an exome array analysis on 106,101 SNPs for 9721 ischemic stroke cases from the SiGN Consortium, and 12,345 subjects with no history of stroke from the Health Retirement Study and SiGN consortium. We identified 15 coding variants significantly associated with all ischemic stroke at array-wide threshold (i.e., p < 4.7 × 10-7), including two common SNPs in ABO that have previously been associated with stroke. Twelve of the remaining 13 variants were extremely rare in European Caucasians (MAF < 0.1%) and the associations were driven by African American samples. There was no evidence for replication of these associations in either TOPMed Stroke samples (n = 5613 cases) or UK Biobank (n = 5874 stroke cases), although power to replicate was very low given the low allele frequencies of the associated variants and a shortage of samples from diverse ancestries. Our study highlights the need for acquiring large, well-powered diverse cohorts to study rare variants, and the technical challenges using array-based genotyping technologies for rare variant genotyping.
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Affiliation(s)
- Huichun Xu
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kevin Nguyen
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Brady J. Gaynor
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hua Ling
- Center for Inherited Disease Research, Dept. of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wei Zhao
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Patrick F. McArdle
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Timothy D. O’Connor
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - O. Colin Stine
- Department of Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kathleen A. Ryan
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Megan Lynch
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jennifer A. Smith
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yao Hu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jeffrey W. Haessler
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - James A. Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Charles C. Hong
- Department of Cardiology Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John W. Cole
- Department of Neurology Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elizabeth Pugh
- Center for Inherited Disease Research, Dept. of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kimberly Doheny
- Center for Inherited Disease Research, Dept. of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48109, USA
| | - Steven J. Kittner
- Department of Neurology Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
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Guimarães Alves AC, Sukow NM, Adelman Cipolla G, Mendes M, Leal TP, Petzl-Erler ML, Lehtonen Rodrigues Souza R, Rainha de Souza I, Sanchez C, Santolalla M, Loesch D, Dean M, Machado M, Moon JY, Kaplan R, North KE, Weiss S, Barreto ML, Lima-Costa MF, Guio H, Cáceres O, Padilla C, Tarazona-Santos E, Mata IF, Dieguez E, Raggio V, Lescano A, Tumas V, Borges V, Ferraz HB, Rieder CR, Schumacher-Schuh A, Santos-Lobato BL, Chana-Cuevas P, Fernandez W, Arboleda G, Arboleda H, Arboleda-Bustos CE, O’Connor TD, Beltrame MH, Borda V. Tracing the Distribution of European Lactase Persistence Genotypes Along the Americas. Front Genet 2021; 12:671079. [PMID: 34630506 PMCID: PMC8493957 DOI: 10.3389/fgene.2021.671079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2021] [Indexed: 01/26/2023] Open
Abstract
In adulthood, the ability to digest lactose, the main sugar present in milk of mammals, is a phenotype (lactase persistence) observed in historically herder populations, mainly Northern Europeans, Eastern Africans, and Middle Eastern nomads. As the -13910∗T allele in the MCM6 gene is the most well-characterized allele responsible for the lactase persistence phenotype, the -13910C > T (rs4988235) polymorphism is commonly evaluated in lactase persistence studies. Lactase non-persistent adults may develop symptoms of lactose intolerance when consuming dairy products. In the Americas, there is no evidence of the consumption of these products until the arrival of Europeans. However, several American countries' dietary guidelines recommend consuming dairy for adequate human nutrition and health promotion. Considering the extensive use of dairy and the complex ancestry of Pan-American admixed populations, we studied the distribution of -13910C > T lactase persistence genotypes and its flanking haplotypes of European origin in 7,428 individuals from several Pan-American admixed populations. We found that the -13910∗T allele frequency in Pan-American admixed populations is directly correlated with allele frequency of the European sources. Moreover, we did not observe any overrepresentation of European haplotypes in the -13910C > T flanking region, suggesting no selective pressure after admixture in the Americas. Finally, considering the dominant effect of the -13910∗T allele, our results indicate that Pan-American admixed populations are likely to have higher frequency of lactose intolerance, suggesting that general dietary guidelines deserve further evaluation across the continent.
