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DeWoody JA, Fernandez NB, Brüniche-Olsen A, Antonides JD, Doyle JM, San Miguel P, Westerman R, Vertyankin VV, Godard-Codding CAJ, Bickham JW. Characterization of the Gray Whale Eschrichtius robustus Genome and a Genotyping Array Based on Single-Nucleotide Polymorphisms in Candidate Genes. Biol Bull 2017; 232:186-197. [PMID: 28898601 DOI: 10.1086/693483] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genetic and genomic approaches have much to offer in terms of ecology, evolution, and conservation. To better understand the biology of the gray whale Eschrichtius robustus (Lilljeborg, 1861), we sequenced the genome and produced an assembly that contains ∼95% of the genes known to be highly conserved among eukaryotes. From this assembly, we annotated 22,711 genes and identified 2,057,254 single-nucleotide polymorphisms (SNPs). Using this assembly, we generated a curated list of candidate genes potentially subject to strong natural selection, including genes associated with osmoregulation, oxygen binding and delivery, and other aspects of marine life. From these candidate genes, we queried 92 autosomal protein-coding markers with a panel of 96 SNPs that also included 2 sexing and 2 mitochondrial markers. Genotyping error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed heterozygosity was 0.33 averaged over all autosomal markers. This level of variability provides substantial discriminatory power across loci (mean probability of identity of 1.6 × 10-25 and mean probability of exclusion >0.999 with neither parent known), indicating that these markers provide a powerful means to assess parentage and relatedness in gray whales. We found 29 unique multilocus genotypes represented among our 36 biopsies (indicating that we inadvertently sampled 7 whales twice). In total, we compiled an individual data set of 28 western gray whales (WGSs) and 1 presumptive eastern gray whale (EGW). The lone EGW we sampled was no more or less related to the WGWs than expected by chance alone. The gray whale genomes reported here will enable comparative studies of natural selection in cetaceans, and the SNP markers should be highly informative for future studies of gray whale evolution, population structure, demography, and relatedness.
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Key Words
- EGW, eastern gray whale
- EST, expressed sequence tag
- HWE, Hardy-Weinberg equilibrium
- IUCN, International Union for Conservation of Nature
- IWC, International Whaling Commission
- LD, linkage disequilibrium
- MP, mate paired
- PCR, polymerase chain reaction
- PE, paired end
- SNP, single-nucleotide polymorphism
- STA, specific target amplification
- WGW, western gray whale
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Zhang Z, Wang J, He J, Zeng X, Chen X, Xiong M, Zhou Q, Guo M, Li D, Lu W. Identification of TRPCs genetic variants that modify risk for lung cancer based on the pathway and two-stage study. Meta Gene 2016; 9:191-6. [PMID: 27617218 PMCID: PMC5006132 DOI: 10.1016/j.mgene.2016.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 12/08/2015] [Revised: 06/26/2016] [Accepted: 07/07/2016] [Indexed: 10/28/2022] Open
Abstract
OBJECTIVE Store operated calcium channels (SOCCs) and Receptor-operated calcium channels (ROCCs) are important pathways participating in regulation of intracellular Ca(2 +) concentration in various cell types. The purpose of our study is to determine whether genetic variations in key components of SOCCs and ROCCs are associated with lung cancer risk. METHODS We identified 236 tagSNPs in 9 key genes related to SOCCs and ROCCs (TRPC1, TRPC3, TRPC4, TRPC6, TRPC7, ORAI1, ORAI2, STIM1, and STIM2) and evaluated their association with lung cancer risk in a two-stage case-control study with a total of 2433 lung cancer cases and 2433 cancer-free controls using Illumina high throughput genotyping platform. RESULTS We found consistently significant associations of TRPC4 rs9547991 and rs978156, and TRPC7 rs11748198 with increased risk of lung cancer among the three kinds of sources of populations (additive model in combined population: adjusted OR = 1.33, 95% CI = 1.11-1.59 for rs9547991; adjusted OR = 1.21, 95% CI = 1.08-1.35 for rs978156; and adjusted OR = 1.28, 95% CI = 1.10-1.47 for rs11748198). When combining the effects of TRPC7 rs11748198, and TRPC4 rs9547991 and rs978156, subjects carrying "≥ 1" variant alleles had a 1.29-fold increased risk of lung cancer (95% CI = 1.15-1.46), compared with those carrying "0" variant allele. Lung cancer risk significantly increased with the increasing number of variant alleles of the three SNPs in a dose-dependent manner (P for trend = 7.2 × 10(- 7)). CONCLUSION These findings suggested that TRPC4 rs9547991 and rs978156, and TRPC7 rs11748198 were candidate susceptibility markers for lung cancer in Chinese population. Our study provides the epidemiological evidence supporting a connection between TRPC members and lung cancer risks.
