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Al‐Ali AK, Alsulaiman A, Alfarhan M, Safaya S, Vatte CB, Albuali WM, Qutub HO, Alzahrani AJ, Milton JN, Steinberg MH. Sickle cell disease in the Eastern Province of Saudi Arabia: Clinical and laboratory features. Am J Hematol 2021; 96:E117-E121. [PMID: 33460474 DOI: 10.1002/ajh.26096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Amein K. Al‐Ali
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
- Department of Clinical Biochemistry College of Medicine, Imam Abdulrahman bin Faisal University Dammam Saudi Arabia
| | - Ahmed Alsulaiman
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
- Department of Internal Medicine King Fahd Hospital Al‐Ahsa Saudi Arabia
| | - Mohammed Alfarhan
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
- Department of Orthopedic Surgery College of Medicine, King Faisal University Al‐Ahsa Saudi Arabia
| | - Surinder Safaya
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
| | - Chitti Babu Vatte
- Department of Clinical Biochemistry College of Medicine, Imam Abdulrahman bin Faisal University Dammam Saudi Arabia
| | - Waleed M. Albuali
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
| | - Hatem O. Qutub
- Alomran Scientific Chair, King Faisal University Al‐Ahsa Saudi Arabia
| | | | - Jacqueline N. Milton
- Department of Statistics Boston University School of Public Health Boston Massachusetts
| | - Martin H. Steinberg
- Department of Medicine, Center of Excellence in Sickle Cell Disease Boston University and Boston Medical Center Boston Massachusetts
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Milton JN, Shaikho EM, Steinberg MH. Haemolysis in sickle cell anaemia: effects of polymorphisms in α-globin gene regulatory elements. Br J Haematol 2019; 186:363-364. [PMID: 30854637 DOI: 10.1111/bjh.15852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacqueline N Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Elmutaz M Shaikho
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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Vathipadiekal V, Alsultan A, Baltrusaitis K, Farrell JJ, Al-Rubaish AM, Al-Muhanna F, Naserullah Z, Suliman A, Patra P, Milton JN, Farrer LA, Chui DH, Al-Ali AK, Sebastiani P, Steinberg MH. Homozygosity for a haplotype in the HBG2-OR51B4 region is exclusive to Arab-Indian haplotype sickle cell anemia. Am J Hematol 2016; 91:E308-11. [PMID: 27185208 DOI: 10.1002/ajh.24368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/10/2016] [Accepted: 03/13/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Vinod Vathipadiekal
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdulrahman Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics; College of Medicine, King Saud University; Riyadh Saudi Arabia
| | - Kristin Baltrusaitis
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - John J. Farrell
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Abdullah M. Al-Rubaish
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Fahad Al-Muhanna
- Department of Internal Medicine; College of Medicine, University of Dammam; Dammam Kingdom of Saudi Arabia
| | - Zaki Naserullah
- Alomran Scientific Chair for Hematological Diseases, King Faisal University, King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
- Department of Pediatrics, Maternity & Child Hospital; Dammam Kingdom of Saudi Arabia
| | - Ahmed Suliman
- Alomran Scientific Chair; King Faisal University, King Fahd Hospital; Hafof Al-Ahsa Kingdom of Saudi Arabia
| | - P.K. Patra
- Department of Biochemistry; Pt. J.N.M. Medical College; Raipur Chhattisgarh India
| | - Jacqueline N. Milton
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Lindsay A. Farrer
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - David H.K. Chui
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | - Amein K. Al-Ali
- Center for Research & Medical Consultation; University of Dammam; Dammam Saudi Arabia
| | - Paola Sebastiani
- Department of Biostatistics; Boston University School of Public Health; Boston Massachusetts
| | - Martin. H. Steinberg
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
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Sebastiani P, Farrell JJ, Alsultan A, Wang S, Edward HL, Shappell H, Bae H, Milton JN, Baldwin CT, Al-Rubaish AM, Naserullah Z, Al-Muhanna F, Alsuliman A, Patra PK, Farrer LA, Ngo D, Vathipadiekal V, Chui DHK, Al-Ali AK, Steinberg MH. BCL11A enhancer haplotypes and fetal hemoglobin in sickle cell anemia. Blood Cells Mol Dis 2015; 54:224-30. [PMID: 25703683 DOI: 10.1016/j.bcmd.2015.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 02/04/2023]
Abstract