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Affiliation(s)
- Ana Cecília Guimarães Alves
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Natalie Mary Sukow
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Gabriel Adelman Cipolla
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Marla Mendes
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thiago P. Leal
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Luiza Petzl-Erler
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ricardo Lehtonen Rodrigues Souza
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratório de Polimorfismos e Ligação, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Ilíada Rainha de Souza
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratório de Polimorfismos Genéticos, Departamento de Biologia Celular, Embriologia e Genética, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Cesar Sanchez
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Meddly Santolalla
- Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Douglas Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Moara Machado
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Scott Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Mauricio L. Barreto
- Universidade Federal da Bahia, Instituto de Saúde Coletiva, Salvador, Brazil
- Fundação Oswaldo Cruz, Centro de Integração de Dados e Conhecimentos para Saúde (Cidacs), Salvador, Brazil
| | - M. Fernanda Lima-Costa
- Fundação Oswaldo Cruz, Instituto René Rachou, Belo Horizonte, Brazil
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Saúde Pública, Belo Horizonte, Brazil
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
- Facultad de Ciencias de la Salud, Universidad de Huánuco, Huánuco, Peru
| | - Omar Cáceres
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
- Carrera de Medicina Humana, Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima, Peru
| | - Carlos Padilla
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Eduardo Tarazona-Santos
- Laboratório de Diversidade Genética Humana, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ignacio F. Mata
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Department of Neurology, University of Washington, Seattle, WA, United States
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Elena Dieguez
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Víctor Raggio
- Department of Genetics, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Andres Lescano
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Vitor Tumas
- Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanderci Borges
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Henrique B. Ferraz
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos R. Rieder
- Departamento de Neurologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Artur Schumacher-Schuh
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Departamento de Farmacologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Pedro Chana-Cuevas
- CETRAM, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| | - William Fernandez
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Humberto Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos E. Arboleda-Bustos
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
- Program for Personalized and Genomic Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- Department of Medicine, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Marcia Holsbach Beltrame
- Laboratório de Genética Molecular Humana, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
- Programa de Pós-Graduação em Genética, Departamento de Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
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Sarihan EI, Pérez-Palma E, Niestroj LM, Loesch D, Inca-Martinez M, Horimoto AR, Cornejo-Olivas M, Torres L, Mazzetti P, Cosentino C, Sarapura-Castro E, Rivera-Valdivia A, Dieguez E, Raggio V, Lescano A, Tumas V, Borges V, Ferraz HB, Rieder CR, Schumacher-Schuh AF, Santos-Lobato BL, Velez-Pardo C, Jimenez-Del-Rio M, Lopera F, Moreno S, Chana-Cuevas P, Fernandez W, Arboleda G, Arboleda H, Arboleda-Bustos CE, Yearout D, Zabetian CP, Thornton TA, O’Connor TD, Lal D, Mata IF. Genome-Wide Analysis of Copy Number Variation in Latin American Parkinson's Disease Patients. Mov Disord 2021; 36:434-441. [PMID: 33150996 PMCID: PMC8059262 DOI: 10.1002/mds.28353] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Parkinson's disease is the second most common neurodegenerative disorder and affects people from all ethnic backgrounds, yet little is known about the genetics of Parkinson's disease in non-European populations. In addition, the overall identification of copy number variants at a genome-wide level has been understudied in Parkinson's patients. The objective of this study was to understand the genome-wide burden of copy number variants in Latinos and its association with Parkinson's disease. METHODS We used genome-wide genotyping data from 747 Parkinson's disease patients and 632 controls from the Latin American Research Consortium on the Genetics of Parkinson's disease. RESULTS Genome-wide copy number burden analysis showed that patients were significantly enriched for copy number variants overlapping known Parkinson's disease genes compared with controls (odds ratio, 3.97; 95%CI, 1.69-10.5; P = 0.018). PRKN showed the strongest copy number burden, with 20 copy number variant carriers. These patients presented an earlier age of disease onset compared with patients with other copy number variants (median age at onset, 31 vs 57 years, respectively; P = 7.46 × 10-7 ). CONCLUSIONS We found that although overall genome-wide copy number variant burden was not significantly different, Parkinson's disease patients were significantly enriched with copy number variants affecting known Parkinson's disease genes. We also identified that of 250 patients with early-onset disease, 5.6% carried a copy number variant on PRKN in our cohort. Our study is the first to analyze genome-wide copy number variant association in Latino Parkinson's disease patients and provides insights about this complex disease in this understudied population. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Elif Irem Sarihan
