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Das B, Das M, Kalita A, Baro MR. The role of Wnt pathway in obesity induced inflammation and diabetes: a review. J Diabetes Metab Disord 2021; 20:1871-1882. [PMID: 34900830 PMCID: PMC8630176 DOI: 10.1007/s40200-021-00862-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/17/2021] [Indexed: 02/06/2023]
Abstract
Diabetes has become a major killer worldwide and at present, millions are affected by it. Being a chronic disease it increases the risk of other diseases ranging from pulmonary disorders to soft tissue infections. The loss of insulin-producing capacity of the pancreatic β-cells is the main reason for the development of the disease. Obesity is a major complication that can give rise to several other diseases such as cancer, diabetes, etc. Visceral adiposity is one of the major factors that play a role in the development of insulin resistance. Obesity causes a chronic low-grade inflammation in the tissues that further increases the chances of developing diabetes. Several pathways have been associated with the development of diabetes due to inflammation caused by obesity. The Wnt pathway is one such candidate pathway that is found to have a controlling effect on the development of insulin resistance. Moreover, the pathway has also been linked to obesity and inflammation. This review aims to find a connection between obesity, inflammation, and diabetes by taking the wnt pathway as the connecting link.
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Affiliation(s)
- Bhabajyoti Das
- Department of Zoology, Animal Physiology and Biochemistry Laboratory, Gauhati University, Guwahati, 781014 Assam India
| | - Manas Das
- Department of Zoology, Animal Physiology and Biochemistry Laboratory, Gauhati University, Guwahati, 781014 Assam India
| | - Anuradha Kalita
- Department of Zoology, Animal Physiology and Biochemistry Laboratory, Gauhati University, Guwahati, 781014 Assam India
| | - Momita Rani Baro
- Department of Zoology, Animal Physiology and Biochemistry Laboratory, Gauhati University, Guwahati, 781014 Assam India
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Tang Y, Li Z, Wang C, Liu Y, Yu H, Wang A, Zhou Y. LDkit: a parallel computing toolkit for linkage disequilibrium analysis. BMC Bioinformatics 2020; 21:461. [PMID: 33066733 PMCID: PMC7565767 DOI: 10.1186/s12859-020-03754-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linkage disequilibrium (LD) analysis is broadly utilized in genetics to understand the evolutionary and demographic history and helps geneticists identify genes associated with interested inherited traits, such as diseases. There are some tools for linkage disequilibrium analysis either in a local or online way; however, there has been no such tool supporting both graphical user interface (GUI) and parallel computing. RESULTS We developed a GUI software called LDkit for LD analysis, which supports parallel computing. The LDkit supports both variant call format (VCF) and PLINK 'ped + map' format. At the same time, users could also just analyze a subset of individuals from the whole population. The LDkit reads the data by block and then paralleled the computation process by monitoring the usage of processes. Assessment on the Human 1000 genome data showed that when paralleled with 32 threads, the running time was reduced to less than 6 minutes from ~77 minutes using the chromosome 22 dataset with 1,103,547 SNPs and 2504 individuals. CONCLUSIONS The software LDkit can be effectively used to calculate and plot LD decay, LD block, and linkage disequilibrium analysis between a site and a given region. Most importantly, both graphical user interface (GUI) and stand-alone packages are available for users' convenience. LDkit was written in JAVA language under cross-platform support.
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Affiliation(s)
- You Tang
- Electrical and Information Engineering College, Jilin Agricultural Science and Technology University, Jilin, China.,Information Technology Academy, Jilin Agricultural University, Changchun, China
| | - Zhuo Li
- Electrical and Information Engineering College, Jilin Agricultural Science and Technology University, Jilin, China.,Information Technology Academy, Jilin Agricultural University, Changchun, China
| | - Chao Wang
- Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture, Beidahuang Kenfeng Seed Co., Ltd., Harbin, China
| | - Yuxin Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Helong Yu
- Information Technology Academy, Jilin Agricultural University, Changchun, China
| | - Aoxue Wang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yao Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Fernández-Torres J, Pérez-Hernández N, Hernández-Molina G, Martínez-Nava GA, Garrido-Rodríguez D, López-Reyes A, Rodríguez-Pérez JM. Risk of Wnt/β-catenin signalling pathway gene polymorphisms in primary Sjögren's syndrome. Rheumatology (Oxford) 2020; 59:418-425. [PMID: 31302686 DOI: 10.1093/rheumatology/kez269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/05/2019] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVE To explore genetic polymorphisms of the Wnt/β-catenin signalling pathway in primary SS (PSS). METHODS We included 98 patients with PSS and 165 healthy volunteers. Genomic DNA was extracted from peripheral blood samples. Through an open-array platform of low density, we genotyped 25 polymorphisms from 14 genes (WISP1, DKK1, SOST, FRZB, LRP1, LRP4, LRP5, LRP6, GSKB, ADAMTS5, GDF5, FMN2, ADIPOQ and COL11A1) involved in the Wnt/β-catenin signalling pathway. We compared the allelic and genotypic frequencies with Fisher's exact test and logistic regression analysis adjusted by age, gender and individual admixture, as well as bootstrap-resampling analysis. We assessed the gene-gene interaction by the multifactor dimensionality reduction method. RESULTS We found a positive significant association with four polymorphisms: LRP5 rs606989, FRZB rs409238, GSK3B rs2037547 and ADIPOQ rs2241766. All of them conferred risk for PSS, being the highest among subjects carrying three to four risk alleles (P < 0.001). According to a multifactor dimensionality reduction analysis, the best models included the LRP5 (rs606989), FRZB (rs409238) and ADIPOQ (rs2241766) polymorphisms. CONCLUSION LRP5, FRZB and ADIPOQ genes related in the Wnt/β-catenin signalling pathway increased the risk of PSS. Further research is needed to establish their functional role in this clinical entity.
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Affiliation(s)
- Javier Fernández-Torres
- Synovial Fluid Laboratory, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra
| | | | - Gabriela Hernández-Molina
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán
| | | | - Daniela Garrido-Rodríguez
- Center of Research in Infectious Diseases (CIENI), Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Alberto López-Reyes
- Synovial Fluid Laboratory, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra
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Abstract
Developmental signaling pathways control a vast array of biological processes during embryogenesis and in adult life. The WNT pathway was discovered simultaneously in cancer and development. Recent advances have expanded the role of WNT to a wide range of pathologies in humans. Here, we discuss the WNT pathway and its role in human disease and some of the advances in WNT-related treatments.
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He L, Xiao J, Rashid KY, Yao Z, Li P, Jia G, Wang X, Cloutier S, You FM. Genome-Wide Association Studies for Pasmo Resistance in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2019; 9:1982. [PMID: 30693010 PMCID: PMC6339956 DOI: 10.3389/fpls.2018.01982] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/20/2018] [Indexed: 05/04/2023]
Abstract
Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype × environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3-23%), were stable across all datasets and explained 32-64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of QTL with positive-effect or favorite alleles (NPQTL) in accessions was significantly correlated with PR (R 2 = 0.55), suggesting that these QTL effects are mainly additive. NPQTL was also significantly associated with morphotype (R 2 = 0.52) and major QTL with positive effect alleles were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding.
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Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Gaofeng Jia
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xiue Wang
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
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Souza KSCD, Ururahy MAG, Oliveira YMDC, Loureiro MB, Silva HPVD, Bortolin RH, Luchessi AD, Arrais RF, Hirata RDC, Almeida MDG, Hirata MH, Rezende AAD. The low-density lipoprotein receptor-related protein 5 (LRP5) 4037C>T polymorphism: candidate for susceptibility to type 1 diabetes mellitus. ARCHIVES OF ENDOCRINOLOGY AND METABOLISM 2018; 62:480-484. [PMID: 30304114 PMCID: PMC10118729 DOI: 10.20945/2359-3997000000057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 05/09/2018] [Indexed: 04/22/2023]
Abstract
OBJECTIVE The present study has investigated the association between low-density lipoprotein receptor-related protein 5 (LRP5) 4037C>T polymorphism and type 1 diabetes mellitus (T1DM) susceptibility in a Brazilian population. SUBJECTS AND METHODS A total number of 134 T1DM patients and 180 normoglycemic individuals (NG) aged 6-20 years were studied. Glycated hemoglobin and glucose levels were determined. Genotyping of LRP5 4037C>T (rs3736228) was performed. RESULTS T1DM patients showed poor glycemic control. Genotypes in the codominant (CT: OR = 2.99 [CI 95%: 1.71-5.24], p < 0.001; TT: OR = 5.34 [CI 95%: 1.05-2702], p < 0.001), dominant (CT + TT: OR = 3.16 [CI 95%: 1.84-5.43], p < 0.001) and log-additive (OR = 2.78 [CI 95%: 1.70-4.52], p < 0.001) models, and LRP5 4037T allele (OR = 2.88, [CI 95%: 1.78-4.77], p < 0.001) were associated with an increased risk of developing T1DM. LRP5 4037CT and CT+TT carriers in T1DM group showed higher concentrations of serum glucose and glycated hemoglobin when compared with CC carriers. CONCLUSION The LRP5 4037C>T may represent a candidate for T1DM susceptibility, as well as poor glycemic control.
