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Park CS, De T, Xu Y, Zhong Y, Smithberger E, Alarcon C, Gamazon ER, Perera MA. Hepatocyte gene expression and DNA methylation as ancestry-dependent mechanisms in African Americans. NPJ Genom Med 2019; 4:29. [PMID: 31798965 PMCID: PMC6877651 DOI: 10.1038/s41525-019-0102-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/11/2019] [Accepted: 09/27/2019] [Indexed: 12/13/2022] Open
Abstract
African Americans (AAs) are an admixed population with widely varying proportion of West African ancestry (WAA). Here we report the correlation of WAA to gene expression and DNA methylation in AA-derived hepatocytes, a cell type important in disease and drug response. We perform mediation analysis to test whether methylation is a mediator of the effect of ancestry on expression. GTEx samples and a second cohort are used as validation. One hundred and thirty-one genes are associated with WAA (FDR < 0.10), 28 of which replicate and represent 220 GWAS phenotypes. Among PharmGKB pharmacogenes, VDR, PTGIS, ALDH1A1, CYP2C19, and P2RY1 nominally associate with WAA (p < 0.05). We find 1037 WAA-associated, differentially methylated regions (FDR < 0.05), with hypomethylated genes enriched in drug-response pathways. In conclusion, WAA contributes to variability in hepatocyte expression and DNA methylation with identified genes previously implicated for diseases disproportionately affecting AAs, including cardiovascular (PTGIS, PLAT) and renal (APOL1) disease, and drug response (CYP2C19).
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Affiliation(s)
- C. S. Park
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - T. De
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Y. Xu
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
- Center for Translational Data Science, University of Chicago, Chicago, IL USA
| | - Y. Zhong
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - E. Smithberger
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC USA
| | - C. Alarcon
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - E. R. Gamazon
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Vanderbilt University School of Medicine, Nashville, TN USA
- Data Science Institute, Vanderbilt University, Nashville, TN USA
- Clare Hall, University of Cambridge, Cambridge, UK
| | - M. A. Perera
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
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2
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Hernandez W, Gamazon ER, Aquino-Michaels K, Smithberger E, O'Brien TJ, Harralson AF, Tuck M, Barbour A, Cavallari LH, Perera MA. Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans. J Thromb Haemost 2017; 15:735-743. [PMID: 28135054 PMCID: PMC5862636 DOI: 10.1111/jth.13639] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 02/12/2016] [Indexed: 11/26/2022]
Abstract
Essentials Genetic variants controlling gene regulation have not been explored in pharmacogenomics. We tested liver expression quantitative trait loci for association with warfarin dose response. A novel predictor for increased warfarin dose response in African Americans was identified. Precision medicine must take into account population-specific variation in gene regulation. SUMMARY Background Warfarin is commonly used to control and prevent thromboembolic disorders. However, because of warfarin's complex dose-requirement relationship, safe and effective use is challenging. Pharmacogenomics-guided warfarin dosing algorithms that include the well-established VKORC1 and CYP2C9 polymorphisms explain only a small proportion of inter-individual variability in African Americans (AAs). Objectives We aimed to assess whether transcriptomic analyses could be used to identify regulatory variants associated with warfarin dose response in AAs. Patients/Methods We identified a total of 56 expression quantitative trait loci (eQTLs) for CYP2C9, VKORC1 and CALU derived from human livers and evaluated their association with warfarin dose response in two independent AA warfarin patient cohorts. Results We found that rs4889606, a strong cis-eQTL for VKORC1 (log10 Bayes Factor = 12.02), is significantly associated with increased warfarin daily dose requirement (β = 1.1; 95% confidence interval [CI] 0.46 to 1.8) in the discovery cohort (n = 305) and in the replication cohort (β = 1.04; 95% CI 0.33 -1.7; n = 141) after conditioning on relevant covariates and the VKORC1 -1639G>A (rs9923231) variant. Inclusion of rs4889606 genotypes, along with CYP2C9 alleles, rs9923231 genotypes and clinical variables, explained 31% of the inter-patient variability in warfarin dose requirement. We demonstrate different linkage disequilibrium patterns in the region encompassing rs4889606 and rs9923231 between AAs and European Americans, which may explain the increased dose requirement found in AAs. Conclusion Our approach of interrogating eQTLs identified in liver has revealed a novel predictor of warfarin dose response in AAs. Our work highlights the utility of leveraging information from regulatory variants mapped in the liver to uncover novel variants associated with drug response and the importance of population-specific research.