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eduardo Pérez-Palma
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Douglas Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Miguel Inca-Martinez
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Andrea R.V.R. Horimoto
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Mario Cornejo-Olivas
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luis Torres
- Movement Disorders Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- School of Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Pilar Mazzetti
- Neurogenetics Research Center, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- School of Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carlos Cosentino
- Movement Disorders Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Peru
- School of Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | | | | | - Elena Dieguez
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Victor Raggio
- Department of Genetics, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Andres Lescano
- Neurology Institute, Universidad de la República, Montevideo, Uruguay
| | - Vitor Tumas
- Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanderci Borges
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Henrique B. Ferraz
- Movement Disorders Unit, Department of Neurology and Neurosurgery, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Carlos R. Rieder
- Departamento de Neurologia, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Artur F. Schumacher-Schuh
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre and Departamento de Farmacologia Universidade Federal do Rio Grande do Su, Porto Alegre, Brazil
| | | | - Carlos Velez-Pardo
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Marlene Jimenez-Del-Rio
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Francisco Lopera
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Sonia Moreno
- Neuroscience Research Group, Medical Research Institute, Faculty of Medicine, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Pedro Chana-Cuevas
- CETRAM, Facultad de Ciencias Medicas, Universidad de Santiago de Chile, Santiago de Chile, Chile
| | - William Fernandez
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Humberto Arboleda
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Carlos E. Arboleda-Bustos
- Neuroscience and Cell Death Research Groups, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Dora Yearout
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Cyrus P. Zabetian
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dennis Lal
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, Massachusetts, USA
- Epilepsy Center & Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ignacio F. Mata
- Lerner Research Institute, Genomic Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Veterans Affairs Puget Sound Health Care System, Seattle, Washington, USA
- Department of Neurology, University of Washington, Seattle, Washington, USA
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Li Y, Shetty AC, Lon C, Spring M, Saunders DL, Fukuda MM, Hien TT, Pukrittayakamee S, Fairhurst RM, Dondorp AM, Plowe CV, O’Connor TD, Takala-Harrison S, Stewart K. Detecting geospatial patterns of Plasmodium falciparum parasite migration in Cambodia using optimized estimated effective migration surfaces. Int J Health Geogr 2020; 19:13. [PMID: 32276636 PMCID: PMC7149848 DOI: 10.1186/s12942-020-00207-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/01/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Understanding the genetic structure of natural populations provides insight into the demographic and adaptive processes that have affected those populations. Such information, particularly when integrated with geospatial data, can have translational applications for a variety of fields, including public health. Estimated effective migration surfaces (EEMS) is an approach that allows visualization of the spatial patterns in genomic data to understand population structure and migration. In this study, we developed a workflow to optimize the resolution of spatial grids used to generate EEMS migration maps and applied this optimized workflow to estimate migration of Plasmodium falciparum in Cambodia and bordering regions of Thailand and Vietnam. METHODS The optimal density of EEMS grids was determined based on a new workflow created using density clustering to define genomic clusters and the spatial distance between genomic clusters. Topological skeletons were used to capture the spatial distribution for each genomic cluster and to determine the EEMS grid density; i.e., both genomic and spatial clustering were used to guide the optimization of EEMS grids. Model accuracy for migration estimates using the optimized workflow was tested and compared to grid resolutions selected without the optimized workflow. As a test case, the optimized workflow was applied to genomic data generated from P. falciparum sampled in Cambodia and bordering regions, and migration maps were compared to estimates of malaria endemicity, as well as geographic properties of the study area, as a means of validating observed migration patterns. RESULTS Optimized grids displayed both high model accuracy and reduced computing time compared to grid densities selected in an unguided manner. In addition, EEMS migration maps generated for P. falciparum using the optimized grid corresponded to estimates of malaria endemicity and geographic properties of the study region that might be expected to impact malaria parasite migration, supporting the validity of the observed migration patterns. CONCLUSIONS Optimized grids reduce spatial uncertainty in the EEMS contours that can result from user-defined parameters, such as the resolution of the spatial grid used in the model. This workflow will be useful to a broad range of EEMS users as it can be applied to analyses involving other organisms of interest and geographic areas.