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Affiliation(s)
- Karla Simone Costa de Souza
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
| | - Marcela Abbott Galvão Ururahy
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
| | - Yonara Monique da Costa Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
- Centro de Educação e Saúde, Universidade Federal de Campina Grande (UFCG), Cuité, PB, Brasil
| | - Melina Bezerra Loureiro
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
| | | | - Raul Hernandes Bortolin
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
| | - André Ducati Luchessi
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
| | - Ricardo Fernando Arrais
- Departamento de Pediatria, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
| | | | - Maria das Graças Almeida
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
| | - Mário Hiroyuki Hirata
- Departamento de Análises Clínicas e Toxicológicas, Universidade de São Paulo (USP), São Paulo, SP, Brasil
| | - Adriana Augusto de Rezende
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brasil
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Kim SA, Cho CS, Kim SR, Bull SB, Yoo YJ. A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs. Bioinformatics 2018; 34:388-397. [PMID: 29028986 PMCID: PMC5860363 DOI: 10.1093/bioinformatics/btx609] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 09/11/2017] [Accepted: 09/28/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation. Results We present Big-LD, a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive. Big-LD uses an agglomerative approach that starts by identifying small communities of SNPs, i.e. the SNPs in each LD bin region, and proceeds by merging these communities. We determine the number of blocks using a method to find maximum-weight independent set. Big-LD produces larger LD blocks compared to existing methods such as MATILDE, Haploview, MIG ++, or S-MIG ++ and the LD blocks better agree with recombination hotspot locations determined by sperm-typing experiments. The observed average runtime of Big-LD for 13 288 240 non-monomorphic SNPs from 1000 Genomes Project autosome data (286 East Asians) is about 5.83 h, which is a significant improvement over the existing methods. Availability and implementation Source code and documentation are available for download at http://github.com/sunnyeesl/BigLD. Contact yyoo@snu.ac.kr. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sun Ah Kim
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Chang-Sung Cho
- Department of Mathematics Education, Seoul National University, Seoul, South Korea
| | - Suh-Ryung Kim
- Department of Mathematics Education, Seoul National University, Seoul, South Korea
| | - Shelley B Bull
- Prosserman Centre for Health Research, The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Yun Joo Yoo
- Department of Mathematics Education, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
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Kim SA, Yoo YJ. Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition. Genomics Inform 2016; 14:196-204. [PMID: 28154511 PMCID: PMC5287124 DOI: 10.5808/gi.2016.14.4.196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 12/03/2016] [Accepted: 12/06/2016] [Indexed: 11/20/2022] Open
Abstract
Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.9 and S-MIG++. We used several experimental datasets obtained by sampling subsets of single nucleotide polymorphism (SNP) markers of chromosome 22 region in the 1000 Genomes Project data and also the HapMap phase 3 data to compare the results of haplotype block partitions by five methods. With decreasing sampling ratio down to 20% of the original SNP markers, the total number of haplotype blocks decreases and the length of haplotype blocks increases for all algorithms. When we examined the marker-independence of the haplotype block locations constructed from the datasets of different density, the results using below 50% of the entire SNP markers were very different from the results using the entire SNP markers. We conclude that the haplotype block construction results should be used and interpreted carefully depending on the selection of markers and the purpose of the study.
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Affiliation(s)
- Sun Ah Kim
- Department of Mathematics Education, Seoul National University, Seoul 08826, Korea
| | - Yun Joo Yoo
- Department of Mathematics Education, Seoul National University, Seoul 08826, Korea.; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea
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Adipose- and muscle-derived Wnts trigger pancreatic β-cell adaptation to systemic insulin resistance. Sci Rep 2016; 6:31553. [PMID: 27527335 PMCID: PMC4985739 DOI: 10.1038/srep31553] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/19/2016] [Indexed: 01/09/2023] Open
Abstract
Wnt signaling molecules are associated with obesity, hyperlipidemia, and type 2 diabetes (T2D). Here, we show that two Wnt proteins, WNT3a and WNT4, are specifically secreted by skeletal muscle and adipose tissue during the development of insulin resistance and play an important role in cross-talk between insulin-resistant tissues and pancreatic beta cells. The activation of Frizzled receptor and Wnt signaling in pancreatic islets via circulating WNT3a in blood resulted in higher insulin secretion and an increase in beta cell proliferation, thus leading to islet adaptation in a pre-diabetic state. Interestingly, in fully developed T2D, the expression profiles of Wnt3a and Wnt4 in adipose tissue and muscle cells and blood plasma levels of these proteins were opposite to the pre-diabetic state, thus favoring the downregulation of Wnt signaling in beta cells and resulting in dysfunctional pancreatic islets. These results demonstrate that alterations in the secretion profile of a canonical Wnt activator (WNT3a) and inhibitor (WNT4) from insulin-resistant tissues during the development of T2D are responsible for triggering progression from a pre-diabetic to a diabetic state. We also show here that WNT3a and WNT4 are potent myokines, and their expression and secretion are regulated in response to nutritional and metabolic changes.
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Yi J, Cai Y, Yao Z, Lin J. Genetic analysis of the relationship between bone mineral density and low-density lipoprotein receptor-related protein 5 gene polymorphisms. PLoS One 2013; 8:e85052. [PMID: 24376863 PMCID: PMC3871666 DOI: 10.1371/journal.pone.0085052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/21/2013] [Indexed: 12/03/2022] Open
Abstract
Background A number of studies have examined the association between the polymorphisms of the low-density lipoprotein receptor-related protein 5 gene (LRP5), but previous results have been inconclusive. Thus we performed a meta-analysis of studies on the association between the LRP5 polymorphisms and bone mineral density (BMD) to assess their pooled effects. Methods Published literature from PubMed, EMBASE and ISI web of science were searched for eligible publications. Weighted mean difference (WMD) and 95% confidence interval (CI) was calculated using fixed- or random-effects model. Results A total of 19 studies with 25773 subjects were considered in this meta-analysis. Of them, 17 examined the association between the A1330V polymorphism and BMD, 8 were focused on the V667M polymorphism, and 2 analyzed the Q89R polymorphism. Individuals with the A1330V AA genotype showed significantly higher BMD than those with the AV/VV genotypes [at lumbar spine (LS): WMD = 0.02g/cm2, 95% CI = 0.01-0.03, P < 10-4; at femur neck (FN): WMD = 0.01g/cm2, 95% CI = 0.00-0.02, P = 0.01] or VV genotype (at LS: WMD = 0.02g/cm2, 95% CI = 0.01-0.04, P = 0.01). Significant associations were also detected in the analysis for V667M (VV vs. VM/MM: WMD at LS = 0.02g/cm2, 95% CI = 0.02-0.03, P < 10-5; WMD at FN = 0.01g/cm2, 95% CI = 0.01-0.02, P = 0.0002). As for Q89R, subjects with the QQ genotype tended to have higher BMD than those with the QR/RR genotypes at FN (WMD = 0.03g/cm2, 95% CI = 0.01-0.05, P = 0.005). Conclusion This meta-analysis demonstrated that the LRP5 polymorphisms may be modestly associated with BMD of LS and FN.
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Affiliation(s)
- Jiayong Yi
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, P. R. China
| | - Yu Cai
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, P. R. China
| | - Zhenjun Yao
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, P. R. China
| | - Jianping Lin
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, P. R. China
- * E-mail:
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Lin WY, Yi N, Lou XY, Zhi D, Zhang K, Gao G, Tiwari HK, Liu N. Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants. Genet Epidemiol 2013; 37:560-70. [PMID: 23740760 DOI: 10.1002/gepi.21740] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 05/01/2013] [Accepted: 05/06/2013] [Indexed: 01/09/2023]
Abstract
For most complex diseases, the fraction of heritability that can be explained by the variants discovered from genome-wide association studies is minor. Although the so-called "rare variants" (minor allele frequency [MAF] < 1%) have attracted increasing attention, they are unlikely to account for much of the "missing heritability" because very few people may carry these rare variants. The genetic variants that are likely to fill in the "missing heritability" include uncommon causal variants (MAF < 5%), which are generally untyped in association studies using tagging single-nucleotide polymorphisms (SNPs) or commercial SNP arrays. Developing powerful statistical methods can help to identify chromosomal regions harboring uncommon causal variants, while bypassing the genome-wide or exome-wide next-generation sequencing. In this work, we propose a haplotype kernel association test (HKAT) that is equivalent to testing the variance component of random effects for distinct haplotypes. With an appropriate weighting scheme given to haplotypes, we can further enhance the ability of HKAT to detect uncommon causal variants. With scenarios simulated according to the population genetics theory, HKAT is shown to be a powerful method for detecting chromosomal regions harboring uncommon causal variants.
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Affiliation(s)
- Wan-Yu Lin
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
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Ip W, Chiang YTA, Jin T. The involvement of the wnt signaling pathway and TCF7L2 in diabetes mellitus: The current understanding, dispute, and perspective. Cell Biosci 2012; 2:28. [PMID: 22892353 PMCID: PMC3468386 DOI: 10.1186/2045-3701-2-28] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 06/19/2012] [Indexed: 12/17/2022] Open
Abstract
The Wnt signaling pathway was initially discovered for its role in tumorigenesis and the development of Drosophila and other eukaryotic organisms. The key effector of this pathway, the bipartite transcription factor β-cat/TCF, is formed by free β-catenin (β-cat) and a TCF protein, including TCF7L2. Extensive recent investigations have highlighted the role of the Wnt signaling pathway in metabolic homeostasis and its implication in diabetes and other metabolic diseases. Genome-wide association studies have shown that several key components of the Wnt signaling pathway are implicated in metabolic homeostasis and the development of type 2 diabetes (T2D). Despite controversial observations regarding the role of Wnt signaling in the development and function of pancreatic islets, the discovery of the association between certain single nucleotide polymorphisms of TCF7L2 and T2D susceptibility has fueled great efforts to explore the role of Wnt signaling in the function of pancreatic β-cells and glucose homeostasis. Here we have introduced our basic understanding of the canonical Wnt signaling pathway, summarized our current knowledge on its implication in metabolic homeostasis and T2D, discussed the work on TCF7L2 as a T2D susceptibility gene, and presented the controversial role of Wnt signaling and TCF7L2 in pancreatic islets as well as their potential metabolic function in other organs. We then expanded our view into the crosstalk among Wnt, insulin and FOXO signaling cascades, which further illustrates the complexity of the Wnt signaling pathway in metabolic homeostasis. Finally, we have presented our perspectives.
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Affiliation(s)
- Wilfred Ip
- Institute of Medical Science, University of Toronto, Toronto, Canada.
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Lin WY, Tiwari HK, Gao G, Zhang K, Arcaroli JJ, Abraham E, Liu N. Similarity-based multimarker association tests for continuous traits. Ann Hum Genet 2012; 76:246-60. [PMID: 22497480 DOI: 10.1111/j.1469-1809.2012.00706.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Testing multiple markers simultaneously not only can capture the linkage disequilibrium patterns but also can decrease the number of tests and thus alleviate the multiple-testing penalty. If a gene is associated with a phenotype, subjects with similar genotypes in this gene should also have similar phenotypes. Based on this concept, we have developed a general framework that is applicable to continuous traits. Two similarity-based tests (namely, SIMc and SIMp tests) were derived as special cases of the general framework. In our simulation study, we compared the power of the two tests with that of the single-marker analysis, a standard haplotype regression, and a popular and powerful kernel machine regression. Our SIMc test outperforms other tests when the average R(2) (a measure of linkage disequilibrium) between the causal variant and the surrounding markers is larger than 0.3 or when the causal allele is common (say, frequency = 0.3). Our SIMp test outperforms other tests when the causal variant was introduced at common haplotypes (the maximum frequency of risk haplotypes >0.4). We also applied our two tests to an adiposity data set to show their utility.