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Affiliation(s)
- W Hernandez
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - E R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
- Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - K Aquino-Michaels
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - E Smithberger
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - T J O'Brien
- Department of Pharmacology and Physiology, George Washington University, Washington, DC, USA
| | - A F Harralson
- Department of Medicine, George Washington University, Washington, DC, USA
- Bernard J. Dunn School of Pharmacy, Shenandoah University, Winchester, VA, USA
| | - M Tuck
- Veterans Affairs Medical Center, Washington, DC, USA
| | - A Barbour
- Department of Medicine, George Washington University, Washington, DC, USA
| | - L H Cavallari
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - M A Perera
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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3
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Huo D, Hu H, Rhie SK, Gamazon ER, Cherniack AD, Liu J, Yoshimatsu TF, Pitt JJ, Hoadley KA, Troester M, Ru Y, Lichtenberg T, Sturtz LA, Shelley CS, Mills GB, Laird PW, Shriver CD, Perou CM, Olopade OI. Abstract P1-05-11: Comprehensive comparison of breast cancer molecular portraits by African and European ancestry in the cancer genome atlas. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-05-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: African American breast cancer patients have worse survival rates than European American patients. Although racial differences in the distribution of breast cancer intrinsic subtype are known, it is unclear if there are other inherent genomic differences contributing to this racial outcome disparity.
Methods: We defined patient race based on genomic ancestry and compared multiple molecular features of breast cancer between 154 black and 776 white patients in The Cancer Genome Atlas (TCGA). We examined the contribution of these molecular features to survival outcomes using Cox proportional hazards models. We also estimated the heritability of breast cancer subtypes using a mixed effect model.
Results: Compared to whites, black patients had higher odds of basal-like (odds ratio=3.80, p<0.001) and HER2-enriched (odds ratio=2.22, p=0.027) breast cancers in reference to luminal A subtype. Beyond differences in relative frequency of intrinsic subtypes, black and white patients had distinct gene expression, protein expression, and somatic mutation landscapes. However, the majority of these molecular differences were eliminated after adjusting for subtype; in the subtype-adjusted models, we found 142 genes, 16 methylation probes, 4 copy number segments, 1 protein, and no somatic mutation were differentially expressed or present between black and white patients. Using the top 40 differentially expressed genes, we built a race-enriched gene signature, which had excellent capacity of distinguishing breast tumors from black versus white patients (c-index=0.852 in the validation dataset). We also estimated the heritability of breast cancer subtype (basal vs. non-basal) to be 0.436 (p=1.5x10-14) and showed that two genetic variants (rs1078806 in FGFR2, rs34084277 in BABAM1) were associated with intrinsic subtype and can partially explain racial differences in subtype frequencies.
Conclusion: On the molecular level, once intrinsic subtype frequency differences are accounted for, there are few genomic or proteomic differences observed between blacks and whites. More than 40% of breast cancer subtype frequency differences may be due to genetic ancestry. These results suggest that future studies are warranted to investigate genetic and non-genetic factors that contribute to the development and progression of breast cancer subtypes in order to reduce racial disparity.
Citation Format: Huo D, Hu H, Rhie SK, Gamazon ER, Cherniack AD, Liu J, Yoshimatsu TF, Pitt JJ, Hoadley KA, Troester M, Ru Y, Lichtenberg T, Sturtz LA, Shelley CS, Mills GB, Laird PW, Shriver CD, Perou CM, Olopade OI. Comprehensive comparison of breast cancer molecular portraits by African and European ancestry in the cancer genome atlas [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-11.