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Affiliation(s)
- Yao Li
- Center for Geospatial Information Science, Department of Geographical Sciences, University of Maryland, College Park, 20742 MD USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Michele Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - David L. Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mark M. Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Arjen M. Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | | | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Kathleen Stewart
- Center for Geospatial Information Science, Department of Geographical Sciences, University of Maryland, College Park, 20742 MD USA
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9
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Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O’Connor TD. Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences. Cancer 2019; 125:2076-2088. [PMID: 30865299 PMCID: PMC6541501 DOI: 10.1002/cncr.32020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
Abstract
Background Although cell lines are an essential resource for studying cancer biology, many are of unknown ancestral origin, and their use may not be optimal for evaluating the biology of all patient populations. Methods An admixture analysis was performed using genome‐wide chip data from the Catalogue of Somatic Mutations in Cancer (COSMIC) Cell Lines Project to calculate genetic ancestry estimates for 1018 cancer cell lines. After stratifying the analyses by tissue and histology types, linear models were used to evaluate the influence of ancestry on gene expression and somatic mutation frequency. Results For the 701 cell lines with unreported ancestry, 215 were of East Asian origin, 30 were of African or African American origin, and 453 were of European origin. Notable imbalances were observed in ancestral representation across tissue type, with the majority of analyzed tissue types having few cell lines of African American ancestral origin, and with Hispanic and South Asian ancestry being almost entirely absent across all cell lines. In evaluating gene expression across these cell lines, expression levels of the genes neurobeachin line 1 (NBEAL1), solute carrier family 6 member 19 (SLC6A19), HEAT repeat containing 6 (HEATR6), and epithelial cell transforming 2 like (ECT2L) were associated with ancestry. Significant differences were also observed in the proportions of somatic mutation types across cell lines with varying ancestral proportions. Conclusions By estimating genetic ancestry for 1018 cancer cell lines, the authors have produced a resource that cancer researchers can use to ensure that their cell lines are ancestrally representative of the populations they intend to affect. Furthermore, the novel ancestry‐specific signal identified underscores the importance of ancestral awareness when studying cancer. Preclinical cancer cell line research is often conducted without an awareness of ancestral background, which results in incongruities between the genetic backgrounds of used cell lines and the patient populations they are intended to represent. By calculating genetic ancestry for 1018 common cancer cell lines and identifying ancestry‐specific expression and somatic mutation patterns, the importance of ancestral awareness is emphasized, and a resource is provided that can be used by cancer researchers to ensure that their cell lines are ancestrally representative of the populations they aim to impact.
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Affiliation(s)
- Michael D. Kessler
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- Department of MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- Program in Personalized and Genomic MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
- Department of Obstetrics and GynecologyInova Fairfax Medical CampusFalls ChurchVirginia
| | - George L. Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
- Department of Obstetrics and GynecologyInova Fairfax Medical CampusFalls ChurchVirginia
| | - Julie C. Dunning Hotopp
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
- Department of Microbiology and ImmunologyUniversity of Maryland School of MedicineBaltimoreMaryland
| | - Timothy D. O’Connor
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- Department of MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- Program in Personalized and Genomic MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
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10
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Johnston HR, Hu YJ, Gao J, O’Connor TD, Abecasis GR, Wojcik GL, Gignoux CR, Gourraud PA, Lizee A, Hansen M, Genuario R, Bullis D, Lawley C, Kenny EE, Bustamante C, Beaty TH, Mathias RA, Barnes KC, Qin ZS. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. Sci Rep 2017; 7:46398. [PMID: 28429804 PMCID: PMC5399604 DOI: 10.1038/srep46398] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/17/2017] [Indexed: 12/15/2022] Open
Abstract
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry.
