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Roman TS, Marvelle AF, Fogarty MP, Vadlamudi S, Gonzalez AJ, Buchkovich ML, Huyghe JR, Fuchsberger C, Jackson AU, Wu Y, Civelek M, Lusis AJ, Gaulton KJ, Sethupathy P, Kangas AJ, Soininen P, Ala-Korpela M, Kuusisto J, Collins FS, Laakso M, Boehnke M, Mohlke KL. Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol. Am J Hum Genet 2015; 97:801-15. [PMID: 26637976 PMCID: PMC4678431 DOI: 10.1016/j.ajhg.2015.10.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [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: 05/04/2015] [Accepted: 10/28/2015] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified more than 150 loci associated with blood lipid and cholesterol levels; however, the functional and molecular mechanisms for many associations are unknown. We examined the functional regulatory effects of candidate variants at the GALNT2 locus associated with high-density lipoprotein cholesterol (HDL-C). Fine-mapping and conditional analyses in the METSIM study identified a single locus harboring 25 noncoding variants (r(2) > 0.7 with the lead GWAS variants) strongly associated with total cholesterol in medium-sized HDL (e.g., rs17315646, p = 3.5 × 10(-12)). We used luciferase reporter assays in HepG2 cells to test all 25 variants for allelic differences in regulatory enhancer activity. rs2281721 showed allelic differences in transcriptional activity (75-fold [T] versus 27-fold [C] more than the empty-vector control), as did a separate 780-bp segment containing rs4846913, rs2144300, and rs6143660 (49-fold [AT(-) haplotype] versus 16-fold [CC(+) haplotype] more). Using electrophoretic mobility shift assays, we observed differential CEBPB binding to rs4846913, and we confirmed this binding in a native chromatin context by performing chromatin-immunoprecipitation (ChIP) assays in HepG2 and Huh-7 cell lines of differing genotypes. Additionally, sequence reads in HepG2 DNase-I-hypersensitivity and CEBPB ChIP-seq signals spanning rs4846913 showed significant allelic imbalance. Allelic-expression-imbalance assays performed with RNA from primary human hepatocyte samples and expression-quantitative-trait-locus (eQTL) data in human subcutaneous adipose tissue samples confirmed that alleles associated with increased HDL-C are associated with a modest increase in GALNT2 expression. Together, these data suggest that at least rs4846913 and rs2281721 play key roles in influencing GALNT2 expression at this HDL-C locus.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Amanda F Marvelle
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marie P Fogarty
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arlene J Gonzalez
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martin L Buchkovich
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeroen R Huyghe
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ying Wu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mete Civelek
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biomedical Engineering, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Aldons J Lusis
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Deparment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kyle J Gaulton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antti J Kangas
- Computational Medicine, Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland
| | - Pasi Soininen
- Computational Medicine, Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland; Nuclear Magnetic Resonance Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Mika Ala-Korpela
- Computational Medicine, Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland; Nuclear Magnetic Resonance Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland; Oulu University Hospital, 90220 Oulu, Finland; Computational Medicine, School of Social and Community Medicine and Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Francis S Collins
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Wu Y, Marvelle AF, Li J, Croteau-Chonka DC, Feranil AB, Kuzawa CW, Li Y, Adair LS, Mohlke KL. Genetic association with lipids in Filipinos: waist circumference modifies an APOA5 effect on triglyceride levels. J Lipid Res 2013; 54:3198-205. [PMID: 24023260 DOI: 10.1194/jlr.p042077] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [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: 12/25/2022] Open
Abstract
Blood levels of lipoprotein cholesterol and triglycerides (TGs) are highly heritable and are major risk factors for cardiovascular disease (CVD). Approximately 100 lipid-associated loci have been identified in populations of European ancestry. We performed a genome-wide association study of lipid traits in 1,782 Filipino women from the Cebu Longitudinal Health and Nutrition Survey, and tested for evidence of interactions with waist circumference. We conducted additional association and interaction analyses in 1,719 of their young adult offspring. Genome-wide significant associations (P < 5 × 10⁻⁸) were detected at APOE for low density lipoprotein cholesterol and total cholesterol, and at APOA5 for TGs. Suggestive associations (P < 10⁻⁶) were detected at GCKR for TGs, and at CETP and TOM1 for high density lipoprotein cholesterol. Our data also supported the existence of allelic heterogeneity at APOA5, CETP, LIPC, and APOE. The secondary signal (Gly185Cys) at APOA5 exhibited a single nucleotide polymorphism (SNP)-by-waist circumference interaction affecting TGs (Pinteraction = 1.6 × 10⁻⁴), manifested by stronger SNP effects as waist circumference increased. These findings provide the first evidence that central obesity may accentuate the effect of the TG-increasing allele of the APOA5 signal, emphasizing that CVD risk could be reduced by central obesity control.