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Affiliation(s)
- Wan-Yu Lin
- Department of Biostatistics, University of Alabama at Birmingham, USA
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Harada K, Miyamoto Y, Morisaki H, Ohta N, Yamanaka I, Kokubo Y, Makino H, Harada-Shiba M, Okayama A, Tomoike H, Tomonori O, Saito Y, Yoshimasa Y, Morisaki T. A Novel Thr56Met Mutation of the Autosomal Recessive Hypercholesterolemia Gene Associated with Hypercholesterolemia. J Atheroscler Thromb 2010; 17:131-40. [DOI: 10.5551/jat.2873] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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15
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Luo HB, Ye Y, Wang YY, Liang WB, Yun LB, Liao M, Yan J, Wu J, Li YB, Hou YP. Characteristics of eight X-STR loci for forensic purposes in the Chinese population. Int J Legal Med 2009; 125:127-31. [DOI: 10.1007/s00414-009-0386-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 10/23/2009] [Indexed: 10/20/2022]
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16
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Suwazono Y, Kobayashi E, Uetani M, Miura K, Morikawa Y, Ishizaki M, Kido T, Nakagawa H, Nogawa K. Low‐density lipoprotein receptor‐related protein 5 variant Q89R is associated with hypertension in Japanese females. Blood Press 2009; 15:80-7. [PMID: 16754270 DOI: 10.1080/08037050600650191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
We examined the influence of the Q89R variant in low-density lipoprotein receptor-related protein 5 on hypertension in a large Japanese cohort. We used multivariate logistic regression analysis to adjust for the effects of other factors known to influence hypertension such as age, body mass index, blood chemistry and lifestyle. Our cohort consisted of 1444 males and 1161 females selected from 3834 male and 2591 female workers in a single company. Hypertension was defined as systolic blood pressure 140 mmHg and/or diastolic blood pressure 90 mmHg or the use of antihypertensive medication. Because the RR genotype was so rare (three normotensive males and three normotensive females), they were excluded from analyses. Genotype distributions for Q89R in hypertensive females (QR = 14, QQ = 60) were significantly different (p = 0.033) from normotensive females (QR = 113, QQ = 971). In contrast, those in hypertensive males (QR = 26, QQ = 230) and in normotensive males (QR = 145, QQ = 1040) were similar. Allele distributions were not significantly different in either gender. In females, multivariate logistic regression showed that the QR genotype was associated with hypertension with odds ratio of 2.1 compared to the QQ genotype. This study indicates that the Q89R polymorphism is an independent factor for hypertension in Japanese females.
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Affiliation(s)
- Yasushi Suwazono
- Department of Occupational and Environmental Medicine, Graduate School of Medicine, Chiba University, Japan.
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17
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Kauppi L, May CA, Jeffreys AJ. Analysis of meiotic recombination products from human sperm. Methods Mol Biol 2009; 557:323-55. [PMID: 19799191 DOI: 10.1007/978-1-59745-527-5_20] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Traditional methods for surveying meiotic recombination in humans are limited to pedigree and linkage disequilibrium analyses. We have developed assays that allow the direct detection of crossover and gene conversion molecules in batches of sperm DNA. To date, we have characterized 26 recombination hotspots by allele-specific PCR and selectively amplified recombinant DNA molecules from these regions. These analyses have revealed that meiotic crossover hotspots in humans are highly localized and flanked by DNA segments where recombination is suppressed. The centers of crossover hotspots are also active in noncrossover recombination, displaying short conversion tracts.
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Affiliation(s)
- Liisa Kauppi
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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18
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A haplotype-based analysis of the LRP5 gene in relation to osteoporosis phenotypes in Spanish postmenopausal women. J Bone Miner Res 2008; 23:1954-63. [PMID: 18684085 DOI: 10.1359/jbmr.080806] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
LRP5 encodes the low-density lipoprotein receptor-related protein 5, a transmembrane protein involved in Wnt signaling. LRP5 is an important regulator of osteoblast growth and differentiation, affecting bone mass in vertebrates. Whether common variations in LRP5 are associated with normal BMD variation or osteoporotic phenotypes is of great relevance. We used a haplotype-based approach to search for common disease-associated variants in LRP5 in a cohort of 964 Spanish postmenopausal women. Twenty-four SNPs were selected, covering the LRP5 region, including the missense changes p.V667M and p.A1330V. The SNPs were genotyped and evaluated for association with BMD at the lumbar spine (LS) or femoral neck (FN) and with osteoporotic fracture, at single SNP and haplotype levels, by regression methods. Association with LS BMD was found for SNP 1, rs312009, located in the 5'-flanking region (p = 0.011, recessive model). SNP 6, rs2508836, in intron 1, was also associated with BMD, both at LS (p = 0.025, additive model) and FN (p = 0.031, recessive model). Two polymorphisms were associated with fracture: SNP 11, rs729635, in intron 1, and SNP 15, rs643892, in intron 5 (p = 0.007 additive model and p = 0.019 recessive model, respectively). Haplotype analyses did not provide additional information, except for haplotype "GC" of the block located at the 3'end of the gene. This haplotype spans intron 22 and the 3' untranslated region and was associated with FN BMD (p = 0.029, one copy of the haplotype versus none). In silico analyses showed that SNP 1 (rs312009) lies in a putative RUNX2 binding site. Electro-mobility shift assays confirmed RUNX2 binding to this site.
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Abstract
The WNT signalling pathway is involved in many physiological and pathophysiological activities. WNT ligands bind to Frizzled receptors and co-receptors (LDL receptor-related protein 5/6), triggering a cascade of signalling events. The major effector of the canonical WNT signalling pathway is the bipartite transcription factor beta-catenin/T cell transcription factor (beta-cat/TCF), formed by free beta-cat and one of the four TCFs. The WNT pathway is involved in lipid metabolism and glucose homeostasis, and mutations in LRP5 may lead to the development of diabetes and obesity. beta-Cat/TCF is also involved in the production of the incretin hormone glucagon-like peptide-1 in the intestinal endocrine L cells. More recently, genome-wide association studies have identified TCF7L2 as a diabetes susceptibility gene, and individuals carrying certain TCF7L2 single nucleotide polymorphisms could be more susceptible to the development of type 2 diabetes. Furthermore, beta-cat is able to interact with forkhead box transcription factor subgroup O (FOXO) proteins. Since FOXO and TCF proteins compete for a limited pool of beta-cat, enhanced FOXO activity during ageing and oxidative stress may attenuate WNT-mediated activities. These observations shed new light on the pathogenesis of type 2 diabetes as an age-dependent disease.
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Affiliation(s)
- T Jin
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Grundberg E, Lau EM, Lorentzon M, Karlsson M, Holmberg A, Groop L, Mellström D, Orwoll E, Mallmin H, Ohlsson C, Ljunggren O, Akesson K. Large-scale association study between two coding LRP5 gene polymorphisms and bone phenotypes and fractures in men. Osteoporos Int 2008; 19:829-37. [PMID: 18026682 DOI: 10.1007/s00198-007-0512-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 10/24/2007] [Indexed: 11/25/2022]
Abstract
UNLABELLED Herein we investigated the association between polymorphisms in the LRP5 gene and bone phenotypes and fractures in three large male cohorts based on the rationale that mutations in LRP5 cause severe bone phenotypes. Results showed an association of the Val667Met SNP with spine BMD in 3,800 young and elderly men. INTRODUCTION The low-density lipoprotein receptor-related protein 5 (LRP5)-Wnt signalling system is of importance for regulating osteoblastic activity, which became clear after findings that inactivating mutations in LRP5 cause osteoporosis. The overall aim of this study was to investigate the association between polymorphisms in the LRP5 gene and bone mineral density (BMD) in three large cohorts of young and elderly men. METHODS The cohorts used were MrOS Sweden (n = 3014, aged 69-81 years) and MrOs Hong Kong (n = 2000, aged > 65 years) and the Swedish GOOD study (n = 1068, aged 18-20 years). The polymorphisms Val667Met and Ala1330Val were genotyped using a TaqMan assay. RESULTS When combining the data from the Swedish cohorts in a meta-analysis (n = 3,800), men carrying the 667Met-allele had 3% lower BMD at lumbar spine compared with non-carriers (p < 0.05). The Val667Met SNP was not polymorphic in the Hong Kong population and thus were not included. There were no associations between the Ala1330Val SNP and bone phenotypes in the study populations. No associations between the LRP5 polymorphisms and self-reported fractures were seen in MrOs Sweden. CONCLUSIONS Results from these three large cohorts indicate that the Val667Met polymorphism but not the Ala1330Val contributes to the observed variability in BMD in the Swedish populations.
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Affiliation(s)
- E Grundberg
- Department of Medical Sciences, Uppsala University Hospital, 75185 Uppsala, Sweden.
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Abstract
Our understanding of the details of mammalian meiotic recombination has recently advanced significantly. Sperm typing technologies, linkage studies, and computational inferences from population genetic data have together provided information in unprecedented detail about the location and activity of the sites of crossing-over in mice and humans. The results show that the vast majority of meiotic recombination events are localized to narrow DNA regions (hot spots) that constitute only a small fraction of the genome. The data also suggest that the molecular basis of hot spot activity is unlikely to be strictly determined by specific DNA sequence motifs in cis. Further molecular studies are needed to understand how hot spots originate, function and evolve.
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Affiliation(s)
- Norman Arnheim
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA.
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22
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Cheung CL, Huang QY, Chan V, Kung AWC. Association of low-density lipoprotein receptor-related protein 5 (LRP5) promoter SNP with peak bone mineral density in Chinese women. Hum Hered 2007; 65:232-9. [PMID: 18073493 DOI: 10.1159/000112370] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 08/14/2007] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Low-density lipoprotein receptor-related protein 5 (LRP5) is important for osteoblast differentiation and mutations of the gene are associated with both low and high bone mass syndromes. Our study aimed to evaluate the importance of LRP5 in the determination of peak bone mass acquisition in Chinese females in the general population. METHODS A total of 286 young southern Chinese females (aged 22-44 years) with low bone mineral density (BMD) (defined by a BMD Z score < or =-1.28 at either the hip or spine) or high BMD (Z score > or =+1) were studied. The LRP5 gene was sequenced for single nucleotide polymorphisms (SNPs) and 4 SNPs were tagged from 8 genotyped SNPs for this study. RESULTS Single locus allele association tests revealed significant associations of rs682429 and rs686921 with BMD variation (p < 0.05). Omnibus test (likelihood ratio test) revealed overall significant association between LRP5 gene locus and total hip BMD, with rs682429 being most predictive. rs682429 is located in 5'UTR, 2 bases adjacent to a consensus recognition site for the Elk-1 binding element. CONCLUSION Common variations of the LRP5 promoter are associated with BMD in young women. These significant associations appear to be driven by rs682429. Functional studies are necessary to elucidate the role of this SNP on the effect of Elk-1 binding element transcriptional activity of LRP5 gene.