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Affiliation(s)
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Jingjing Gao
- Data and Statistical Sciences, AbbVie, North Chicago, IL, USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gonçalo R. Abecasis
- Department of Biostatistics, SPH, University of Michigan, Ann Arbor, MI, USA
| | - Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Antoine Lizee
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | - Eimear E. Kenny
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A. Mathias
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C. Barnes
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Zhaohui S. Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
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11
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O’Connor TD, Mundy NI. Evolutionary Modeling of Genotype-Phenotype Associations, and Application to Primate Coding and Non-coding mtDNA Rate Variation. Evol Bioinform Online 2013; 9:301-16. [PMID: 23926418 PMCID: PMC3733722 DOI: 10.4137/ebo.s11600] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Variation in substitution rates across a phylogeny can be indicative of shifts in the evolutionary dynamics of a protein or non-protein coding regions. One way to understand these signals is to seek the phenotypic correlates of rate variation. Here, we extended a previously published likelihood method designed to detect evolutionary associations between genotypic evolutionary rate and phenotype over a phylogeny. In simulation with two discrete categories of phenotype, the method has a low false-positive rate and detects greater than 80% of true-positives with a tree length of three or greater and a three-fold or greater change in substitution rate given the phenotype. In addition, we successfully extend the test from two to four phenotype categories and evaluated its performance. We then applied the method to two major hypotheses for rate variation in the mitochondrial genome of primates-longevity and generation time as well as body mass which is correlated with many aspects of life history-using three categories of phenotype through discretization of continuous values. Similar to previous results for mammals, we find that the majority of mitochondrial protein-coding genes show associations consistent with the longevity and body mass predictions and that the predominant signal of association comes from the third codon position. We also found a significant association between maximum lifespan and the evolutionary rate of the control region of the mtDNA. In contrast, 24 protein-coding genes from the nuclear genome do not show a consistent pattern of association, which is inconsistent with the generation time hypothesis. These results show the extended method can robustly identify genotype-phenotype associations up to at least four phenotypic categories, and demonstrate the successful application of the method to study factors affecting neutral evolutionary rate in protein-coding and non-coding loci.
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Affiliation(s)
- Timothy D. O’Connor
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas I. Mundy
- Department of Zoology, Downing Street, University of Cambridge, Cambridge CB2 3EJ, UK
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12
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O’Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E, Leal SM, Akey JM. Fine-scale patterns of population stratification confound rare variant association tests. PLoS One 2013; 8:e65834. [PMID: 23861739 PMCID: PMC3701690 DOI: 10.1371/journal.pone.0065834] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/29/2013] [Indexed: 11/18/2022] Open
Abstract
Advances in next-generation sequencing technology have enabled systematic exploration of the contribution of rare variation to Mendelian and complex diseases. Although it is well known that population stratification can generate spurious associations with common alleles, its impact on rare variant association methods remains poorly understood. Here, we performed exhaustive coalescent simulations with demographic parameters calibrated from exome sequence data to evaluate the performance of nine rare variant association methods in the presence of fine-scale population structure. We find that all methods have an inflated spurious association rate for parameter values that are consistent with levels of differentiation typical of European populations. For example, at a nominal significance level of 5%, some test statistics have a spurious association rate as high as 40%. Finally, we empirically assess the impact of population stratification in a large data set of 4,298 European American exomes. Our results have important implications for the design, analysis, and interpretation of rare variant genome-wide association studies.
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Affiliation(s)
- Timothy D. O’Connor
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Adam Kiezun
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Emily Turner
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | | | | | - Suzanne M. Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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