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Affiliation(s)
- D Huo
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - H Hu
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - SK Rhie
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - ER Gamazon
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - AD Cherniack
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - J Liu
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - TF Yoshimatsu
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - JJ Pitt
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - KA Hoadley
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - M Troester
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - Y Ru
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - T Lichtenberg
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - LA Sturtz
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - CS Shelley
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - GB Mills
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - PW Laird
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - CD Shriver
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - CM Perou
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
| | - OI Olopade
- University of Chicago; Chan Soon-Shiong Institute of Molecular Medicine at Windber; University of Southern California; Vanderbilt University; The Eli and Edythe L. Broad Institute of MIT and Harvard; University of North Carolina at Chapel Hill; Nationwide Children's Hospital, Columbus; University of Wisconsin; University of Texas MD Anderson Cancer Center; Van Andel Research Institute; Walter Reed National Military Medical Center
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Chang SW, McDonough CW, Gong Y, Johnson TA, Tsunoda T, Gamazon ER, Perera MA, Takahashi A, Tanaka T, Kubo M, Pepine CJ, Johnson JA, Cooper-DeHoff RM. Genome-wide association study identifies pharmacogenomic loci linked with specific antihypertensive drug treatment and new-onset diabetes. Pharmacogenomics J 2016; 18:106-112. [PMID: 27670767 PMCID: PMC5368017 DOI: 10.1038/tpj.2016.67] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 07/11/2016] [Accepted: 08/25/2016] [Indexed: 01/14/2023]
Abstract
We conducted a discovery genome-wide association study with expression quantitative trait loci (eQTL) annotation of new-onset diabetes (NOD) among European Americans, who were exposed to a calcium channel blocker-based strategy (CCB strategy) or a β-blocker-based strategy (β-blocker strategy) in the INternational VErapamil SR Trandolapril STudy. Replication of the top signal from the SNP*treatment interaction analysis was attempted in Hispanic and African Americans, and a joint meta-analysis was performed (total 334 NOD cases and 806 matched controls). PLEKHH2 rs11124945 at 2p21 interacted with antihypertensive exposure for NOD (meta-analysis p=5.3×10−8). rs11124945 G allele carriers had lower odds for NOD when exposed to the β-blocker strategy compared with the CCB strategy [OR=0.38 (0.24-0.60), p=4.0×10−5], while A/A homozygotes exposed to the β-blocker strategy had increased odds for NOD compared with the CCB strategy [OR=2.02 (1.39-2.92), p=2.0×10−4]. eQTL annotation of the 2p21 locus provides functional support for regulating gene expression.
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Affiliation(s)
- S-W Chang
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - C W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Y Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - T A Johnson
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - T Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - E R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - M A Perera
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - A Takahashi
- Laboratory for Statistical Analysis, SNP Research Center, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - T Tanaka
- Laboratory for Cardiovascular Diseases, SNP Research Center, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - M Kubo
- Laboratory for Genotyping Development, SNP Research Center, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - C J Pepine
- Division of Cardiovascular Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - J A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA.,Division of Cardiovascular Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - R M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL, USA.,Division of Cardiovascular Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
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5
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Evans PD, Mueller KL, Gamazon ER, Cox NJ, Tomblin JB. A genome-wide sib-pair scan for quantitative language traits reveals linkage to chromosomes 10 and 13. Genes Brain Behav 2016; 14:387-97. [PMID: 25997078 DOI: 10.1111/gbb.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 02/03/2023]
Abstract
Although there is considerable evidence that individual differences in language development are highly heritable, there have been few genome-wide scans to locate genes associated with the trait. Previous analyses of language impairment have yielded replicable evidence for linkage to regions on chromosomes 16q, 19q, 13q (within lab) and at 13q (between labs). Here we report the first linkage study to screen the continuum of language ability, from normal to disordered, as found in the general population. 383 children from 147 sib-ships (214 sib-pairs) were genotyped on the Illumina(®) Linkage IVb Marker Panel using three composite language-related phenotypes and a measure of phonological memory (PM). Two regions (10q23.33; 13q33.3) yielded genome-wide significant peaks for linkage with PM. A peak suggestive of linkage was also found at 17q12 for the overall language composite. This study presents two novel genetic loci for the study of language development and disorders, but fails to replicate findings by previous groups. Possible reasons for this are discussed.