BACKGROUND Fetal hemoglobin (HbF) levels in sickle cell anemia patients vary. We genotyped polymorphisms in the erythroid-specific enhancer of BCL11A to see if they might account for the very high HbF associated with the Arab-Indian (AI) haplotype and Benin haplotype of sickle cell anemia. METHODS AND RESULTS Six BCL112A enhancer SNPs and their haplotypes were studied in Saudi Arabs from the Eastern Province and Indian patients with AI haplotype (HbF ~20%), African Americans (HbF ~7%), and Saudi Arabs from the Southwestern Province (HbF ~12%). Four SNPs (rs1427407, rs6706648, rs6738440, and rs7606173) and their haplotypes were consistently associated with HbF levels. The distributions of haplotypes differ in the 3 cohorts but not their genetic effects: the haplotype TCAG was associated with the lowest HbF level and the haplotype GTAC was associated with the highest HbF level and differences in HbF levels between carriers of these haplotypes in all cohorts were approximately 6%. CONCLUSIONS Common HbF BCL11A enhancer haplotypes in patients with African origin and AI sickle cell anemia have similar effects on HbF but they do not explain their differences in HbF.
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Affiliation(s)
- P Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States.
| | - J J Farrell
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - A Alsultan
- Sickle Cell Disease Research Center and Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - S Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - H L Edward
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - H Shappell
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - H Bae
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, United States
| | - J N Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - C T Baldwin
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - A M Al-Rubaish
- Department of Internal Medicine, College of Medicine, University of Dammam, Dammam, Saudi Arabia
| | - Z Naserullah
- Department of Pediatrics, Maternity & Child Hospital, Dammam, Saudi Arabia
| | - F Al-Muhanna
- Department of Internal Medicine, College of Medicine, University of Dammam, Dammam, Saudi Arabia
| | - A Alsuliman
- Department of Hematology, King Fahd Hospital, Hafof, Al-Ahsa, Saudi Arabia
| | - P K Patra
- Deptartment of Biochemistry, Pt. J.N.M. Medical College, Raipur, Chattisgarh, India
| | - L A Farrer
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - D Ngo
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - V Vathipadiekal
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - D H K Chui
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - A K Al-Ali
- Prince Mohammed Center for Research & Consultation Studies, University of Dammam, Dammam, Saudi Arabia
| | - M H Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, MA, United States
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Milton JN, Steinberg MH, Sebastiani P. Evaluation of an ensemble of genetic models for prediction of a quantitative trait. Front Genet 2015; 5:474. [PMID: 25628649 PMCID: PMC4292739 DOI: 10.3389/fgene.2014.00474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 08/26/2014] [Accepted: 12/20/2014] [Indexed: 01/09/2023] Open
Abstract
Many genetic markers have been shown to be associated with common quantitative traits in genome-wide association studies. Typically these associated genetic markers have small to modest effect sizes and individually they explain only a small amount of the variability of the phenotype. In order to build a genetic prediction model without fitting a multiple linear regression model with possibly hundreds of genetic markers as predictors, researchers often summarize the joint effect of risk alleles into a genetic score that is used as a covariate in the genetic prediction model. However, the prediction accuracy can be highly variable and selecting the optimal number of markers to be included in the genetic score is challenging. In this manuscript we present a strategy to build an ensemble of genetic prediction models from data and we show that the ensemble-based method makes the challenge of choosing the number of genetic markers more amenable. Using simulated data with varying heritability and number of genetic markers, we compare the predictive accuracy and inclusion of true positive and false positive markers of a single genetic prediction model and our proposed ensemble method. The results show that the ensemble of genetic models tends to include a larger number of genetic variants than a single genetic model and it is more likely to include all of the true genetic markers. This increased sensitivity is obtained at the price of a lower specificity that appears to minimally affect the predictive accuracy of the ensemble.