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Affiliation(s)
- Ching-Lung Cheung
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
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23
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Forensic STRs as potential disease markers: A study of VWA and von Willebrand's Disease. Forensic Sci Int Genet 2007; 1:253-61. [DOI: 10.1016/j.fsigen.2007.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 05/11/2007] [Accepted: 06/01/2007] [Indexed: 11/22/2022]
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24
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Suwazono Y, Kobayashi E, Dochi M, Miura K, Morikawa Y, Ishizaki M, Kido T, Nakagawa H, Nogawa K. Combination of the C1429T polymorphism in the G-protein beta-3 subunit gene and the A1330V polymorphism in the low-density lipoprotein receptor-related protein 5 gene is a risk factor for hypercholesterolaemia. Clin Exp Med 2007; 7:108-14. [DOI: 10.1007/s10238-007-0131-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 06/12/2007] [Indexed: 10/22/2022]
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Horne BD, Camp NJ, Anderson JL, Mower CP, Clarke JL, Kolek MJ, Carlquist JF. Multiple less common genetic variants explain the association of the cholesteryl ester transfer protein gene with coronary artery disease. J Am Coll Cardiol 2007; 49:2053-60. [PMID: 17512363 DOI: 10.1016/j.jacc.2007.02.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 01/29/2007] [Accepted: 02/05/2007] [Indexed: 11/27/2022]
Abstract
OBJECTIVES The objective of this study was to identify associations of the cholesteryl ester transfer protein (CETP) gene with coronary artery disease (CAD) with tagging (t) single nucleotide polymorphisms (SNPs) chosen to optimally account for intra-genic variation. BACKGROUND The CETP gene plays a critical role in lipoprotein metabolism, but the common and well-studied TaqIB variant is inconsistently predictive of CAD. METHODS From a deoxyribonucleic acid bank of 10,020 individuals, nondiabetic nonsmoking patients (n = 4,811) with angiographically defined, clinically significant CAD (> or =70% stenosis) or normal coronaries were genotyped for 11 CETP tSNPs. Myocardial infarction (MI) and lipid levels were evaluated as secondary end points. RESULTS Analysis of single tSNPs, corrected for multiple comparisons (p < 0.00485), identified allele +1086A to be associated with CAD (p = 0.0034). Suggestive allelic and significant genotypic associations were found for -631AA (odds ratio [OR] = 3.95, p = 0.004 vs. CC) and +2389GA (OR = 1.21, p = 0.003 vs. GG). Haplotype analysis by linkage disequilibrium (LD) group revealed a CAD association for LD group B (p = 0.0025 across T+1086A, C+878T, C+408T) and near significance for LD group A (p = 0.013 across C-631A, MspI, G+2389A). A weak protective trend for TaqIB was eliminated by adjustment for other tSNPs, and haplotype analyses suggested that TaqIB was simply a marker for other tSNPs or haplotypes. No tSNP or haplotype associations with MI were found. CONCLUSIONS Multiple, less common SNPs and haplotype variants underlie CETP-related CAD risk, for which the common TaqIB variant is simply a poor marker. The occurrence of risk-related variants on separate haplotypes suggests genetic-risk complexity and allelic heterogeneity. (Database Registry of the Intermountain Heart Collaborative Study; http://clinicaltrials.gov/ct/show/NCT00406185?order=1; NCT00406185).
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Affiliation(s)
- Benjamin D Horne
- Cardiovascular Department, LDS Hospital, Intermountain Medical Center, University of Utah, Salt Lake City, Utah 84143, USA.
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Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JAL, Barris W, McClintock AE, McClintock S, Thomson PC, Tier B, Nicholas FW, Raadsma HW. A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle. Genetics 2007; 176:763-72. [PMID: 17435229 PMCID: PMC1894606 DOI: 10.1534/genetics.106.069369] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Analysis of data on 1000 Holstein-Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy-Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05-0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage disequilibrium. A total of 727 haplotype blocks consisting of > or =3 SNPs were identified. The average block length was 69.7 +/- 7.7 kb, which is approximately 5-10 times larger than in humans. These blocks comprised a total of 2964 SNPs and covered 50,638 kb of the sequence map, which constitutes 2.18% of the length of all autosomes. A set of tag SNPs, which will be useful for further fine-mapping studies, has been identified. Overall, the results suggest that as many as 75,000-100,000 tag SNPs would be needed to track all important haplotype blocks in the bovine genome. This would require approximately 250,000 SNPs in the discovery phase.
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Affiliation(s)
- Mehar S Khatkar
- Centre for Advanced Technologies in Animal Genetics and Reproduction (ReproGen), University of Sydney, Camden NSW 2570, Australia.
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Xiong DH, Lei SF, Yang F, Wang L, Peng YM, Wang W, Recker RR, Deng HW. Low-density lipoprotein receptor-related protein 5 (LRP5) gene polymorphisms are associated with bone mass in both Chinese and whites. J Bone Miner Res 2007; 22:385-93. [PMID: 17241106 DOI: 10.1359/jbmr.061116] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
UNLABELLED In this study, the associations of novel LRP5 variants with BMD variation were detected and some replicated in the two ethnic groups of Chinese and white origins, respectively. These data support the concept that LRP5 variation can contribute to minor and major variation in bone structure. INTRODUCTION Mutations in the low-density lipoprotein receptor-related protein 5 (LRP5) gene have been shown to cause both high and low bone mass. However, it is still controversial whether LRP5 is associated with normal BMD variation. This study explored the association of LRP5 with BMD phenotypes at three clinically important skeletal sites-the spine, hip, and ultradistal radius (UD)-in two independent populations of Chinese and white ethnicities, respectively. MATERIALS AND METHODS The Chinese sample consisted of 733 unrelated subjects. The white sample was made up of 1873 subjects from 405 nuclear families. High-density single nucleotide polymorphisms (SNPs) across the whole LRP5 gene were genotyped and analyzed in both samples. RESULTS Linkage disequilibrium (LD) analyses showed that the haplotype structures of LRP5 between Chinese and whites were in good agreement. Association tests showed that polymorphisms in block 5 spanning intron 7 to intron 19 of LRP5 significantly associated with spine BMD variation in both samples. Particularly, the significant association of SNP rs491347 in intron 7 with spine BMD in the Chinese sample (p=0.002) was replicated in whites, even after adjusting for multiple testing (p=0.005). Its strongly associated SNP rs1784235 could cause the loss of an estrogen receptor alpha (ERalpha) binding site in LRP5, which could partially explain the above replicated association. However, we did not observe any significant replication with BMD variation at the hip and UD. After accounting for multiple testing, associations with BMD variation at these two sites were mainly found in Chinese. Sex-stratified analyses further revealed that the LRP5 associations with BMD in Chinese and whites were driven by male and female subjects, respectively. CONCLUSIONS Our work supported LRP5 genetic variants as possible susceptibility factors for osteoporosis and fractures in humans. Especially, the SNP rs491347 and its strongly associated SNPs (e.g., rs1784235) could be important to human osteoporosis phenotypes.
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Affiliation(s)
- Dong-Hai Xiong
- Osteoporosis Research Center and Department of Biomedical Sciences, Creighton University, Omaha, NE, USA
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Kiel DP, Ferrari SL, Cupples LA, Karasik D, Manen D, Imamovic A, Herbert AG, Dupuis J. Genetic variation at the low-density lipoprotein receptor-related protein 5 (LRP5) locus modulates Wnt signaling and the relationship of physical activity with bone mineral density in men. Bone 2007; 40:587-96. [PMID: 17137849 PMCID: PMC1845172 DOI: 10.1016/j.bone.2006.09.029] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 09/25/2006] [Accepted: 09/28/2006] [Indexed: 10/23/2022]
Abstract
Polymorphisms in the LRP5 gene have been associated with bone mineral density (BMD) in men and/or women. However, the functional basis for this association remains obscure. We hypothesized that LRP5 alleles could modulate Wnt signaling and the relationship between physical activity and BMD. This genetic association study was performed in the population-based Framingham Study Offspring Cohort, and included a subset of 1797 unrelated individuals who provided blood samples for DNA and who had BMD measurements of the hip and spine. Ten single-nucleotide polymorphisms (SNPs) spanning the LRP5 gene were genotyped and used for association and interaction analyses with BMD by regression methods. LRP5 haplotypes were transiently co-expressed with Wnt3a, MesD and Dkk1 in HEK293 cells and their activity evaluated by the TCF-Lef reporter assay. Six out of ten SNPs in LRP5 were associated with one or more of the femur or spine BMDs in men or women after adjustment for covariates, and these associations differed between genders. In men< or =age 60 years, 3 SNPs were significantly associated with BMD: rs2306862 on Exon 10 with femoral neck BMD (p=0.01) and Ward's BMD (p=0.01); rs4988321/p. V667M with Ward's BMD (p=0.02); and intronic rs901825 with trochanter BMD (p=0.03). In women, 3 SNPs in intron 2 were significantly associated with BMD: rs4988330 for trochanter (p=0.01) and spine BMD (p=0.003); rs312778 with femoral neck BMD (p=0.05); and rs4988331 with spine BMD (p=0.04). For each additional rare allele, BMD changed by 3-5% in males and 2-4% in females. Moreover, there was a significant interaction between physical activity and rs2306862 in exon 10 (p for interaction=0.02) and rs3736228/p. A1330V in exon 18 (p for interaction=0.05) on spine BMD in men. In both cases, the TT genotype was associated with lower BMD in men with higher physical activity scores, conversely with higher BMD in men with lower physical activity scores. In vitro, TCF-Lef activity in presence of Wnt3a was significantly reduced in cells expressing LRP5 haplotypes carrying the T allele of exon 10 and 18 compared to the wild-type allele, whereas co-expression of Dkk1 completely inhibited Wnt3a response through all LRP5 haplotypes. In summary, genetic variation in exons 10 and 18 of the LRP5 gene modulates Wnt signaling and the relationship between physical activity and BMD in men. These observations suggest that Wnt-LRP5 may play a role in the adaptation of bone to mechanical load in humans, and may explain some gender-related differences in bone mass.