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Key Words
- CI, confidence interval
- Genetic variants
- HWE, Hardy-Weinberg equilibrium
- LD, linkage disequilibrium
- Lung cancer
- MAF, minor allele frequency
- OR, odds ratio
- ROCCs
- ROCCs, receptor-operated Ca2 + channels
- SNP, single nucleotide polymorphism
- SOCCs
- SOCCs, Store-operated Ca2 + channels
- SOCE, Store-operated Ca2 + entry channels
- TRPCs
- tagSNPs, tagging single nucleotide polymorphisms
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Affiliation(s)
- Zili Zhang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jian Wang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jianxing He
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiansheng Zeng
- Department of Respiratory Medicine, Xiangyang Central Hospital, Xiangyang, China
| | - Xindong Chen
- The First Municipal Hospital of Lufeng, Lufeng, China
| | - Mingmei Xiong
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qipeng Zhou
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Meihua Guo
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Defu Li
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wenju Lu
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China; Department of Laboratory Medicine, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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Antony HA, Das S, Parija SC, Padhi S. Sequence analysis of pfcrt and pfmdr1 genes and its association with chloroquine resistance in Southeast Indian Plasmodium falciparum isolates. Genom Data 2016; 8:85-90. [PMID: 27222806 PMCID: PMC4856815 DOI: 10.1016/j.gdata.2016.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/13/2016] [Accepted: 04/16/2016] [Indexed: 01/13/2023]
Abstract
BACKGROUND Due to the widespread resistance of Plasmodium falciparum to chloroquine drug, artemisinin-based combination therapy (ACT) has been recommended as the first-line treatment. This study aims to evaluate the extent of chloroquine resistance in P. falciparum infection after the introduction of ACT. This study was carried out based on the mutation analysis in P. falciparum chloroquine resistant transporter (pfcrt) and P. falciparum multidrug resistance 1 (pfmdr1) genes. Identification of these molecular markers plays a significant role in monitoring and assessment of drug resistance as well as in designing an effective antimalarial drug policy in India. METHODS Sixty blood samples were collected from patients infected with P. falciparum from JIPMER, Puducherry and MKCG Medical College, Odisha. Polymerase chain reaction-restriction fragment length polymorphism was performed, targeting the point mutation of K76T in pfcrt and N86Y in pfmdr1 gene. The PCR products were sequenced, genotyped and further analysed for amino acid changes in these codons. RESULTS The frequency of pfcrt mutation at 76th position was dominant for mutant T allele with 56.7% and wild type K, 43.3%. Majority of pfmdr1 86 allele were wild type, with N (90%) and mutant, Y (10%). Additionally, we found three haplotypes for CQ resistance, SVMNT, CVIET and CVIKT in association with the pfcrt gene. However, a poorly studied SNP in pfmdr1 gene (Y184F) associated with CQ resistance showed high frequency (70%) in P. falciparum isolates. CONCLUSIONS The point mutation K76T of pfcrt is high in P. falciparum suggesting a sustained high CQ resistance even after five years of the introduction of ACTs for antimalarial therapy. The present study suggests a strong association of CQ resistance with pfcrt T76, but not with the pfmdr1 Y86 mutation. However, sequence analysis showed that Y184F mutation on pfmdr1 gene was found to be associated with high resistance. Also, a new pfcrt haplotype 'CVIKT' associated with CQ resistance was found to be present in Indian strains of P. falciparum. The data obtained from this study helps in continuous monitoring of drug resistance in malaria and also suggests the need for careful usage of CQ in Plasmodium vivax malarial treatment.