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Affiliation(s)
- Ying Wu
- Departments of Genetics, University of North Carolina, Chapel Hill, NC 27599
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Croteau-Chonka DC, Marvelle AF, Lange EM, Lee NR, Adair LS, Lange LA, Mohlke KL. Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women. Obesity (Silver Spring) 2011; 19:1019-27. [PMID: 20966902 PMCID: PMC3046220 DOI: 10.1038/oby.2010.256] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [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] [Indexed: 11/08/2022]
Abstract
Increased values of multiple adiposity-related anthropometric traits are important risk factors for many common complex diseases. We performed a genome-wide association (GWA) study for four quantitative traits related to body size and adiposity (BMI, weight, waist circumference, and height) in a cohort of 1,792 adult Filipino women from the Cebu Longitudinal Health and Nutrition Survey (CLHNS). This is the first GWA study of anthropometric traits in Filipinos, a population experiencing a rapid transition into a more obesogenic environment. In addition to identifying suggestive evidence of additional single-nucleotide polymorphism (SNP) association signals (P < 10(-5)), we replicated (P < 0.05, same direction of additive effect) associations previously reported in European populations of both BMI and weight with MC4R and FTO, of BMI with BDNF, and of height with EFEMP1, ZBTB38, and NPPC, but none with waist circumference. We also replicated loci reported in Japanese or Korean populations as associated with BMI (OTOL1) and height (HIST1H1PS2, C14orf145, GPC5). A difference in local linkage disequilibrium (LD) between European and Asian populations suggests a narrowed association region for BDNF, while still including a proposed functional nonsynonymous amino acid substitution variant (rs6265, Val66Met). Finally, we observed significant evidence (P < 0.0042) for age-by-genotype interactions influencing BMI for rs17782313 (MC4R) and rs9939609 (FTO), and for a study year-by-genotype interaction for rs4923461 (BDNF). Our results show that several genetic risk factors are associated with anthropometric traits in Filipinos and provide further insight into the effects of BDNF, FTO, and MC4R on BMI.
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Affiliation(s)
- Damien C. Croteau-Chonka
- Department of Genetics, University of North Carolina, Chapel Hill, NC
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC
- Bioinformatics and Computational Biology Training Program, University of North Carolina, Chapel Hill, NC
| | - Amanda F. Marvelle
- Department of Genetics, University of North Carolina, Chapel Hill, NC
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC
| | - Ethan M. Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC
| | - Nanette R. Lee
- Office of Population Studies Foundation Inc., University of San Carlos, Cebu City, Philippines
| | - Linda S. Adair
- Department of Nutrition, University of North Carolina, Chapel Hill, NC
| | - Leslie A. Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC
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Martiniova L, Perera SM, Brouwers FM, Alesci S, Abu-Asab M, Marvelle AF, Kiesewetter DO, Thomasson D, Morris JC, Kvetnansky R, Tischler AS, Reynolds JC, Fojo AT, Pacak K. Increased uptake of [¹²³I]meta-iodobenzylguanidine, [¹⁸F]fluorodopamine, and [³H]norepinephrine in mouse pheochromocytoma cells and tumors after treatment with the histone deacetylase inhibitors. Endocr Relat Cancer 2011; 18:143-57. [PMID: 21098082 PMCID: PMC4110720 DOI: 10.1677/erc-10-0090] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [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] [Indexed: 11/27/2022]
Abstract
[¹³¹I]meta-iodobenzylguanidine ([¹³¹I]MIBG) is the most commonly used treatment for metastatic pheochromocytoma and paraganglioma. It enters the chromaffin cells via the membrane norepinephrine transporter; however, its success has been modest. We studied the ability of histone deacetylase (HDAC) inhibitors to enhance [¹²³I]MIBG uptake by tumors in a mouse metastatic pheochromocytoma model. HDAC inhibitors are known to arrest growth, induce differentiation and apoptosis in various cancer cells, and further inhibit tumor growth. We report the in vitro and in vivo effects of two HDAC inhibitors, romidepsin and trichostatin A, on the uptake of [(3)H]norepinephrine, [¹²³I]MIBG, and [(18)F]fluorodopamine in a mouse model of metastatic pheochromocytoma. The effects of both inhibitors on norepinephrine transporter activity were assessed in mouse pheochromocytoma (MPC) cells by using the transporter-blocking agent desipramine and the vesicular-blocking agent reserpine. HDAC inhibitors increased [(3)H]norepinephrine, [¹²³I]MIBG, and [(18)F]fluorodopamine uptake through the norepinephrine transporter in MPC cells. In vivo, inhibitor treatment resulted in significantly increased uptake of [(18)F]fluorodopamine positron emission tomography (PET) in pheochromocytoma liver metastases (19.1 ± 3.2% injected dose per gram of tumor (%ID/g) compared to liver metastases in pretreatment scans 5.9 ± 0.6%; P<0.001). Biodistribution analysis after inhibitors treatment confirmed the PET results. The uptake of [(123)I]MIBG was significantly increased in liver metastases 9.5 ± 1.1% compared to 3.19 ± 0.4% in untreated control liver metastases (P<0.05). We found that HDAC inhibitors caused an increase in the amount of norepinephrine transporter expressed in tumors. HDAC inhibitors may enhance the therapeutic efficacy of [(131)I]MIBG treatment in patients with advanced malignant pheochromocytoma and paraganglioma.