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Affiliation(s)
- Douglas P Kiel
- Institute for Aging Research, Hebrew SeniorLife, Harvard Medical School, Boston, MA 02131, USA.
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Mander AP, Bansal A. Stepwise haplotype analysis: are LD patterns repeatable? Hum Genomics 2006; 2:376-82. [PMID: 16848975 PMCID: PMC3525156 DOI: 10.1186/1479-7364-2-6-376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A variety of techniques exist to describe and depict patterns of pairwise linkage disequilibrium (LD). In the current paper, a new log-linear framework is proposed for the summarisation of local interactions among single nucleotide polymorphisms (SNPs). Our approach provides a straightforward means of capturing the diversity of higher-order LD relationships for small numbers of loci by investigating inter-marker interactions. Our method was applied to a dataset of 76 SNP markers spanning a genomic interval of length 2.8 megabases. The analysis of three short sub-regions is described in detail here. Model and graphical representations of contiguous markers in medium to high LD are presented. In the regions studied, evidence for sub-structure was detected, supporting the view that the genomic reality is complex. Interestingly, a critical evaluation of the method by bootstrapping showed that while some LD relationships were captured in a highly repeatable fashion, the majority were not. Large numbers of small interactions, both direct and indirect, mean that many models can adequately summarise the data at hand. Our results suggest that repeatability should be further investigated in the application of LD-based approaches.
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Affiliation(s)
- A P Mander
- MRC Human Nutrition Research, Elsie Widdowson Laboratory, 120 Fulbourn Road, Cambridge, CB1 9NL, UK.
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30
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Suwazono Y, Kobayashi E, Uetani M, Miura K, Morikawa Y, Ishizaki M, Kido T, Nakagawa H, Nogawa K. G-protein beta 3 subunit polymorphism C1429T and low-density lipoprotein receptor-related protein 5 polymorphism A1330V are risk factors for hypercholesterolemia in Japanese males--a prospective study over 5 years. Metabolism 2006; 55:751-7. [PMID: 16713434 DOI: 10.1016/j.metabol.2006.01.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 01/18/2006] [Indexed: 11/21/2022]
Abstract
We examined the relationship between the C825T, C1429T, and A-350G variants in the G-protein beta 3 subunit (GNB3) gene, the A1330V and Q89R variants in the low-density lipoprotein receptor-related protein 5 (LRP5) gene, and the risk of hypercholesterolemia in a prospective study in Japanese workers. This study included observations over a 5-year period from 1997 to 2002 on 936 males and 662 females who were not hypercholesterolemic on entry. Hypercholesterolemia was defined as a serum total cholesterol level of 240 mg/dL or higher. Pooled logistic regression analyses were performed using either of the gene variants with age, body mass index, smoking, alcohol consumption, and habitual exercise as the covariates. The risk of the development of hypercholesterolemia was 2.27 times higher in males with the TT genotype of GNB3/C1429T than in males with the CC genotype (95% confidence interval, 1.04-4.94), after adjustment for the effects of other potential covariates. Simultaneously, the risk was 1.49 times higher in males with the AV genotype of LRP5/A1330V than in males with the AA genotype (95% confidence interval, 1.04-2.12) after adjustment for the effects of other potential covariates. This study indicates the GNB3/C1429T and LRP5/A1330V are independent risk factors for hypercholesterolemia in Japanese males and suggests that targeting these polymorphisms may be beneficial when attempting to prevent hypercholesterolemia in the general Japanese male population.
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Affiliation(s)
- Yasushi Suwazono
- Department of Occupational and Environmental Medicine (A2), Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan.
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Weikard R, Kühn C, Goldammer T, Freyer G, Schwerin M. The bovine PPARGC1A gene: molecular characterization and association of an SNP with variation of milk fat synthesis. Physiol Genomics 2006; 21:1-13. [PMID: 15781588 DOI: 10.1152/physiolgenomics.00103.2004] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Several studies in a variety of breeds have reported at least two QTL for milk production traits, including milk fat synthesis on bovine chromosome 6 (BTA6), comprising a region that comparatively has been mapped to equivalent syntenic chromosome intervals in human, pig, and mouse harboring loci associated with type II diabetes and obesity-related traits. We identified the bovine peroxysome proliferator-activated receptor-gamma coactivator-1alpha gene (PPARGC1A) as a plausible positional and functional candidate gene for a previously described QTL for milk fat yield on BTA6 because of its chromosomal position and its key role in energy, fat, and glucose metabolism. To analyze the role of the bovine PPARGC1A gene in regulation of milk fat synthesis in dairy cattle, we determined its cDNA sequence, genomic organization, chromosomal localization, and expression pattern. The bovine PPARGC1A gene is organized in 13 exons comprising 6,261 bp and is expressed at different levels in a large number of tissues. Bovine PPARGC1A cDNA and protein sequences showed substantial similarity (92-95%) to its respective orthologs from human, rat, and mouse. Screening for polymorphisms in the coding sequence, exon/intron boundaries, 5'- and 3'-untranslated regions, and promoter region of the PPARGC1A gene in sires with a different genotype at the QTL for milk fat yield as well as in a multibreed panel revealed a total of 11 polymorphic loci. A significant association between an SNP in intron 9 of the PPARGC1A gene and milk fat yield was observed in a major dairy cattle population, indicating that the PPARGC1A gene could be involved in genetic variation underlying the QTL for milk fat synthesis on BTA6.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cattle
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- DNA, Complementary/metabolism
- Exons
- Fats/metabolism
- Female
- Gene Frequency
- Genetic Markers
- Genetic Variation
- Genotype
- Haplotypes
- History, 20th Century
- Humans
- Introns
- Lactation
- Mice
- Milk/metabolism
- Models, Genetic
- Models, Statistical
- Molecular Sequence Data
- Oligonucleotide Array Sequence Analysis
- Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha
- Phenotype
- Polymorphism, Genetic
- Polymorphism, Single Nucleotide
- Quantitative Trait Loci
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Species Specificity
- Trans-Activators/genetics
- Transcription Factors
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Affiliation(s)
- Rosemarie Weikard
- Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere, Dummerstorf, Germany.
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Suwazono Y, Kobayashi E, Uetani M, Miura K, Morikawa Y, Ishizaki M, Kido T, Nakagawa H, Nogawa K. Low-density lipoprotein receptor-related protein 5 variant A1330V is a determinant of blood pressure in Japanese males. Life Sci 2006; 78:2475-9. [PMID: 16289238 DOI: 10.1016/j.lfs.2005.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 09/30/2005] [Accepted: 10/03/2005] [Indexed: 11/22/2022]
Abstract
We examined the influence of the A1330V variant in the low-density lipoprotein receptor-related protein 5 gene on blood pressure in a large cohort of Japanese workers. This study used analysis of covariance in a multivariate general linear model to adjust for other potential factors such as age, body mass index, blood chemistry and lifestyle. The target subjects were 1440 males and 1169 females selected from 3834 male and 2591 female workers in a single company. Hypertension was defined as systolic blood pressure >or=140 mm Hg and/or diastolic blood pressure >or=90 mm Hg or the use of antihypertensive medications. Genotype distributions for A1330V in hypertensive males (AA=139(54.5%), AV=101(39.6%), VV=15(5.9%)) and females (AA=48(63.2%), AV=24(31.6%), VV=4(5.3%)) were not significantly different from normotensive males (AA=594(50.1%), AV=488(41.2%), VV=103(8.7%)) and females (AA=568(52.0%), AV=441(40.3%), VV=84(7.7%)). Allele distributions were not significantly different in either sex. In males, analysis of covariance showed that the VV genotype was associated with a 2.5 mm Hg lower diastolic blood pressure and a 2.3 mm Hg lower mean blood pressure than the AA genotype. This study indicates that the 1330V allele is an independent factor for lower diastolic and mean blood pressure in Japanese males.
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Affiliation(s)
- Yasushi Suwazono
- Department of Occupational and Environmental Medicine (A2), Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba 260-8670, Japan.
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33
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Greenawalt DM, Cui X, Wu Y, Lin Y, Wang HY, Luo M, Tereshchenko IV, Hu G, Li JY, Chu Y, Azaro MA, Decoste CJ, Chimge NO, Gao R, Shen L, Shih WJ, Lange K, Li H. Strong correlation between meiotic crossovers and haplotype structure in a 2.5-Mb region on the long arm of chromosome 21. Genome Res 2005; 16:208-14. [PMID: 16385099 PMCID: PMC1361716 DOI: 10.1101/gr.4641706] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although the haplotype structure of the human genome has been studied in great detail, very little is known about the mechanisms underlying its formation. To investigate the role of meiotic recombination on haplotype block formation, single nucleotide polymorphisms were selected at a high density from a 2.5-Mb region of human chromosome 21. Direct analysis of meiotic recombination by high-throughput multiplex genotyping of 662 single sperm identifies 41 recombinants. The crossovers were nonrandomly distributed within 16 small areas. All, except one, of these crossovers fall in areas where the haplotype structure exhibits breakdown, displaying a strong statistically positive association between crossovers and haplotype block breaks. The data also indicate a particular clustered distribution of recombination hotspots within the region. This finding supports the hypothesis that meiotic recombination makes a primary contribution to haplotype block formation in the human genome.
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Affiliation(s)
- Danielle M Greenawalt
- Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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Abstract
Models of background variation in genomic regions form the basis of linkage disequilibrium mapping methods. In this work we analyze a background model that groups SNPs into haplotype blocks and represents the dependencies between blocks by a Markov chain. We develop an error measure to compare the performance of this model against the common model that assumes that blocks are independent. By examining data from the International Haplotype Mapping project, we show how the Markov model over haplotype blocks is most accurate when representing blocks in strong linkage disequilibrium. This contrasts with the independent model, which is rendered less accurate by linkage disequilibrium. We provide a theoretical explanation for this surprising property of the Markov model and relate its behavior to allele diversity.
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Affiliation(s)
- G Greenspan
- Computer Science Department, Technion, Haifa 32000, Israel.