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Affiliation(s)
- Hiasindh Ashmi Antony
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry 605006, India
| | - Sindhusuta Das
- Department of Microbiology, Maharaja Krishna Chandra Gajapati Medical College (MKCG Medical College), Odisha 760004, India
| | - Subhash Chandra Parija
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry 605006, India
| | - Sanghamitra Padhi
- Department of Microbiology, Maharaja Krishna Chandra Gajapati Medical College (MKCG Medical College), Odisha 760004, India
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Forni D, Mozzi A, Pontremoli C, Vertemara J, Pozzoli U, Biasin M, Bresolin N, Clerici M, Cagliani R, Sironi M. Diverse selective regimes shape genetic diversity at ADAR genes and at their coding targets. RNA Biol 2015; 12:149-61. [PMID: 25826567 DOI: 10.1080/15476286.2015.1017215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A-to-I RNA editing operated by ADAR enzymes is extremely common in mammals. Several editing events in coding regions have pivotal physiological roles and affect protein sequence (recoding events) or function. We analyzed the evolutionary history of the 3 ADAR family genes and of their coding targets. Evolutionary analysis indicated that ADAR evolved adaptively in primates, with the strongest selection in the unique N-terminal domain of the interferon-inducible isoform. Positively selected residues in the human lineage were also detected in the ADAR deaminase domain and in the RNA binding domains of ADARB1 and ADARB2. During the recent history of human populations distinct variants in the 3 genes increased in frequency as a result of local selective pressures. Most selected variants are located within regulatory regions and some are in linkage disequilibrium with eQTLs in monocytes. Finally, analysis of conservation scores of coding editing sites indicated that editing events are counter-selected within regions that are poorly tolerant to change. Nevertheless, a minority of recoding events occurs at highly conserved positions and possibly represents the functional fraction. These events are enriched in pathways related to HIV-1 infection and to epidermis/hair development. Thus, both ADAR genes and their targets evolved under variable selective regimes, including purifying and positive selection. Pressures related to immune response likely represented major drivers of evolution for ADAR genes. As for their coding targets, we suggest that most editing events are slightly deleterious, although a minority may be beneficial and contribute to antiviral response and skin homeostasis.
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Key Words
- 1000G,1000 Genomes Pilot Project
- A to I, adenosine to inosine
- A-to-I editing
- ADAR
- ADAR editing sites
- AGS, Aicardi-Goutières Syndrome
- BEB, Bayes Empirical Bayes
- BS-REL, branch site-random effects likelihood
- CEU, Europeans
- CHBJPT, Chinese plus Japanese
- DAF, derived allele frequency
- DIND, Derived Intra-allelic Nucleotide Diversity
- DSH, dyschromatosis symmetrica hereditaria
- FDR, false discovery rate
- GARD, Genetic Algorithm Recombination Detection
- GERP Genomic Evolutionary Rate Profiling
- IFN, Interferon
- LD, linkage disequilibrium
- LRT, likelihood ratio test
- MAF, minor allele frequency
- MEME, Mixed Effects Model of Evolution
- RBD, dsRNA binding domain
- SLAC, single-likelihood ancestor counting
- YRI, Yoruba
- eQTL, Expression quantitative trait loci
- evolutionary analysis
- iHS, Integrated Haplotype Score
- positive selection
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Affiliation(s)
- Diego Forni
- a Bioinformatics ; Scientific Institute IRCCS E. MEDEA ; Bosisio Parini , Italy
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Lundbo LF, Harboe ZB, Clausen LN, Hollegaard MV, Sørensen HT, Hougaard DM, Konradsen HB, Nørgaard M, Benfield T. Genetic Variation in NFKBIE Is Associated With Increased Risk of Pneumococcal Meningitis in Children. EBioMedicine 2016; 3:93-9. [PMID: 26870821 DOI: 10.1016/j.ebiom.2015.11.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 11/29/2022] Open
Abstract