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Affiliation(s)
- Jacqueline N Milton
- Department of Biostatistics, School of Public Health, Boston University Boston, MA, USA
| | - Martin H Steinberg
- Department of Medicine, School of Medicine, Boston University Boston, MA, USA
| | - Paola Sebastiani
- Department of Biostatistics, School of Public Health, Boston University Boston, MA, USA
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Abstract
The genetic variants associated with blood pressure identified so far explain only a small proportion of the total heritability of this trait. With recent advances in sequencing technology and statistical methodology, it becomes feasible to study the association between blood pressure and rare genetic variants. Using real baseline phenotype data and imputed dosage data from Genetic Analysis Workshop 18, we performed a candidate gene association analysis. We focused on 8 genes shown to be associated with either systolic or diastolic blood pressure to identify the association with both common and rare genetic variants, and then did a genome-wide rare-variant analysis on blood pressure. We performed association analysis for rare coding and splicing variants within each gene region and all rare variants in each sliding window, using either burden tests or sequence kernel association tests accounting for familial correlation. With a sample size of only 747, we failed to find any novel associated genetic loci. Consequently, we performed analyses on simulated data, with knowledge of the underlying simulating model, to evaluate the type I error rate and power for the methods used in real data analysis.
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Affiliation(s)
- Han Chen
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Seung Hoan Choi
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Jaeyoung Hong
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Chen Lu
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Jacqueline N Milton
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Catherine Allard
- Département de Mathématiques, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - Sean M Lacey
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
| | - Honghuang Lin
- Department of Medicine, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, 801 Massachusetts Avenue, Boston, MA 02118, USA
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Milton JN, Gordeuk VR, Taylor JG, Gladwin MT, Steinberg MH, Sebastiani P. Prediction of fetal hemoglobin in sickle cell anemia using an ensemble of genetic risk prediction models. ACTA ACUST UNITED AC 2014; 7:110-5. [PMID: 24585758 DOI: 10.1161/circgenetics.113.000387] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Fetal hemoglobin (HbF) is the major modifier of the clinical course of sickle cell anemia. Its levels are highly heritable, and its interpersonal variability is modulated in part by 3 quantitative trait loci that affect HbF gene expression. Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) in these quantitative trait loci that are highly associated with HbF but explain only 10% to 12% of the variance of HbF. Combining SNPs into a genetic risk score can help to explain a larger amount of the variability of HbF level, but the challenge of this approach is to select the optimal number of SNPs to be included in the genetic risk score. METHODS AND RESULTS We developed a collection of 14 models with genetic risk score composed of different numbers of SNPs and used the ensemble of these models to predict HbF in patients with sickle cell anemia. The models were trained in 841 patients with sickle cell anemia and were tested in 3 independent cohorts. The ensemble of 14 models explained 23.4% of the variability in HbF in the discovery cohort, whereas the correlation between predicted and observed HbF in the 3 independent cohorts ranged between 0.28 and 0.44. The models included SNPs in BCL11A, the HBS1L-MYB intergenic region, and the site of the HBB gene cluster, quantitative trait loci previously associated with HbF. CONCLUSIONS An ensemble of 14 genetic risk models can predict HbF levels with accuracy between 0.28 and 0.44, and the approach may also prove useful in other applications.