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Affiliation(s)
- Lucia Martiniova
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
- Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Shiromi M. Perera
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Frederieke M. Brouwers
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Salvatore Alesci
- Clinical Neuroendocrinology Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mones Abu-Asab
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amanda F. Marvelle
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dale O. Kiesewetter
- Intramural Science PRGMS, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Thomasson
- Laboratory of Diagnostic Radiology, Warren Grant Magnuson Clinical Center, Bethesda, MD, 20892 USA
| | - John C. Morris
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Richard Kvetnansky
- Institute of Experimental Endocrinology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Arthur S. Tischler
- Department of Pathology, Tufts University School of Medicine and Tufts Medical Center, Boston, MA, 02111, USA
| | - James C Reynolds
- Nuclear Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A. Tito Fojo
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
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Lange LA, Croteau-Chonka DC, Marvelle AF, Qin L, Gaulton KJ, Kuzawa CW, McDade TW, Wang Y, Li Y, Levy S, Borja JB, Lange EM, Adair LS, Mohlke KL. Genome-wide association study of homocysteine levels in Filipinos provides evidence for CPS1 in women and a stronger MTHFR effect in young adults. Hum Mol Genet 2010; 19:2050-8. [PMID: 20154341 DOI: 10.1093/hmg/ddq062] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plasma homocysteine (Hcy) level is associated with cardiovascular disease and may play an etiologic role in vascular damage, a precursor for atherosclerosis. We performed a genome-wide association study for Hcy in 1786 unrelated Filipino women from the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The most strongly associated single-nucleotide polymorphism (SNP) (rs7422339, P = 4.7 x 10(-13)) encodes Thr1405Asn in the gene CPS1 and explained 3.0% of variation in the Hcy level. The widely studied MTHFR C677T SNP (rs1801133) was also highly significant (P = 8.7 x 10(-10)) and explained 1.6% of the trait variation. We also genotyped these two SNPs in 1679 CLHNS young adult offspring. The MTHFR C677T SNP was strongly associated with Hcy (P = 1.9 x 10(-26)) and explained approximately 5.1% of the variation in the offspring. In contrast, the CPS1 variant was significant only in females (P = 0.11 in all; P = 0.0087 in females). Combined analysis of all samples confirmed that the MTHFR variant was more strongly associated with Hcy in the offspring (interaction P = 1.2 x 10(-5)). Furthermore, although there was evidence for a positive synergistic effect between the CPS1 and MTHFR SNPs in the offspring (interaction P = 0.0046), there was no significant evidence for an interaction in the mothers (P = 0.55). These data confirm a recent finding that CPS1 is a locus influencing Hcy levels in women and suggest that genetic effects on Hcy may differ across developmental stages.
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Affiliation(s)
- Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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Zinman L, Liu HN, Sato C, Wakutani Y, Marvelle AF, Moreno D, Morrison KE, Mohlke KL, Bilbao J, Robertson J, Rogaeva E. A mechanism for low penetrance in an ALS family with a novel SOD1 deletion. Neurology 2009; 72:1153-9. [PMID: 19332692 DOI: 10.1212/01.wnl.0000345363.65799.35] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND About 20% of familial amyotrophic lateral sclerosis (ALS) is caused by mutations in SOD1 and is typically transmitted as an autosomal dominant trait. However, due to reduced mutation penetrance, the disease may present in a recessive or sporadic manner. OBJECTIVE To determine the factors responsible for the low penetrance of the SOD1 mutation. METHODS Twelve members of a Canadian ALS family of Filipino origin were recruited for the study. SOD1 was sequenced in the proband. SOD1 expression was assessed by real-time-PCR and immunoblotting. RESULTS The proband was a homozygous carrier of a novel 6 bp deletion in exon 2 (DeltaG27/P28), the pathologic significance of which was confirmed by immunohistochemistry. Eight living family members are heterozygotes and remain unaffected at ages ranging between 48 and 85 years. Haplotype analysis showed that the deletion is a single founder mutation likely common in the Cagayan province (Philippines). The low penetrance of the mutation is explained by the fact that it enhances the naturally occurring alternative splicing of exon 2 of the SOD1 mRNA, leading to reduced transcription of the mutant allele. Indeed, Western blot analysis demonstrated the low level of SOD1 protein in carriers of the DeltaG27/P28 compared to wild-type individuals or a carrier of the A4V SOD1 mutation. CONCLUSION The enhanced splicing of exon 2 acts as a natural knock-down of the mutant SOD1 allele in the Filipino amyotrophic lateral sclerosis (ALS) family. There is a need for careful investigation of splicing isoforms of SOD1 and other ALS genes as factors influencing the severity of disease.