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Affiliation(s)
- P D Evans
- Department of Medicine, The University of Chicago, IL, USA
| | - K L Mueller
- Murdoch Childrens Research Institute, Melbourne, Australia.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
| | - E R Gamazon
- Department of Medicine, The University of Chicago, IL, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - N J Cox
- Department of Medicine, The University of Chicago, IL, USA.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - J B Tomblin
- Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
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Hernandez W, Gamazon ER, Aquino-Michaels K, Patel S, O'Brien TJ, Harralson AF, Kittles RA, Barbour A, Tuck M, McIntosh SD, Douglas JN, Nicolae D, Cavallari LH, Perera MA. Ethnicity-specific pharmacogenetics: the case of warfarin in African Americans. Pharmacogenomics J 2013; 14:223-8. [PMID: 24018621 DOI: 10.1038/tpj.2013.34] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/18/2013] [Accepted: 07/22/2013] [Indexed: 01/05/2023]
Abstract
Using a derivation cohort (N=349), we developed the first warfarin dosing algorithm that includes recently discovered polymorphisms in VKORC1 and CYP2C9 associated with warfarin dose requirement in African Americans (AAs). We tested our novel algorithm in an independent cohort of 129 AAs and compared the dose prediction to the International Warfarin Pharmacogenetics Consortium (IWPC) dosing algorithms. Our algorithm explains more of the phenotypic variation (R(2)=0.27) than the IWPC pharmacogenomics (R(2)=0.15) or clinical (R(2)=0.16) algorithms. Among high-dose patients, our algorithm predicted a higher proportion of patients within 20% of stable warfarin dose (45% vs 29% and 2% in the IWPC pharmacogenomics and clinical algorithms, respectively). In contrast to our novel algorithm, a significant inverse correlation between predicted dose and percent West African ancestry was observed for the IWPC pharmacogenomics algorithm among patients requiring ⩾60 mg per week (β=-2.04, P=0.02).
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Affiliation(s)
- W Hernandez
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - E R Gamazon
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - K Aquino-Michaels
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - S Patel
- Department of Pharmacy, University of Illinois, Chicago, IL, USA
| | - T J O'Brien
- Department of Pharmacology and Physiology, The George Washington University, Washington DC, USA
| | - A F Harralson
- 1] Department of Pharmacology and Physiology, The George Washington University, Washington DC, USA [2] Department of Pharmacogenomics, Bernard J. Dunn School of Pharmacy, Shenandoah University, Ashburn, VA, USA
| | - R A Kittles
- Department of Medicine, Institute of Human Genetics, University of Illinois, Chicago, IL, USA
| | - A Barbour
- Department of Medicine, The George Washington University, Washington DC, USA
| | - M Tuck
- Department of Veterans Affairs, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - S D McIntosh
- 1] Department of Medicine, The George Washington University, Washington DC, USA [2] Department of Veterans Affairs, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - J N Douglas
- Department of Veterans Affairs, Uniformed Services University of the Health Sciences, Washington DC, USA
| | - D Nicolae
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | - L H Cavallari
- Department of Pharmacy, University of Illinois, Chicago, IL, USA
| | - M A Perera
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
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7
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Weng L, Ziliak D, Im HK, Gamazon ER, Philips S, Nguyen AT, Desta Z, Skaar TC, Flockhart DA, Huang RS. Genome-wide discovery of genetic variants affecting tamoxifen sensitivity and their clinical and functional validation. Ann Oncol 2013; 24:1867-1873. [PMID: 23508821 PMCID: PMC3690911 DOI: 10.1093/annonc/mdt125] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 01/18/2013] [Revised: 02/12/2013] [Accepted: 02/14/2013] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Beyond estrogen receptor (ER), there are no validated predictors for tamoxifen (TAM) efficacy and toxicity. We utilized a genome-wide cell-based model to comprehensively evaluate genetic variants for their contribution to cellular sensitivity to TAM. DESIGN Our discovery model incorporates multidimensional datasets, including genome-wide genotype, gene expression, and endoxifen-induced cellular growth inhibition in the International HapMap lymphoblastoid cell lines (LCLs). Genome-wide findings were further evaluated in NCI60 cancer cell lines. Gene knock-down experiments were performed in four breast cancer cell lines. Genetic variants identified in the cell-based model were examined in 245 Caucasian breast cancer patients who underwent TAM treatment. RESULTS We identified seven novel single-nucleotide polymorphisms (SNPs) associated with endoxifen sensitivity through the expression of 10 genes using the genome-wide integrative analysis. All 10 genes identified in LCLs were associated with TAM sensitivity in NCI60 cancer cell lines, including USP7. USP7 knock-down resulted in increasing resistance to TAM in four breast cancer cell lines tested, which is consistent with the finding in LCLs and in the NCI60 cells. Furthermore, we identified SNPs that were associated with TAM-induced toxicities in breast cancer patients, after adjusting for other clinical factors. CONCLUSION Our work demonstrates the utility of a cell-based model in genome-wide identification of pharmacogenomic markers.