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Affiliation(s)
- Jacqueline N Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
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Barbosa CG, Aleluia AC, Pacheco AP, Paz SS, Zanette AM, Lyra IM, Steinberg MH, Milton JN, Goncalves MS. Genetic modulation of HbF in Brazilians with HbSC disease and sickle cell anemia. Am J Hematol 2013; 88:923-4. [PMID: 23828430 DOI: 10.1002/ajh.23538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Cynara G. Barbosa
- Faculdade de Farmácia, Universidade Federal da Bahia; Salvador-BA Brasil
| | | | | | | | | | - Isa M. Lyra
- Fundação de Hematologia e Hemoterapia da Bahia (HEMOBA); Salvador-BA Brasil
| | - Martin H. Steinberg
- Department of Medicine; Boston University School of Medicine; Boston Massachusetts
| | | | - Marilda S. Goncalves
- Faculdade de Farmácia, Universidade Federal da Bahia; Salvador-BA Brasil
- Fundação Oswaldo Cruz Bahia; Salvador-BA Brasil
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Bhatnagar P, Barron-Casella E, Bean CJ, Milton JN, Baldwin CT, Steinberg MH, DeBaun M, Casella JF, Arking DE. Genome-wide meta-analysis of systolic blood pressure in children with sickle cell disease. PLoS One 2013; 8:e74193. [PMID: 24058526 PMCID: PMC3772989 DOI: 10.1371/journal.pone.0074193] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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: 04/25/2013] [Accepted: 07/30/2013] [Indexed: 01/11/2023] Open
Abstract
In pediatric sickle cell disease (SCD) patients, it has been reported that higher systolic blood pressure (SBP) is associated with increased risk of a silent cerebral infarction (SCI). SCI is a major cause of neurologic morbidity in children with SCD, and blood pressure is a potential modulator of clinical manifestations of SCD; however, the risk factors underlying these complications are not well characterized. The aim of this study was to identify genetic variants that influence SBP in an African American population in the setting of SCD, and explore the use of SBP as an endo-phenotype for SCI. We conducted a genome-wide meta-analysis for SBP using two SCD cohorts, as well as a candidate screen based on published SBP loci. A total of 1,617 patients were analyzed, and while no SNP reached genome-wide significance (P-value<5.0 x 10(-8)), a number of suggestive candidate loci were identified. The most significant SNP, rs7952106 (P-value=8.57 x 10(-7)), was in the DRD2 locus on chromosome 11. In a gene-based association analysis, MIR4301 (micro-RNA4301), which resides in an intron of DRD2, was the most significant gene (P-value=5.2 x 10(-5)). Examining 27 of the previously reported SBP associated SNPs, 4 SNPs were nominally significant. A genetic risk score was constructed to assess the aggregated genetic effect of the published SBP variants, demonstrating a significant association (P=0.05). In addition, we also assessed whether these variants are associated with SCI, validating the use of SBP as an endo-phenotype for SCI. Three SNPs were nominally associated, and only rs2357790 (5' CACNB2) was significant for both SBP and SCI. None of these SNPs retained significance after Bonferroni correction. Taken together, our results suggest the importance of DRD2 genetic variation in the modulation of SBP, and extend the aggregated importance of previously reported SNPs in the modulation of SBP in an African American cohort, more specifically in children with SCD.
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Affiliation(s)
- Pallav Bhatnagar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily Barron-Casella
- Department of Pediatrics, Division of Pediatric Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christopher J. Bean
- Clinical and Molecular Hemostasis Laboratory Branch, Division of Blood Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jacqueline N. Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Clinton T. Baldwin
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Martin H. Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Michael DeBaun
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - James F. Casella
- Department of Pediatrics, Division of Pediatric Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Milton JN, Rooks H, Drasar E, McCabe EL, Baldwin CT, Melista E, Gordeuk VR, Nouraie M, Kato GR, Minniti C, Taylor J, Campbell A, Luchtman-Jones L, Rana S, Castro O, Zhang Y, Thein SL, Sebastiani P, Gladwin MT, Steinberg MH. Genetic determinants of haemolysis in sickle cell anaemia. Br J Haematol 2013; 161:270-8. [PMID: 23406172 PMCID: PMC4129543 DOI: 10.1111/bjh.12245] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [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: 10/23/2012] [Accepted: 12/29/2012] [Indexed: 12/31/2022]
Abstract
Haemolytic anaemia is variable among patients with sickle cell anaemia and can be estimated by reticulocyte count, lactate dehydrogenase, aspartate aminotransferase and bilirubin levels. Using principal component analysis of these measurements we computed a haemolytic score that we used as a subphenotype in a genome-wide association study. We identified in one cohort and replicated in two additional cohorts the association of a single nucleotide polymorphism in NPRL3 (rs7203560; chr16p13·3) (P = 6·04 × 10(-07) ). This association was validated by targeted genotyping in a fourth independent cohort. The HBA1/HBA2 regulatory elements, hypersensitive sites (HS)-33, HS-40 and HS-48 are located in introns of NPRL3. Rs7203560 was in perfect linkage disequilibrium (LD) with rs9926112 (r(2) = 1) and in strong LD with rs7197554 (r(2) = 0·75) and rs13336641 (r(2) = 0·77); the latter is located between HS-33 and HS-40 sites and next to a CTCF binding site. The minor allele for rs7203560 was associated with the -∝(3·7) thalassaemia gene deletion. When adjusting for HbF and ∝ thalassaemia, the association of NPRL3 with the haemolytic score was significant (P = 0·00375) and remained significant when examining only cases without gene deletion∝ thalassaemia (P = 0·02463). Perhaps by independently down-regulating expression of the HBA1/HBA2 genes, variants of the HBA1/HBA2 gene regulatory loci, tagged by rs7203560, reduce haemolysis in sickle cell anaemia.