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35
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Crabbe P, Balemans W, Willaert A, van Pottelbergh I, Cleiren E, Coucke PJ, Ai M, Goemaere S, van Hul W, de Paepe A, Kaufman JM. Missense mutations in LRP5 are not a common cause of idiopathic osteoporosis in adult men. J Bone Miner Res 2005; 20:1951-9. [PMID: 16234968 DOI: 10.1359/jbmr.050705] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 06/21/2005] [Accepted: 07/05/2005] [Indexed: 01/29/2023]
Abstract
UNLABELLED We studied whether the LRP5 gene contributes to the clinical phenotype of IO in men. Mutation analysis in 66 IO men revealed a range of sequence variants, of which two missense variants were shown to be of functional relevance. INTRODUCTION Mutations in the LDL receptor-related protein 5 (LRP5) gene have been associated with extreme bone phenotypes, which makes LRP5 a plausible candidate gene for idiopathic osteoporosis (IO). MATERIALS AND METHODS In 66 men with IO, all 23 exons and exon-intron boundaries of the LRP5 gene were screened for mutations, and functional analyses were performed for those that were putatively involved in the phenotype. RESULTS Mutation analysis in the IO probands revealed five missense mutations, of which 1067C>T (S356L), 1364C>T (S455L), and 4609G>A (A1537T) were of potential functional significance because they were located in highly conserved regions of LRP5 and not found in a control panel. Segregation analysis in the respective families could not exclude their possible causality for IO. Furthermore, functional analyses clearly showed an inhibitory effect of mutations 1067C>T and 1364C>T on Wnt signal transduction. These effects are most likely caused by impaired LRP5 synthesis in the case of 1067C>T and failure of protein trafficking to the cell surface for 1364C>T. CONCLUSIONS For 2 of 66 IO probands, a mutation in the LRP5 gene with proven functionality was found. The findings indicate that carrying an LRP5 mutation is a risk factor for IO, but that overall, IO in men is infrequently underlied by such a mutation.
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Affiliation(s)
- Patricia Crabbe
- Department of Endocrinology, Ghent University Hospital, Ghent, Belgium.
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Lee HJ, Kim KJ, Park MH, Kimm K, Park C, Oh B, Lee JY. Single-nucleotide polymorphisms and haplotype LD analysis of the 29-kb IGF2 region on chromosome 11p15.5 in the Korean population. Hum Hered 2005; 60:73-80. [PMID: 16166779 DOI: 10.1159/000088269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Accepted: 07/13/2005] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE We investigated sequence variations of the 29-kb insulin-like growth factor 2 (IGF2) region in human chromosome region 11p15.5 in the Korean population. This region consists of IGF2, insulin-like growth factor 2 antisense (IGF2AS), and the insulin gene, all important candidate genes for various diseases, including cancer, obesity, diabetes, and coronary disease. While single nucleotide polymorphisms (SNPs) have been identified for this region and used in association studies, ethnic differences in genetic variation at this site have not been addressed. To date, SNPs for the entire 29-kb region in the Korean population have not been reported. METHODS We surveyed a population of 108 Koreans for SNPs in the 29-kb IGF2 region. RESULTS We identified 62 SNPs, consisting of 6 SNPs in the promoter region, 17 in the untranslated region, 19 in introns, and 20 in the intergenic region. We also analyzed linkage disequilibrium (LD) patterns and haplotypes using 36 high-frequency (> 5%)SNPs and found a well-defined LD block spanning about 13 kb that includes 8 kb of the IGF2AS gene, with two hot-spot regions flanking the LD block. CONCLUSION These SNPs may be useful as genetic markers in disease association studies in the Korean population.
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Affiliation(s)
- Hye-Ja Lee
- Division of Structural and Functional Genome Research, National Genome Research Institute, NIH Korea, Seoul, Korea
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37
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Zhang ZL, Qin YJ, He JW, Huang QR, Li M, Hu YQ, Liu YJ. Association of polymorphisms in low-density lipoprotein receptor-related protein 5 gene with bone mineral density in postmenopausal Chinese women. Acta Pharmacol Sin 2005; 26:1111-6. [PMID: 16115379 DOI: 10.1111/j.1745-7254.2005.00173.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
AIM To investigate the possible association of Q89R, N740N and A1330V polymorphisms in low-density lipoprotein receptor-related protein 5 (LRP5) gene with bone mineral density (BMD) in postmenopausal Chinese women. METHODS Q89R, N740N and A1330V genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 647 unrelated healthy postmenopausal Han Chinese women aged 43-76 years in Shanghai. BMD at lumbar spine 1-4 and the left proximal femur including the femoral neck, trochanter and Ward's triangle were measured by dual-energy X-ray absorptionmetry in all subjects. RESULTS The distribution of the Q89R, N740N and A1330V genotypes in this population was as follows: QQ 80.5%, QR 18.7%, and RR 0.8%; TT 66.9%, TC 31.1%, and CC 2.0%; AA 68.0%, AV 29.7%, and VV 2.3%. The frequencies of the Q89R, N740N and A1330V genotypes and alleles did not deviate from the Hardy-Weinberg equilibrium. We found that the Q89R and A1330V polymorphisms were in linkage disequilibrium in our population (kappa2=13.50, P<0.01). Both before and after adjusting for age, years since menopause, height, and weight, the Q89R or N740N genotypes were significantly associated with BMD at the femoral neck (P<0.05). Subjects with the Q89R QQ genotype or the N740N TT genotype had a significantly higher BMD at the femoral neck, compared with those with the QR/RR or TC/CC genotypes, respectively. No significant association was found between A1330V polymorphism and BMD at any site. CONCLUSION Our findings suggest that the LRP5 gene is a candidate for the genetic determination of BMD in postmenopausal Chinese women.
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Affiliation(s)
- Zhen-lin Zhang
- Center for Preventing and Treating Osteoporosis, Osteoporosis Research Unit, the Sixth People's Hospital, Shanghai Jiaotong University, Shanghai 200233, China.
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38
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Smith AJP, Gidley J, Sandy JR, Perry MJ, Elson CJ, Kirwan JR, Spector TD, Doherty M, Bidwell JL, Mansell JP. Haplotypes of the low-density lipoprotein receptor-related protein 5 (LRP5) gene: are they a risk factor in osteoarthritis? Osteoarthritis Cartilage 2005; 13:608-13. [PMID: 15979013 DOI: 10.1016/j.joca.2005.01.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Accepted: 01/24/2005] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Several genome-wide scans have revealed an osteoarthritis (OA)-susceptibility locus on chromosome 11q in close proximity to the low-density lipoprotein receptor-related protein 5 (LRP5) gene. The regulation of bone mass is under the control of LRP5 and since increased bone mass is thought to play a role in the pathology of OA we examined LRP5 polymorphisms and haplotypes to determine if variants of this locus may predispose to OA. METHODS A UK control population of 187 individuals was examined for five commonly occurring polymorphisms against a cohort of 158 DNAs from patients with knee OA. An additional UK cohort was also examined to confirm the findings of the first study; this second group consisted of 110 knee OA patients. Haplotype analysis was also performed on patient and control DNAs. RESULTS A study of individual polymorphisms revealed no association with disease. However, haplotype analysis of the initial two populations revealed a common haplotype (C-G-C-C-A) that provided a 1.6-fold increased risk of OA (P(c)=0.021). The data obtained from the second cohort confirmed the initial findings, with a 1.6-fold increased risk observed within this cohort for the risk haplotype (P=0.012). CONCLUSIONS A closer investigation of LRP5 and associated Wnt signalling molecules in OA will help determine disease aetiology and the development of novel treatment strategies that specifically target the bone compartment.
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Affiliation(s)
- A J P Smith
- University of Bristol Department of Pathology and Microbiology, Homoeopathic Hospital Site, Cotham, Bristol BS6 6JU, UK
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Ferrari SL, Deutsch S, Antonarakis SE. Pathogenic mutations and polymorphisms in the lipoprotein receptor-related protein 5 reveal a new biological pathway for the control of bone mass. Curr Opin Lipidol 2005; 16:207-14. [PMID: 15767861 DOI: 10.1097/01.mol.0000162326.62419.e4] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW This review summarizes recent findings concerning the genomic variations of the lipoprotein receptor-related protein 5 (LPR5) in relation to bone biology. RECENT FINDINGS Mutations in the LRP5 gene causing high bone mass (HBM) and osteoporosis-pseudoglioma (OPPG) underscored the role of the Wnt-LRP5 canonical signaling on bone formation. Additional LRP5 activating mutations have been identified in a variety of sclerosing bone dysplasias, improving the diagnostic classification of these disorders. Association of polymorphisms in LRP5 with bone mineral density indicate that LRP5 genetic variation contribute to the risk of osteoporosis. Transgenic mice carrying the LRP5 HBM mutation have improved bone biomechanical properties, and the molecular mechanisms by which this mutation exerts its effects have been clarified. A number of KO mice have shown the complex effects of the Wnt-LRP5 pathway on bone mass and skeletal morphology. In vitro studies indicate that osteoblasts produce a variety of Wnts, the LRP5 co-receptor frizzled (Fzd), as well as LRP5 and Wnt inhibitors, i.e. dickkopf (Dkk1) and frizzled-related proteins (Sfrps), respectively, and delineate the role of these molecules in regulating the commitment of mesenchymal stem cells along the osteoblastic lineage. SUMMARY Identification of pathogenic mutations and allelic variations in LRP5 has improved our understanding of the physiology of bone mass acquisition and the pathophysiology of several bone diseases, including osteoporosis. Understanding how complex interactions between agonistic and inhibitory factors in the Wnt-LRP5 canonical pathway influence osteoblast functions has the potential of providing new anabolic treatments for osteoporosis.
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Affiliation(s)
- Serge L Ferrari
- Division of Bone Diseases, Department of Rehabilitation and Geriatrics, Geneva University Hospital, Geneva, Switzerland.
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Sivakumaran TA, Shen P, Wall DP, Do BH, Kucheria K, Oefner PJ. Conservation of theRB1gene in human and primates. Hum Mutat 2005; 25:396-409. [PMID: 15776430 DOI: 10.1002/humu.20154] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mutations in the RB1 gene are associated with retinoblastoma, which has served as an important model for understanding hereditary predisposition to cancer. Despite the great scrutiny that RB1 has enjoyed as the prototypical tumor suppressor gene, it has never been the object of a comprehensive survey of sequence variation in diverse human populations and primates. Therefore, we analyzed the coding (2,787 bp) and adjacent intronic and untranslated (7,313 bp) sequences of RB1 in 137 individuals from a wide range of ethnicities, including 19 Asian Indian hereditary retinoblastoma cases, and five primate species. Aside from nine apparently disease-associated mutations, 52 variants were identified. They included six singleton, coding variants that comprised five amino acid replacements and one silent site. Nucleotide diversity of the coding region (pi=0.0763+/-1.35 x 10(-4)) was 52 times lower than that of the noncoding regions (pi=3.93+/-5.26 x 10(-4)), indicative of significant sequence conservation. The occurrence of purifying selection was corroborated by phylogeny-based maximum likelihood analysis of the RB1 sequences of human and five primates, which yielded an estimated ratio of replacement to silent substitutions (omega) of 0.095 across all lineages. RB1 displayed extensive linkage disequilibrium over 174 kb, and only four unique recombination events, two in Africa and one each in Europe and Southwest Asia, were observed. Using a parsimony approach, 15 haplotypes could be inferred. Ten were found in Africa, though only 12.4% of the 274 chromosomes screened were of African origin. In non-Africans, a single haplotype accounted for from 63 to 84% of all chromosomes, most likely the consequence of natural selection and a significant bottleneck in effective population size during the colonization of the non-African continents.