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Affiliation(s)
| | | | - H K Im
- Health Studies, University of Chicago, Chicago
| | | | - S Philips
- Department of Medicine, Division of Clinical Pharmacology, School of Medicine, Indiana University, Indianapolis, USA
| | - A T Nguyen
- Department of Medicine, Division of Clinical Pharmacology, School of Medicine, Indiana University, Indianapolis, USA
| | - Z Desta
- Department of Medicine, Division of Clinical Pharmacology, School of Medicine, Indiana University, Indianapolis, USA
| | - T C Skaar
- Department of Medicine, Division of Clinical Pharmacology, School of Medicine, Indiana University, Indianapolis, USA
| | - D A Flockhart
- Department of Medicine, Division of Clinical Pharmacology, School of Medicine, Indiana University, Indianapolis, USA
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Gamazon ER, Badner JA, Cheng L, Zhang C, Zhang D, Cox NJ, Gershon ES, Kelsoe JR, Greenwood TA, Nievergelt CM, Chen C, McKinney R, Shilling PD, Schork NJ, Smith EN, Bloss CS, Nurnberger JI, Edenberg HJ, Foroud T, Koller DL, Scheftner WA, Coryell W, Rice J, Lawson WB, Nwulia EA, Hipolito M, Byerley W, McMahon FJ, Schulze TG, Berrettini WH, Potash JB, Zandi PP, Mahon PB, McInnis MG, Zöllner S, Zhang P, Craig DW, Szelinger S, Barrett TB, Liu C. Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. Mol Psychiatry 2013; 18:340-6. [PMID: 22212596 PMCID: PMC3601550 DOI: 10.1038/mp.2011.174] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We conducted a systematic study of top susceptibility variants from a genome-wide association (GWA) study of bipolar disorder to gain insight into the functional consequences of genetic variation influencing disease risk. We report here the results of experiments to explore the effects of these susceptibility variants on DNA methylation and mRNA expression in human cerebellum samples. Among the top susceptibility variants, we identified an enrichment of cis regulatory loci on mRNA expression (eQTLs), and a significant excess of quantitative trait loci for DNA CpG methylation, hereafter referred to as methylation quantitative trait loci (mQTLs). Bipolar disorder susceptibility variants that cis regulate both cerebellar expression and methylation of the same gene are a very small proportion of bipolar disorder susceptibility variants. This finding suggests that mQTLs and eQTLs provide orthogonal ways of functionally annotating genetic variation within the context of studies of pathophysiology in brain. No lymphocyte mQTL enrichment was found, suggesting that mQTL enrichment was specific to the cerebellum, in contrast to eQTLs. Separately, we found that using mQTL information to restrict the number of single-nucleotide polymorphisms studied enhances our ability to detect a significant association. With this restriction a priori informed by the observed functional enrichment, we identified a significant association (rs12618769, P(bonferroni)<0.05) from two other GWA studies (TGen+GAIN; 2191 cases and 1434 controls) of bipolar disorder, which we replicated in an independent GWA study (WTCCC). Collectively, our findings highlight the importance of integrating functional annotation of genetic variants for gene expression and DNA methylation to advance the biological understanding of bipolar disorder.