Background Streptococcus pneumoniae and Neisseria meningitidis are frequent pathogens in life-threatening infections. Genetic variation in the immune system may predispose to these infections. Nuclear factor-κB is a key component of the TLR-pathway, controlled by inhibitors, encoded by the genes NFKBIA, NFKBIE and NFKBIZ. We aimed to replicate previous findings of genetic variation associated with invasive pneumococcal disease (IPD), and to assess whether similar associations could be found in invasive meningococcal disease (IMD). Methods Cases with IPD and IMD and controls were identified by linking Danish national registries. DNA was obtained from the Danish Neonatal Screening Biobank. The association between SNPs and susceptibility to IPD and IMD, mortality and pneumococcal serotypes was investigated. Results 372 children with pneumococcal meningitis, 907 with pneumococcal bacteremia and 1273 controls were included. We included 406 cases with meningococcal meningitis, 272 with meningococcal bacteremia, and 672 controls. The NFKBIE SNP was associated with increased risk of pneumococcal meningitis (aOR 1.68; 95% CI: 1.20–2.36), but not bacteremia (aOR 1.08; 95% CI: 0.86–1.35). The remaining SNPs were not associated with susceptibility to invasive disease. None of the SNPs were associated with risk of IMD or mortality. Conclusions A NFKBIE polymorphism was associated with increased risk of pneumococcal meningitis. A polymorphism in the NFKBIE gene was associated with an increased risk of pneumococcal meningitis in children. This single nucleotide polymorphism (SNP) was not associated with bacteremia. None of the studied SNPs were associated with risk or severity of invasive meningococcal disease.
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Key Words
- CI, confidence intervals
- CRS, Danish Civil Registration System
- CSF, cerebrospinal fluid
- DNPR, Danish National Patient Registry
- DNSB, Danish Neonatal Screening Biobank
- HWE, Hardy–Weinberg equilibrium
- IMD, invasive meningococcal disease
- IPD, Invasive pneumococcal disease
- IQR, interquartile range
- Invasive Meningococcal Disease
- Invasive Pneumococcal Disease
- LD, linkage disequilibrium
- NF, nuclear factor-κB
- Nuclear Factor-κB
- OR, odds ratio
- Pneumoccoccal Serotypes
- RSV, respiratory syncytial virus
- SNPs, single nucleotide polymorphisms
- SSI, Statens Serum Institut
- WGA, whole-genome-amplification
- aOR, adjusted odds ratio
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Enya M, Horikawa Y, Iizuka K, Takeda J. Association of genetic variants of the incretin-related genes with quantitative traits and occurrence of type 2 diabetes in Japanese. Mol Genet Metab Rep 2014; 1:350-61. [PMID: 27896108 DOI: 10.1016/j.ymgmr.2014.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/26/2014] [Accepted: 07/26/2014] [Indexed: 02/08/2023] Open
Abstract
Background None of the high frequency variants of the incretin-related genes has been found by genome-wide association study (GWAS) for association with occurrence of type 2 diabetes in Japanese. However, low frequency and rare and/or high frequency variants affecting glucose metabolic traits remain to be investigated. Method We screened all exons of the incretin-related genes (GCG, GLP1R, DPP4, PCSK1, GIP, and GIPR) in 96 patients with type 2 diabetes and investigated for association of genetic variants of these genes with quantitative metabolic traits upon test meal with 38 young healthy volunteers and with the occurrence of type 2 diabetes in Japanese subjects comprising 1303 patients with type 2 diabetes and 1014 controls. Result Two mutations of GIPR, p.Thr3Alafsx21 and Arg183Gln, were found only in patients with type 2 diabetes, and both of them were treated with insulin. Of ten tagSNPs, we found that risk allele C of SNP393 (rs6235) of PCSK1 was nominally associated with higher fasting insulin and HOMA-R (P = 0.034 and P = 0.030), but not with proinsulin level, incretin level or BMI. The variant showed significant association with occurrence of type 2 diabetes after adjustment for age, sex, and BMI (P = 0.0043). Conclusion Rare variants of GIPR may contribute to the development of type 2 diabetes, possibly through insulin secretory defects. Furthermore, the genetic variant of PCSK1 might influence glucose homeostasis by altered insulin resistance independently of BMI, incretin level or proinsulin conversion, and may be associated with the occurrence of type 2 diabetes in Japanese.