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Affiliation(s)
- Theru A Sivakumaran
- Division of Genetics, Department of Anatomy, All India Institute of Medical Sciences, New Delhi, India
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Wang WYS, Barratt BJ, Clayton DG, Todd JA. Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 2005; 6:109-18. [PMID: 15716907 DOI: 10.1038/nrg1522] [Citation(s) in RCA: 747] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To fully understand the allelic variation that underlies common diseases, complete genome sequencing for many individuals with and without disease is required. This is still not technically feasible. However, recently it has become possible to carry out partial surveys of the genome by genotyping large numbers of common SNPs in genome-wide association studies. Here, we outline the main factors - including models of the allelic architecture of common diseases, sample size, map density and sample-collection biases - that need to be taken into account in order to optimize the cost efficiency of identifying genuine disease-susceptibility loci.
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Affiliation(s)
- William Y S Wang
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
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42
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Park BL, Cheong HS, Kim LH, Choi YH, Namgoong S, Park HS, Hong SJ, Choi BW, Lee JH, Park CS, Shin HD. Association analysis of signal transducer and activator of transcription 4 (STAT4) polymorphisms with asthma. J Hum Genet 2005; 50:133-138. [PMID: 15744455 DOI: 10.1007/s10038-005-0232-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Accepted: 12/24/2004] [Indexed: 12/21/2022]
Abstract
The signal transducer and activator of transcription 4 (STAT4) on chromosome 2q32.2-q32.3 is known to be essential for mediating responses to interleukin 12 in lymphocytes and regulating the differentiation of T helper cells. In an effort to discover additional polymorphism(s) in genes in which variant(s) have been implicated in asthma, we investigated the genetic polymorphisms in STAT4 to evaluate it as a potential candidate gene for a host genetic study of asthma. By direct DNA sequencing in 24 individuals, we identified 12 sequence variants within introns and their flanking regions, including the 1.5 kb promoter region of STAT4. Among them, seven common polymorphic sites were selected for genotyping in our asthma cohort (502 asthmatic patients, 164 normal controls). Using logistic regression analysis for association with the risk of asthma, while controlling for age, gender, and smoking status as covariates, no significant associations with the risk of asthma were detected. However, one single nucleotide polymorphism (SNP) in intron 11 (+90089T--> C) and two haplotypes showed positive association (P= 0.03, 0.03 and 0.03, respectively) with production of specific IgE to Dermatophagoides farinae (D.f.) or Dermatophagoides pteronyssinus (D.p.) among asthmatic patients. The minor allele frequencies of +90089T--> C and BLOCK2-ht1 were higher (0.54 and 0.47, respectively) among individuals who produced specific IgE to D.f. or D.p. than frequencies (0.47 and 0.39, respectively) among individuals who did not produce specific IgE (OR=1.38 and 1.40, respectively). Our findings suggest that polymorphisms in STAT4 might be one of the genetic factors for the risk of production of specific IgE to mite allergens.
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Affiliation(s)
- Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., 11th Floor, MaeHun B/D, 13 Chongro 4 Ga, Chongro-Gu, Seoul, Korea, 110-834
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., 11th Floor, MaeHun B/D, 13 Chongro 4 Ga, Chongro-Gu, Seoul, Korea, 110-834
| | - Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., 11th Floor, MaeHun B/D, 13 Chongro 4 Ga, Chongro-Gu, Seoul, Korea, 110-834
| | - Yoo Hyun Choi
- Department of Genetic Epidemiology, SNP Genetics, Inc., 11th Floor, MaeHun B/D, 13 Chongro 4 Ga, Chongro-Gu, Seoul, Korea, 110-834
| | - Sohg Namgoong
- Department of Genetic Epidemiology, SNP Genetics, Inc., 11th Floor, MaeHun B/D, 13 Chongro 4 Ga, Chongro-Gu, Seoul, Korea, 110-834
| | - Hae-Sim Park
- Asthma Genome Research Group, Soonchunhyang University Hospital, Ajuo University Hospital, Ulsan University Hospital, and Choong-Ang University Hospital, Korea
| | - Soo-Jong Hong
- Asthma Genome Research Group, Soonchunhyang University Hospital, Ajuo University Hospital, Ulsan University Hospital, and Choong-Ang University Hospital, Korea
| | - Byoung Whui Choi
- Asthma Genome Research Group, Soonchunhyang University Hospital, Ajuo University Hospital, Ulsan University Hospital, and Choong-Ang University Hospital, Korea
| | - June Hyuk Lee
- Asthma Genome Research Group, Soonchunhyang University Hospital, Ajuo University Hospital, Ulsan University Hospital, and Choong-Ang University Hospital, Korea
| | - Choon-Sik Park
- Asthma Genome Research Group, Soonchunhyang University Hospital, Ajuo University Hospital, Ulsan University Hospital, and Choong-Ang University Hospital, Korea.
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, 1174, Jung Dong, Wonmi Ku, Bucheon, Gyeonggi Do, Korea, 420-021.
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., 11th Floor, MaeHun B/D, 13 Chongro 4 Ga, Chongro-Gu, Seoul, Korea, 110-834
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Hu X, Schrodi SJ, Ross DA, Cargill M. Selecting tagging SNPs for association studies using power calculations from genotype data. Hum Hered 2005; 57:156-70. [PMID: 15297809 DOI: 10.1159/000079246] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Accepted: 04/13/2004] [Indexed: 11/19/2022] Open
Abstract
Recent studies have indicated that linkage disequilibrium (LD) between single nucleotide polymorphism (SNP) markers can be used to derive a reduced set of tagging SNPs (tSNPs) for genetic association studies. Previous strategies for identifying tSNPs have focused on LD measures or haplotype diversity, but the statistical power to detect disease-associated variants using tSNPs in genetic studies has not been fully characterized. We propose a new approach of selecting tSNPs based on determining the set of SNPs with the highest power to detect association. Two-locus genotype frequencies are used in the power calculations. To show utility, we applied this power method to a large number of SNPs that had been genotyped in Caucasian samples. We demonstrate that a significant reduction in genotyping efforts can be achieved although the reduction depends on genotypic relative risk, inheritance mode and the prevalence of disease in the human population. The tSNP sets identified by our method are remarkably robust to changes in the disease model when small relative risk and additive mode of inheritance are employed. We have also evaluated the ability of the method to detect unidentified SNPs. Our findings have important implications in applying tSNPs from different data sources in association studies.
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Affiliation(s)
- Xiaolan Hu
- Celera Diagnostics, Harbor Bay Pkwy, Alameda, CA 94502, USA.
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Bernig T, Taylor JG, Foster CB, Staats B, Yeager M, Chanock SJ. Sequence analysis of the mannose-binding lectin (MBL2) gene reveals a high degree of heterozygosity with evidence of selection. Genes Immun 2005; 5:461-76. [PMID: 15306844 DOI: 10.1038/sj.gene.6364116] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human mannose-binding protein (MBL) is a component of innate immunity. To capture the common genetic variants of MBL2, we resequenced a 10.0 kb region that includes MBL2 in 102 individuals representing four major US ethnic groups. In all, 87 polymorphic sites were observed, indicating a high level of heterozygosity (total pi=18.3 x 10(-4)). Estimates of linkage disequilibrium across MBL2 indicate that it is divided into two blocks, with a probable recombination hot spot in the 3' end. Three non-synonymous SNPs in exon 1 of the encoding MBL2 gene and three upstream SNPs form common 'secretor haplotypes' that can predict circulating levels. Common variants have been associated with increased susceptibility to infection and autoimmune diseases. The high frequencies of B, C and D alleles in certain populations suggest a possible selective advantage for heterozygosity. There is limited diversity of haplotype structure; the 'secretor haplotypes' lie on a restricted number of extended haplotypes, which could include additional linked SNPs, which might also have possible functional implications. There is evidence for gene conversion in the region between the two blocks, in the last exon. Our data should form the basis for conducting MBL2 candidate gene association studies using a locus-wide approach.
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Affiliation(s)
- T Bernig
- Section on Genomic Variation, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
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Koller DL, Ichikawa S, Johnson ML, Lai D, Xuei X, Edenberg HJ, Conneally PM, Hui SL, Johnston CC, Peacock M, Foroud T, Econs MJ. Contribution of the LRP5 gene to normal variation in peak BMD in women. J Bone Miner Res 2005; 20:75-80. [PMID: 15619672 DOI: 10.1359/jbmr.041019] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 07/14/2004] [Accepted: 08/20/2004] [Indexed: 02/03/2023]
Abstract
UNLABELLED The role of the LRP5 gene in rare BMD-related traits has recently been shown. We tested whether variation in this gene might play a role in normal variation in peak BMD. Association between SNPs in LRP5 and hip and spine BMD was measured in 1301 premenopausal women. Only a small proportion of the BMD variation was attributable to LRP5 in our sample. INTRODUCTION Mutations in the low-density lipoprotein receptor-related protein 5 (LRP5) gene have been implicated as the cause of multiple distinct BMD-related rare Mendelian phenotypes. We sought to examine whether the LRP5 gene contributes to the observed variation in peak BMD in the normal population. MATERIALS AND METHODS We genotyped 12 single nucleotide polymorphisms (SNPs) in LRP5 using allele-specific PCR and mass spectrometry methods. Linkage disequilibrium between the genotyped LRP5 SNPs was measured. We tested for association between these SNPs and both hip and spine BMD (adjusted for age and body weight) in 1301 healthy premenopausal women who took part in a sibling pair study aimed at identifying the genes underlying peak bone mass. Our study used both population-based (ANOVA) and family-based (quantitative transmission disequilibrium test) association methodology. RESULTS AND CONCLUSIONS The linkage disequilibrium pattern and haplotype block structure within the LRP5 gene were consistent with that observed in other studies. Although significant evidence of association was found between LRP5 SNPs and both hip and spine BMD, only a small proportion of the total variation in these phenotypes was accounted for. The genotyped SNPs accounted for approximately 0.8% of the variation in femoral neck BMD and 1.1% of the variation in spine BMD. Results from our sample suggest that natural variation in and around LRP5 is not a major contributor to the observed variability in peak BMD at either the femoral neck or lumbar spine in white women.