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Affiliation(s)
- ER Gamazon
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - JA Badner
- Department of Psychiatry, University of Chicago, Chicago, IL, USA
| | - L Cheng
- Department of Psychiatry, Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - C Zhang
- Department of Psychiatry, Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - D Zhang
- School of Medicine, University of Zhejiang, Hanzhou, Zhejiang, China
| | - NJ Cox
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - ES Gershon
- Department of Psychiatry, University of Chicago, Chicago, IL, USA
| | - JR Kelsoe
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - TA Greenwood
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - CM Nievergelt
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - C Chen
- Department of Psychiatry, Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - R McKinney
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - PD Shilling
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - NJ Schork
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, CA, USA
| | - EN Smith
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, CA, USA
| | - CS Bloss
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, CA, USA
| | - JI Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - HJ Edenberg
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - T Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - DL Koller
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - WA Scheftner
- Department of Psychiatry, Rush University, Chicago, IL, USA
| | - W Coryell
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - J Rice
- Division of Biostatistics, Washington University, St Louis, MO, USA
| | - WB Lawson
- Department of Psychiatry, Howard University, Washington, DC, USA
| | - EA Nwulia
- Department of Psychiatry, Howard University, Washington, DC, USA
| | - M Hipolito
- Department of Psychiatry, Howard University, Washington, DC, USA
| | - W Byerley
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - FJ McMahon
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - TG Schulze
- Genetic Basis of Mood and Anxiety Disorders Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA,Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - WH Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - JB Potash
- Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - PP Zandi
- Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - PB Mahon
- Department of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - MG McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - S Zöllner
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - P Zhang
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - DW Craig
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - S Szelinger
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - TB Barrett
- Department of Psychiatry, Portland VA Medical Center, Portland, OR, USA
| | - C Liu
- Department of Psychiatry, Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL, USA
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Abstract
The use of cell-based models has emerged as a promising means to discover and validate pharmacologic phenotype-genotype relationships. The availability of large-scale genome studies in both human and model systems is now allowing us an unprecedented opportunity to understand how well cell-based models identify clinically relevant genetic variants associated with drug response and toxicity. Here we review these studies and the emerging translational information.
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Affiliation(s)
- N J Cox
- Committee on Clinical Pharmacology and Pharmacogenomics, Department of Medicine, University of Chicago, Chicago, Illinois, USA
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Wheeler HE, Gamazon ER, Stark AL, O'Donnell PH, Gorsic LK, Huang RS, Cox NJ, Dolan ME. Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations. Pharmacogenomics J 2011; 13:35-43. [PMID: 21844884 PMCID: PMC3370147 DOI: 10.1038/tpj.2011.38] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Platinating agents are used in the treatment of many cancers, yet they can induce toxicities and resistance that limit their utility. Using previously published and additional world population panels of diverse ancestry totaling 608 lymphoblastoid cell lines (LCLs), we performed meta-analyses of over 3 million SNPs for both carboplatin- and cisplatin-induced cytotoxicity. The most significant SNP in the carboplatin meta-analysis is located in an intron of NBAS (p = 5.1 × 10−7). The most significant SNP in the cisplatin meta-analysis is upstream of KRT16P2 (p = 5.8 × 10−7). We also show that cisplatin-susceptibility SNPs are enriched for carboplatin-susceptibility SNPs. Most of the variants that associate with platinum-induced cytotoxicity are polymorphic across multiple world populations; therefore, they could be tested in follow-up studies in diverse clinical populations. Seven genes previously implicated in platinating agent response, including BCL2, GSTM1, GSTT1, ERCC2, and ERCC6 were also implicated in our meta-analyses.