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Affiliation(s)
- L Zinman
- Centre for Neurodegenerative Diseases, Department of Medicine, University of Toronto, 6 Queen's Park Crescent West, Toronto, Ontario, Canada, M5S 3H2
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Marvelle AF, Lange LA, Qin L, Adair LS, Mohlke KL. Association of FTO with obesity-related traits in the Cebu Longitudinal Health and Nutrition Survey (CLHNS) Cohort. Diabetes 2008; 57:1987-91. [PMID: 18426866 PMCID: PMC2453620 DOI: 10.2337/db07-1700] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 04/15/2008] [Indexed: 01/29/2023]
Abstract
OBJECTIVE The underlying genetic component of obesity-related traits is not well understood, and there is limited evidence to support genetic association shared across multiple studies, populations, and environmental contexts. The present study investigated the association between candidate variants and obesity-related traits in a sample of 1,886 adult Filipino women from the Cebu Longitudinal Health and Nutrition Survey (CLHNS) cohort. RESEARCH DESIGN AND METHODS We selected and genotyped 19 single nucleotide polymorphisms in 10 genes (ADRB2, ADRB3, FTO, GNB3, INSIG2, LEPR, PPARG, TNF, UCP2, and UCP3) that had been previously reported to be associated with an obesity-related quantitative trait. RESULTS We observed evidence for association of the A allele of rs9939609 (FTO intron 1) with increased BMI (P = 0.0072 before multiple test correction), baseline BMI (P = 0.0015), longitudinal BMI based on eight surveys from 1983 to 2005 (P = 0.000029), waist circumference (P = 0.0094), and weight (P = 0.021). The increase in average BMI was approximately 0.4 for each additional A allele. We also observed association of the ADRB3 Trp64Arg variant with BMI, waist circumference, percent body fat, weight, fat mass, arm fat area, and arm muscle area (P < 0.05), although the direction of effect is inconsistent with the majority of previous reports. CONCLUSIONS Our study confirms that FTO is a common obesity susceptibility gene in Filipinos, with an effect size similar to that seen in samples of European origin.
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Affiliation(s)
- Amanda F Marvelle
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Marvelle AF, Lange LA, Qin L, Wang Y, Lange EM, Adair LS, Mohlke KL. Comparison of ENCODE region SNPs between Cebu Filipino and Asian HapMap samples. J Hum Genet 2007; 52:729-737. [PMID: 17636361 DOI: 10.1007/s10038-007-0175-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [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: 05/02/2007] [Accepted: 06/22/2007] [Indexed: 10/23/2022]
Abstract
Patterns of linkage disequilibrium (LD) act as the framework for designing efficient association studies; these patterns are being studied and catalogued by The International HapMap Project. The current study assessed the transferability of tag SNPs chosen from HapMap panels to a cohort of 80 individuals from metro Cebu, Philippines, who participated in the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The analyses focused on 627 single nucleotide polymorphisms (SNPs) in the central 40 kb within each of the 10 HapMap ENCODE regions. The similarity between the genetic variants in Cebu Filipino samples and HapMap panels was examined using allele frequency estimates, measures of pairwise linkage disequilibrium (LD), and haplotype frequency estimates. For these measures, strong correlations were observed between the Cebu Filipino samples and the Asian panels from HapMap, with the strongest correlations observed with the Han Chinese from Beijing (CHB) panel. Tag SNPs selected using the HapMap CHB panel were particularly effective at representing the genetic variation in Cebu Filipino samples. These results suggest that the HapMap data will be an effective resource for future studies in Cebu Filipino samples.
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Affiliation(s)
- Amanda F Marvelle
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA
| | - Leslie A Lange
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA
| | - Li Qin
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA
| | - Yunfei Wang
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA
| | - Ethan M Lange
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA
- Department of Biostatistics, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Linda S Adair
- Department of Nutrition, Schools of Medicine and Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Karen L Mohlke
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.
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