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Affiliation(s)
- Daniel L Koller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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Camp NJ, Swensen J, Horne BD, Farnham JM, Thomas A, Cannon-Albright LA, Tavtigian SV. Characterization of linkage disequilibrium structure, mutation history, and tagging SNPs, and their use in association analyses:ELAC2 and familial early-onset prostate cancer. Genet Epidemiol 2005; 28:232-43. [PMID: 15593091 DOI: 10.1002/gepi.20054] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In association analyses, it is critical that informative single-nucleotide polymorphisms (SNPs) be selected for study and utilized appropriately. We sequenced 38 kb, including exons of ELAC2, promoter region and conserved upstream intergenic sequences. A comprehensive characterization of linkage disequilibrium (LD) structure and mutation history was performed using our principal components analysis (PCA) method and a phylogenetic analysis. We identified a complex pattern of LD structure consistent with the occurrence of both recombination and mutation events within ELAC2. Four overlapping and noncontiguous LD groups were defined. Eight tagging SNPs (tSNPs) were identified, accounting for over 90% of the genetic variation of the 19 total variants. We tested associations between familial early-onset prostate cancer (PRCA) and each variant independently and in haplotypes. We performed these tests using all 19 variants and the 8 tSNPs; the results using tSNP haplotypes accurately represent the association evidence for the full haplotypes. We observed increased evidence for association when SNPs were analyzed in haplotypes. The phylogenetic analysis indicated three haplotypes, clustered farthest from the root-node, all of which were found more often in cases than controls. These three haplotypes together showed the best evidence of association with familial, early-onset PRCA (P=0.0024; odds ratio=2.23; 95% CI, 1.33-3.74), indicating possible allelic heterogeneity. Our results suggest that 8 tSNPs are required to comprehensively assess associations in ELAC2, and that haplotypes should be considered for analysis, and that a knowledge of mutation history may be helpful in parsing allelic heterogeneity and suggesting combinations of haplotypes to be tested.
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Affiliation(s)
- Nicola J Camp
- Genetic Epidemiology Division, Department of Medical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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Koay MA, Woon PY, Zhang Y, Miles LJ, Duncan EL, Ralston SH, Compston JE, Cooper C, Keen R, Langdahl BL, MacLelland A, O'Riordan J, Pols HA, Reid DM, Uitterlinden AG, Wass JAH, Brown MA. Influence of LRP5 polymorphisms on normal variation in BMD. J Bone Miner Res 2004; 19:1619-27. [PMID: 15355556 DOI: 10.1359/jbmr.040704] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2003] [Revised: 01/15/2004] [Accepted: 05/18/2004] [Indexed: 11/18/2022]
Abstract
UNLABELLED Genetic studies based on cohorts with rare and extreme bone phenotypes have shown that the LRP5 gene is an important genetic modulator of BMD. Using family-based and case-control approaches, this study examines the role of the LRP5 gene in determining normal population variation of BMD and describes significant association and suggestive linkage between LRP5 gene polymorphisms and BMD in >900 individuals with a broad range of BMD. INTRODUCTION Osteoporosis is a common, highly heritable condition determined by complex interactions of genetic and environmental etiologies. Genetic factors alone can account for 50-80% of the interindividual variation in BMD. Mutations in the LRP5 gene on chromosome 11q12-13 have been associated with rare syndromes characterized by extremely low or high BMD, but little is known about the contribution of this gene to the development of osteoporosis and determination of BMD in a normal population. MATERIALS AND METHODS To examine the entire spectrum of low to high BMD, 152 osteoporotic probands, their families (597 individuals), and 160 women with elevated BMD (T score > 2.5) were recruited. BMD at the lumbar spine, femoral neck, and hip were measured in each subject using DXA. RESULTS PAGE sequencing of the LRP5 gene revealed 10 single nucleotide polymorphisms (SNPs), 8 of which had allele frequencies of >5%, in exons 8, 9, 10, 15, and 18 and in introns 6, 7, and 21. Within families, a strong association was observed between an SNP at nucleotide C171346A in intron 21 and total hip BMD (p < 1 x 10(-5) in men only, p = 0.0019 in both men and women). This association was also observed in comparisons of osteoporotic probands and unrelated elevated BMD in women (p = 0.03), along with associations with markers in exons 8 (C135242T, p = 0.007) and 9 (C141759T, p = 0.02). Haplotypes composed of two to three of the SNPs G121513A, C135242T, G138351A, and C141759T were strongly associated with BMD when comparing osteoporotic probands and high BMD cases (p < 0.003). An SNP at nucleotide C165215T in exon 18 was linked to BMD at the lumbar spine, femoral neck, and total hip (parametric LOD scores = 2.8, 2.5, and 2.2 and nonparametric LOD scores = 0.3, 1.1, and 2.2, respectively) but was not genetically associated with BMD variation. CONCLUSION These results show that common LRP5 polymorphisms contribute to the determination of BMD in the general population.
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Affiliation(s)
- M Audrey Koay
- Institute of Musculoskeletal Sciences, University of Oxford, The Botnar Research Centre, Nuffield Orthopaedic Centre, Headington, Oxford, UK
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Kauppi L, Jeffreys AJ, Keeney S. Where the crossovers are: recombination distributions in mammals. Nat Rev Genet 2004; 5:413-24. [PMID: 15153994 DOI: 10.1038/nrg1346] [Citation(s) in RCA: 238] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Liisa Kauppi
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.
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Koh JM, Jung MH, Hong JS, Park HJ, Chang JS, Shin HD, Kim SY, Kim GS. Association between bone mineral density and LDL receptor-related protein 5 gene polymorphisms in young Korean men. J Korean Med Sci 2004; 19:407-12. [PMID: 15201508 PMCID: PMC2816843 DOI: 10.3346/jkms.2004.19.3.407] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Recently, It has been reported that the LDL receptor-related protein 5 (LRP5) regulates bone formation, and that mutations of the gene cause osteoporosis-pseudoglioma syndrome or high bone mass phenotypes. However, the mutations cannot explain a genetic trait for osteoporosis in the general population because of their rarity. From 219 Korean men aged 20-34 yr, we looked for six known polymorphisms causing amino acid changes in the LRP5 coding region, and investigated their association with bone mineral density (BMD) at the following anatomical sites: lumbar spine (L2-L4) and the left proximal femur (femoral neck, Ward's triangle, trochanter and shaft). We found that the Q89R polymorphism was significantly associated with BMD at the femoral neck and Ward's triangle (p=0.004 and <0.001, respectively). However, after adjusting for age, weight and height, a statistically significant association only occurred at the Ward's triangle (p=0.043), and a marginal association was observed at the femoral neck (p=0.098). No A400V, V667M, R1036Q and A1525V polymorphisms were found, and no statistically significant association was found between the A1330V polymorphism and BMD at any sites. Although we failed to demonstrate a clear association between the LRP5 polymorphism and peak bone mass in young men, the present study suggests that larger-scale studies on the Q89R polymorphism need to be performed.
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Affiliation(s)
- Jung-Min Koh
- Department of Genetic Epidemiology SNP Genetics, Seoul, Republic of Korea
| | - Min Hui Jung
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jeong Soo Hong
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyung Joo Park
- Department of Genetic Epidemiology SNP Genetics, Seoul, Republic of Korea
| | - Jae Suk Chang
- Department of Orthopedic Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | - Shin-Yoon Kim
- Department of Orthopedic Surgery, Kyungpook National University, Taegu, Republic of Korea
| | - Ghi Su Kim
- Department of Genetic Epidemiology SNP Genetics, Seoul, Republic of Korea
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Mizuguchi T, Furuta I, Watanabe Y, Tsukamoto K, Tomita H, Tsujihata M, Ohta T, Kishino T, Matsumoto N, Minakami H, Niikawa N, Yoshiura KI. LRP5, low-density-lipoprotein-receptor-related protein 5, is a determinant for bone mineral density. J Hum Genet 2004; 49:80-86. [PMID: 14727154 DOI: 10.1007/s10038-003-0111-6] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Accepted: 11/06/2003] [Indexed: 01/18/2023]
Abstract
Osteoporosis is a multifactorial trait with low bone mineral density (BMD). We report results of an association study between BMD and nine candidate genes ( TGFB1, TGFBR2, SMAD2, SMAD3, SMAD4, IFNB1, IFNAR1, FOS and LRP5), as well as of a case-control study of osteoporosis. Samples for the former association study included 481 general Japanese women. Among the nine candidate genes examined, only LRP5 showed a significant association with BMD. We identified a strong linkage disequilibrium (LD) block within LRP5. Of five LPR5 single nucleotide polymorphisms (SNPs) that are located in the LD block, three gave relatively significant results: Women with the C/C genotype at the c.2220C>T SNP site had higher adjusted BMD (AdjBMD) value compared to those with C/T and T/T (p=0.022); and likewise, G/G at IVS17-30G>A and C/C women at c.3989C>T showed higher AdjBMD than those with G/A or A/A (p=0.039) and with C/T or T/T ( p=0.053), respectively. The case-control study in another series of samples consisting of 126 osteoporotic patients and 131 normal controls also gave a significant difference in allele frequency at c.2220C>T (kappa2=6.737, p=0.009). These results suggest that LRP5 is a BMD determinant and also contributes to a risk of osteoporosis.
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Affiliation(s)
- Takeshi Mizuguchi
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Kawaguchi, Japan
| | - Itsuko Furuta
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yukio Watanabe
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
- Department of Obstetrics and Gynecology, Asahikawa Medical College, Asahikawa, Japan
| | - Kazuhiro Tsukamoto
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Kawaguchi, Japan
- Department of Clinical Pharmacy, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroshi Tomita
- Nagasaki Prefectural Medical Health Center, Nagasaki, Japan
| | | | - Tohru Ohta
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Kawaguchi, Japan
- Division of Functional Genomics, Center for Frontier Life Sciences, Nagasaki University, Nagasaki, Japan
| | - Tatsuya Kishino
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Kawaguchi, Japan
- Division of Functional Genomics, Center for Frontier Life Sciences, Nagasaki University, Nagasaki, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Kawaguchi, Japan
| | - Hisanori Minakami
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Norio Niikawa
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Kawaguchi, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Kawaguchi, Japan.
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