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Key Words
- BMI, body mass index
- CPR, c-peptide immunoreactivity
- DPP4, dipeptidyl peptidase 4
- GCG, proglucagon gene
- GIP, glucose-dependent insulinotropic peptide
- GIPR, GIP receptor
- GLP-1, glucagon-like peptide 1
- GLP1R, GLP-1 receptor
- GWAS, genome-wide association study
- HOMA-B, homeostasis model assessment as an index of insulin secretion
- HOMA-R, homeostasis model assessment as an index of insulin resistance
- HbA1c, hemoglobin A1c
- IRI, immunoreactive insulin
- Incretin
- LD, linkage disequilibrium
- OR, odds ratio
- Obesity
- PCR, polymerase chain reaction
- PCSK1
- PCSK1, prohormone convertase (PC) enzymes. PC1/3
- Polymorphism
- SNP, single nucleotide polymorphism
- Type 2 diabetes
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Sjakste T, Paramonova N, Wu LSS, Zemeckiene Z, Sitkauskiene B, Sakalauskas R, Wang JY, Sjakste N. PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity in Latvians, Lithuanians and Taiwanese. Meta Gene 2014; 2:283-98. [PMID: 25606411 PMCID: PMC4287955 DOI: 10.1016/j.mgene.2014.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 02/26/2014] [Revised: 03/11/2014] [Accepted: 03/17/2014] [Indexed: 11/16/2022] Open
Abstract
PSMA6 (rs2277460, rs1048990), PSMC6 (rs2295826, rs2295827) and PSMA3 (rs2348071) genetic diversity was investigated in 1438 unrelated subjects from Latvia, Lithuania and Taiwan. In general, polymorphism of each individual locus showed tendencies similar to determined previously in HapMap populations. Main differences concern Taiwanese and include presence of rs2277460 rare allele A not found before in Asians and absence of rs2295827 rare alleles homozygotes TT observed in all other human populations. Observed patterns of SNPs and haplotype diversity were compatible with expectation of neutral model of evolution. Linkage disequilibrium between the rs2295826 and rs2295827 was detected to be complete in Latvians and Lithuanians (D´ = 1; r2 = 1) and slightly disrupted in Taiwanese (D´ = 0.978; r2 = 0.901). Population differentiation (FST statistics) was estimated from pairwise population comparisons of loci variability, five locus haplotypes and PSMA6 and PSMC6 two locus haplotypes. Latvians were significantly different from all Asians at each of 5 SNPs and from Lithuanians at the rs1048990 and PSMC6 loci. Lithuanian and Asian populations exhibited similarities at the PSMC6 loci and were different at the PSMA6 and PSMA3 SNPs. Considering five locus haplotypes all European populations were significantly different from Asian; Lithuanian population was different from both Latvian and CEU. Allele specific patterns of transcription factor binding sites and splicing signals were predicted in silico and addressed to eventual functionality of nucleotide substitutions and their potential to be involved in human genome evolution and geographical adaptation. Current study represents a novel step toward a systematic analysis of the proteasomal gene genetic diversity in human populations. SNPs in PSMA6, PSMC6 and PSMA3 differentiate Latvian and Taiwanese populations. rs2277460, rs1048990 and rs2348071 differentiate Lithuanians and Taiwanese. Lithuanians and Taiwanese are similar in rs2295826, rs2295827 diversity. rs1048990, rs2295826 and rs2295827 differentiate Latvians and Lithuanians.