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Affiliation(s)
- H E Wheeler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
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Below JE, Gamazon ER, Morrison JV, Konkashbaev A, Pluzhnikov A, McKeigue PM, Parra EJ, Elbein SC, Hallman DM, Nicolae DL, Bell GI, Cruz M, Cox NJ, Hanis CL. Genome-wide association and meta-analysis in populations from Starr County, Texas, and Mexico City identify type 2 diabetes susceptibility loci and enrichment for expression quantitative trait loci in top signals. Diabetologia 2011; 54:2047-55. [PMID: 21647700 PMCID: PMC3761075 DOI: 10.1007/s00125-011-2188-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 04/14/2011] [Indexed: 12/11/2022]
Abstract
AIMS/HYPOTHESIS We conducted genome-wide association studies (GWASs) and expression quantitative trait loci (eQTL) analyses to identify and characterise risk loci for type 2 diabetes in Mexican-Americans from Starr County, TX, USA. METHOD Using 1.8 million directly interrogated and imputed genotypes in 837 unrelated type 2 diabetes cases and 436 normoglycaemic controls, we conducted Armitage trend tests. To improve power in this population with high disease rates, we also performed ordinal regression including an intermediate class with impaired fasting glucose and/or glucose tolerance. These analyses were followed by meta-analysis with a study of 967 type 2 diabetes cases and 343 normoglycaemic controls from Mexico City, Mexico. RESULT The top signals (unadjusted p value <1 × 10(-5)) included 49 single nucleotide polymorphisms (SNPs) in eight gene regions (PER3, PARD3B, EPHA4, TOMM7, PTPRD, HNT [also known as RREB1], LOC729993 and IL34) and six intergenic regions. Among these was a missense polymorphism (rs10462020; Gly639Val) in the clock gene PER3, a system recently implicated in diabetes. We also report a second signal (minimum p value 1.52 × 10(-6)) within PTPRD, independent of the previously implicated SNP, in a population of Han Chinese. Top meta-analysis signals included known regions HNF1A and KCNQ1. Annotation of top association signals in both studies revealed a marked excess of trans-acting eQTL in both adipose and muscle tissues. CONCLUSIONS/INTERPRETATION In the largest study of type 2 diabetes in Mexican populations to date, we identified modest associations of novel and previously reported SNPs. In addition, in our top signals we report significant excess of SNPs that predict transcript levels in muscle and adipose tissues.
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Affiliation(s)
- J. E. Below
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - E. R. Gamazon
- Section of Genetic Medicine, KCBD 3220, University of Chicago, 900 E 57th Street, Chicago, IL 60637, USA
| | - J. V. Morrison
- Section of Genetic Medicine, KCBD 3220, University of Chicago, 900 E 57th Street, Chicago, IL 60637, USA
| | - A. Konkashbaev
- Section of Genetic Medicine, KCBD 3220, University of Chicago, 900 E 57th Street, Chicago, IL 60637, USA
| | - A. Pluzhnikov
- Section of Genetic Medicine, KCBD 3220, University of Chicago, 900 E 57th Street, Chicago, IL 60637, USA
| | - P. M. McKeigue
- Public Health Sciences Section, Division of Community Health Sciences, University of Edinburgh Medical School, Edinburgh, UK
| | - E. J. Parra
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - S. C. Elbein
- Section on Endocrinology and Metabolism, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - D. M. Hallman
- Human Genetics Center, University of Texas Health Science Center at Houston, P.O. Box 20186, Houston, TX 77225, USA
| | - D. L. Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, USA. Section of Genetic Medicine, KCBD 3220, University of Chicago, 900 E 57th Street, Chicago, IL 60637, USA. Department of Statistics, University of Chicago, Chicago, IL, USA. Department of Medicine, University of Chicago, Chicago, IL, USA
| | - G. I. Bell
- Department of Human Genetics, University of Chicago, Chicago, IL, USA. Department of Medicine, University of Chicago, Chicago, IL, USA
| | - M. Cruz
- Unidad de Investigacion Medica en Bioquimica, Hospital de Especialidades, Centro Medico ‘Siglo XXI’, IMSS, Mexico City, Mexico
| | - N. J. Cox
- Department of Human Genetics, University of Chicago, Chicago, IL, USA. Section of Genetic Medicine, KCBD 3220, University of Chicago, 900 E 57th Street, Chicago, IL 60637, USA. Department of Medicine, University of Chicago, Chicago, IL, USA. Section of Genetic Medicine, University of Chicago, KCBD 3220, 900 E 57th Street, Chicago, IL 60637, USA
| | - C. L. Hanis
- Human Genetics Center, University of Texas Health Science Center at Houston, P.O. Box 20186, Houston, TX 77225, USA
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