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Affiliation(s)
| | - Helen Rooks
- King’s College School of Medicine, King’s College London, London, UK
| | - Emma Drasar
- King’s College School of Medicine, King’s College London, London, UK
- Molecular Haematology, King’s College London, London, UK
| | | | - Clinton T. Baldwin
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA
| | - Efi Melista
- Center for Human Genetics, Boston University, Boston, MA
| | | | - Mehdi Nouraie
- Center for Sickle Cell Disease, Howard University, Washington, DC
| | - Gregory R. Kato
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Caterina Minniti
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
| | - James Taylor
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
| | - Andrew Campbell
- Pediatric Hematology Oncology, University of Michigan, Ann Arbor, MI
| | - Lori Luchtman-Jones
- Hematology, Children’s National Medical Center, Howard University, Washington, DC
| | - Sohail Rana
- Center for Sickle Cell Disease, Howard University, Washington, DC
| | - Oswaldo Castro
- Sickle Cell Vascular Disease Section, Hematology Branch, National Heart, Lung and Blood Institute, Bethesda, MD
- Center For Sickle Cell Disease, Howard University, Washington, DC
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Swee Lay Thein
- King’s College School of Medicine, King’s College London, London, UK
- Molecular Haematology, King’s College London, London, UK
| | | | - Mark T. Gladwin
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Martin H. Steinberg
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA
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11
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Milton JN, Sebastiani P, Solovieff N, Hartley SW, Bhatnagar P, Arking DE, Dworkis DA, Casella JF, Barron-Casella E, Bean CJ, Hooper WC, DeBaun MR, Garrett ME, Soldano K, Telen MJ, Ashley-Koch A, Gladwin MT, Baldwin CT, Steinberg MH, Klings ES. A genome-wide association study of total bilirubin and cholelithiasis risk in sickle cell anemia. PLoS One 2012; 7:e34741. [PMID: 22558097 PMCID: PMC3338756 DOI: 10.1371/journal.pone.0034741] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [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: 11/14/2011] [Accepted: 03/05/2012] [Indexed: 12/31/2022] Open
Abstract
Serum bilirubin levels have been associated with polymorphisms in the UGT1A1 promoter in normal populations and in patients with hemolytic anemias, including sickle cell anemia. When hemolysis occurs circulating heme increases, leading to elevated bilirubin levels and an increased incidence of cholelithiasis. We performed the first genome-wide association study (GWAS) of bilirubin levels and cholelithiasis risk in a discovery cohort of 1,117 sickle cell anemia patients. We found 15 single nucleotide polymorphisms (SNPs) associated with total bilirubin levels at the genome-wide significance level (p value <5 × 10(-8)). SNPs in UGT1A1, UGT1A3, UGT1A6, UGT1A8 and UGT1A10, different isoforms within the UGT1A locus, were identified (most significant rs887829, p = 9.08 × 10(-25)). All of these associations were validated in 4 independent sets of sickle cell anemia patients. We tested the association of the 15 SNPs with cholelithiasis in the discovery cohort and found a significant association (most significant p value 1.15 × 10(-4)). These results confirm that the UGT1A region is the major regulator of bilirubin metabolism in African Americans with sickle cell anemia, similar to what is observed in other ethnicities.