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Key Words
- Genetic diversity
- HWE, Hardy–Weinberg equilibrium
- HapMap HCB, Han Chinese
- HapMap JPT, Japanese
- HapMap-CEU, NorthWestern Europeans
- Human population
- LD, linkage disequilibrium
- LT, Lithuanian population
- LV, Latvian population
- PSMA3
- PSMA6
- PSMC6
- Proteasome
- SNP
- SNP, single nucleotide polymorphism
- T2DM, type 2 diabetes mellitus
- TF, transcription factor
- TFBS, transcription factor binding site
- TW, Taiwanese population
- UPS, ubiquitin–proteasome system
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Affiliation(s)
- Tatjana Sjakste
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, Miera str. 3, LV2169, Salaspils, Latvia
| | - Natalia Paramonova
- Genomics and Bioinformatics, Institute of Biology of the University of Latvia, Miera str. 3, LV2169, Salaspils, Latvia
| | | | - Zivile Zemeckiene
- Department of Laboratory Medicine, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Brigita Sitkauskiene
- Department of Pulmonology and Immunology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Raimundas Sakalauskas
- Department of Pulmonology and Immunology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jiu-Yao Wang
- Division of Allergy and Clinical Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nikolajs Sjakste
- Faculty of Medicine, University of Latvia, Riga, Latvia ; Latvian Institute of Organic Synthesis, Riga, Latvia
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Beydoun MA, Tanaka T, Beydoun HA, Ding EL, Ferrucci L, Zonderman AB. Vitamin D receptor and megalin gene polymorphisms are associated with central adiposity status and changes among US adults. J Nutr Sci 2013; 2:e33. [PMID: 25191583 DOI: 10.1017/jns.2013.19] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 04/01/2013] [Accepted: 05/03/2013] [Indexed: 01/13/2023] Open
Abstract
We examined longitudinal associations of vitamin D receptor (VDR) and megalin (LRP2; LDL receptor-related protein-2) gene polymorphisms with central adiposity. We used data from the Baltimore Longitudinal Study of Aging (BLSA), an ongoing prospective open cohort study. Study participants consisted of non-Hispanic white adults residing in Baltimore city, with one or more visits at age ≥50 years, and complete data (n 609-617). Repeated assessments on waist circumference (WC) and waist:hip ratio (WHR) were available. Multiple linear mixed models were used to estimate mid-follow-up age central adiposity level and annual rate of change with cut-points set at the sex-specific 80th percentile. The four binary outcomes were: 'elevated central adiposity' (ECA-WC and ECA-WHR) and 'significant increase in central adiposity' (SICA-WC and SICA-WHR). SNP for VDR (four SNP: (1) rs11568820 (CdX-2:T/C); (2) rs1544410 (BsmI:G/A); (3) rs7975232 (ApaI:A/C); (4) rs731236 (TaqI:G/A)) and Megalin (three SNP: (1) rs3755166:G/A; (2) rs2075252:C/T; (3) rs4668123:C/T) genes were selected. SNP latent classes (SNPLC) and SNP haplotypes (SNPHAP) were created. Multiple logistic regression analyses indicated that, in men, higher ECA-WHR odds were associated with SNPLC Megalin2:rs3755166[-]/rs2075252[TT]/rs4668123[T-] (v. Megalin1:rs3755166[-]/rs2075252[CC]/rs4668123[-]) (OR 2·87; 95 % CI 1·15, 7·12; P = 0·023) and that SNPLC Megalin3:rs3755166[-]/rs2075252[CT]/rs4668123[-] (v. Megalin1) was linked to lower SICA-WC odds (OR 0·48; 95 % CI 0·26, 0·88; P = 0·019) (P > 0·05 for sex × SNPLC). In women, VDR3 SNPHAP (GAA:bAT) was related to lower odds of ECA-WC (OR 0·37; 95 % CI 0·16, 0·87; P = 0·023) (P < 0·05 for sex × SNPHAP), VDR1 SNPHAP (GCA:baT) was associated with greater odds and VDR3 SNPHAP (GAA:bAT) with lower odds of SICA-WC (P > 0·05 for sex × SNPHAP). Vitamin D-related gene polymorphisms were associated with central adiposity status and change. Future mechanistic studies are needed to confirm those polymorphisms' biological significance to central adiposity.
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Key Words
- Adults
- BLSA, Baltimore Longitudinal Study of Aging
- Central adiposity
- ECA, elevated central adiposity
- LCA, latent class analysis
- LD, linkage disequilibrium
- Megalin
- SICA, significant increase in central adiposity
- SNP
- SNPHAP, SNP halotype
- SNPLC, SNP latent class
- VDR, vitamin D receptor
- Vitamin D receptor
- WC, waist circumference
- WHR, waist:hip ratio
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