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Affiliation(s)
- Jacqueline N. Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Nadia Solovieff
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Stephen W. Hartley
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Pallav Bhatnagar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Daniel A. Dworkis
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - James F. Casella
- Department of Pediatrics, Division of Pediatric Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily Barron-Casella
- Department of Pediatrics, Division of Pediatric Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christopher J. Bean
- Clinical and Molecular Hemostasis Laboratory Branch, Division of Blood Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - W. Craig Hooper
- Clinical and Molecular Hemostasis Laboratory Branch, Division of Blood Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Michael R. DeBaun
- Vanderbilt School of Medicine, Nashville, Tennessee, United States of America
| | - Melanie E. Garrett
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Karen Soldano
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Mark T. Gladwin
- Division of Pulmonary, Allergy and Critical Care Medicine and the Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Clinton T. Baldwin
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Martin H. Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Elizabeth S. Klings
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- The Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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12
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Sebastiani P, Riva A, Montano M, Pham P, Torkamani A, Scherba E, Benson G, Milton JN, Baldwin CT, Andersen S, Schork NJ, Steinberg MH, Perls TT. Whole genome sequences of a male and female supercentenarian, ages greater than 114 years. Front Genet 2012; 2:90. [PMID: 22303384 PMCID: PMC3262222 DOI: 10.3389/fgene.2011.00090] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [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] [Received: 10/20/2011] [Accepted: 12/04/2011] [Indexed: 12/18/2022] Open
Abstract
Supercentenarians (age 110+ years old) generally delay or escape age-related diseases and disability well beyond the age of 100 and this exceptional survival is likely to be influenced by a genetic predisposition that includes both common and rare genetic variants. In this report, we describe the complete genomic sequences of male and female supercentenarians, both age >114 years old. We show that: (1) the sequence variant spectrum of these two individuals' DNA sequences is largely comparable to existing non-supercentenarian genomes; (2) the two individuals do not appear to carry most of the well-established human longevity enabling variants already reported in the literature; (3) they have a comparable number of known disease-associated variants relative to most human genomes sequenced to-date; (4) approximately 1% of the variants these individuals possess are novel and may point to new genes involved in exceptional longevity; and (5) both individuals are enriched for coding variants near longevity-associated variants that we discovered through a large genome-wide association study. These analyses suggest that there are both common and rare longevity-associated variants that may counter the effects of disease-predisposing variants and extend lifespan. The continued analysis of the genomes of these and other rare individuals who have survived to extremely old ages should provide insight into the processes that contribute to the maintenance of health during extreme aging.
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Affiliation(s)
- Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health Boston, MA, USA
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13
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Dworkis DA, Klings ES, Solovieff N, Li G, Milton JN, Hartley SW, Melista E, Parente J, Sebastiani P, Steinberg MH, Baldwin CT. Severe sickle cell anemia is associated with increased plasma levels of TNF-R1 and VCAM-1. Am J Hematol 2011; 86:220-3. [PMID: 21264913 DOI: 10.1002/ajh.21928] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Sickle cell anemia (SCA, HBB glu6val) is characterized by multiple complications and a high degree of phenotypic variability: some subjects have only sporadic pain crises and few acute hospitalizations, while others experience multiple serious complications, high levels of morbidity, and accelerated mortality [1]. The tumor necrosis factor-α (TNF-α) signaling pathway plays important roles in inflammation and the immune response; variation in this pathway might be expected to modify the overall severity of SCA through the pathway's effects on the vascular endothelium [2,3]. We examined plasma biomarkers of TNF-α activity and endothelial cell activation for associations with SCA severity in 24 adults (12 mild, 12 severe). Two biomarkers, tumor necrosis factor-α receptor-1 (TNF-R1) and vascular cell adhesion molecule-1 (VCAM-1) were significantly higher in subjects with severe SCA. Along with these biomarker differences, we also examined data from a genome-wide association study (GWAS) using SCA severity as a disease phenotype, and found evidence of genetic association between disease severity and a single nucleotide polymorphism (SNP) in VCAM1, which codes for VCAM-1, and several SNPs in ARFGEF2, a gene involved in TNF-R1 release [4].
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Affiliation(s)
- Daniel A. Dworkis
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Center for Human Genetics, Boston University School of Medicine, Boston, Massachusetts
| | - Elizabeth S. Klings
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Nadia Solovieff
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Guihua Li
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Jacqueline N. Milton
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Stephen W. Hartley
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Efthymia Melista
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Center for Human Genetics, Boston University School of Medicine, Boston, Massachusetts
| | - Jason Parente
- Center for Human Genetics, Boston University School of Medicine, Boston, Massachusetts
| | - Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Martin H. Steinberg
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Clinton T. Baldwin
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Center for Human Genetics, Boston University School of Medicine, Boston, Massachusetts
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14
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Solovieff N, Milton JN, Hartley SW, Sherva R, Sebastiani P, Dworkis DA, Klings ES, Farrer LA, Garrett ME, Ashley-Koch A, Telen MJ, Fucharoen S, Ha SY, Li CK, Chui DHK, Baldwin CT, Steinberg MH. Fetal hemoglobin in sickle cell anemia: genome-wide association studies suggest a regulatory region in the 5' olfactory receptor gene cluster. Blood 2010; 115:1815-22. [PMID: 20018918 PMCID: PMC2832816 DOI: 10.1182/blood-2009-08-239517] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 11/18/2009] [Indexed: 11/20/2022] Open
Abstract
In a genome-wide association study of 848 blacks with sickle cell anemia, we identified single nucleotide polymorphisms (SNPs) associated with fetal hemoglobin concentration. The most significant SNPs in a discovery sample were tested in a replication set of 305 blacks with sickle cell anemia and in subjects with hemoglobin E or beta thalassemia trait from Thailand and Hong Kong. A novel region on chromosome 11 containing olfactory receptor genes OR51B5 and OR51B6 was identified by 6 SNPs (lowest P = 4.7E-08) and validated in the replication set. An additional olfactory receptor gene, OR51B2, was identified by a novel SNP set enrichment analysis. Genome-wide association studies also validated a previously identified SNP (rs766432) in BCL11A, a gene known to affect fetal hemoglobin levels (P = 2.6E-21) and in Thailand and Hong Kong subjects. Elements within the olfactory receptor gene cluster might play a regulatory role in gamma-globin gene expression.
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MESH Headings
- Adolescent
- Adult
- Black or African American/genetics
- Anemia, Sickle Cell/blood
- Anemia, Sickle Cell/genetics
- Carrier Proteins/genetics
- Child
- Child, Preschool
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, X/genetics
- Female
- Fetal Hemoglobin/genetics
- Fetal Hemoglobin/metabolism
- Genome-Wide Association Study
- Hemoglobin E/genetics
- Hong Kong
- Humans
- Male
- Multigene Family
- Nuclear Proteins/genetics
- Polymorphism, Single Nucleotide
- Receptors, Odorant/genetics
- Regulatory Sequences, Nucleic Acid
- Repressor Proteins
- Thailand
- Young Adult
- beta-Thalassemia/genetics
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Affiliation(s)
- Nadia Solovieff
- Department of Biostatistics, Boston University School of Public Health, MA, USA
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15
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Sebastiani P, Solovieff N, Hartley SW, Milton JN, Riva A, Dworkis DA, Melista E, Klings ES, Garrett ME, Telen MJ, Ashley-Koch A, Baldwin CT, Steinberg MH. Genetic modifiers of the severity of sickle cell anemia identified through a genome-wide association study. Am J Hematol 2010; 85:29-35. [PMID: 20029952 DOI: 10.1002/ajh.21572] [Citation(s) in RCA: 41] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We conducted a genome-wide association study (GWAS) to discover single nucleotide polymorphisms (SNPs) associated with the severity of sickle cell anemia in 1,265 patients with either "severe" or "mild" disease based on a network model of disease severity. We analyzed data using single SNP analysis and a novel SNP set enrichment analysis (SSEA) developed to discover clusters of associated SNPs. Single SNP analysis discovered 40 SNPs that were strongly associated with sickle cell severity (odds for association >1,000); of the 32 that we could analyze in an independent set of 163 patients, five replicated, eight showed consistent effects although failed to reach statistical significance, whereas 19 did not show any convincing association. Among the replicated associations are SNPs in KCNK6 a K(+) channel gene. SSEA identified 27 genes with a strong enrichment of significant SNPs (P < 10(-6)); 20 were replicated with varying degrees of confidence. Among the novel findings identified by SSEA is the telomere length regulator gene TNKS. These studies are the first to use GWAS to understand the genetic diversity that accounts the phenotypic heterogeneity sickle cell anemia as estimated by an integrated model of severity. Additional validation, resequencing, and functional studies to understand the biology and reveal mechanisms by which candidate genes might have their effects are the future goals of this work.
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Affiliation(s)
- Paola Sebastiani
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
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