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Article: Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes

TitlePatterns of linkage disequilibrium and haplotype distribution in disease candidate genes
Authors
Issue Date2004
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenet/
Citation
Bmc Genetics, 2004, v. 5 How to Cite?
AbstractBackground: The adequacy of association studies for complex diseases depends critically on the existence of linkage disequilibrium (LD) between functional alleles and surrounding SNP markers. Results: We examined the patterns of LD and haplotype distribution in eight candidate genes for osteoporosis and/or obesity using 31 SNPs in 1,873 subjects. These eight genes are apolipoprotein E (APOE), type I collagen α1 (COL1A1), estrogen receptor-α (ER-α), leptin receptor (LEPR), parathyroid hormone (PTH)/PTH-related peptide receptor type 1 (PTHR1), transforming growth factor-β1 (TGF-β1), uncoupling protein 3 (UCP3), and vitamin D (1,25-dihydroxyvitamin D 3) receptor (VDR). Yin yang haplotypes, two high-frequency haplotypes composed of completely mismatching SNP alleles, were examined. To quantify LD patterns, two common measures of LD, D' and r 2, were calculated for the SNPs within the genes. The haplotype distribution varied in the different genes. Yin yang haplotypes were observed only in PTHR1 and UCP3. D' ranged from 0.020 to 1.000 with the average of 0.475, whereas the average r 2 was 0.158 (ranging from 0.000 to 0.883). A decay of LD was observed as the intermarker distance increased, however, there was a great difference in LD characteristics of different genes or even in different regions within gene. Conclusion: The differences in haplotype distributions and LD patterns among the genes underscore the importance of characterizing genomic regions of interest prior to association studies. © 2004 Long et al; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/178906
ISSN
2015 Impact Factor: 2.152
2015 SCImago Journal Rankings: 1.185
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLong, JRen_US
dc.contributor.authorZhao, LJen_US
dc.contributor.authorLiu, PYen_US
dc.contributor.authorLu, Yen_US
dc.contributor.authorDvornyk, Ven_US
dc.contributor.authorShen, Hen_US
dc.contributor.authorLiu, YJen_US
dc.contributor.authorZhang, YYen_US
dc.contributor.authorXiong, DHen_US
dc.contributor.authorXiao, Pen_US
dc.contributor.authorDeng, HWen_US
dc.date.accessioned2012-12-19T09:50:38Z-
dc.date.available2012-12-19T09:50:38Z-
dc.date.issued2004en_US
dc.identifier.citationBmc Genetics, 2004, v. 5en_US
dc.identifier.issn1471-2156en_US
dc.identifier.urihttp://hdl.handle.net/10722/178906-
dc.description.abstractBackground: The adequacy of association studies for complex diseases depends critically on the existence of linkage disequilibrium (LD) between functional alleles and surrounding SNP markers. Results: We examined the patterns of LD and haplotype distribution in eight candidate genes for osteoporosis and/or obesity using 31 SNPs in 1,873 subjects. These eight genes are apolipoprotein E (APOE), type I collagen α1 (COL1A1), estrogen receptor-α (ER-α), leptin receptor (LEPR), parathyroid hormone (PTH)/PTH-related peptide receptor type 1 (PTHR1), transforming growth factor-β1 (TGF-β1), uncoupling protein 3 (UCP3), and vitamin D (1,25-dihydroxyvitamin D 3) receptor (VDR). Yin yang haplotypes, two high-frequency haplotypes composed of completely mismatching SNP alleles, were examined. To quantify LD patterns, two common measures of LD, D' and r 2, were calculated for the SNPs within the genes. The haplotype distribution varied in the different genes. Yin yang haplotypes were observed only in PTHR1 and UCP3. D' ranged from 0.020 to 1.000 with the average of 0.475, whereas the average r 2 was 0.158 (ranging from 0.000 to 0.883). A decay of LD was observed as the intermarker distance increased, however, there was a great difference in LD characteristics of different genes or even in different regions within gene. Conclusion: The differences in haplotype distributions and LD patterns among the genes underscore the importance of characterizing genomic regions of interest prior to association studies. © 2004 Long et al; licensee BioMed Central Ltd.en_US
dc.languageengen_US
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.biomedcentral.com/bmcgenet/en_US
dc.relation.ispartofBMC Geneticsen_US
dc.titlePatterns of linkage disequilibrium and haplotype distribution in disease candidate genesen_US
dc.typeArticleen_US
dc.identifier.emailDvornyk, V: dvornyk@hku.hken_US
dc.identifier.authorityDvornyk, V=rp00693en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1186/1471-2156-5-11en_US
dc.identifier.pmid15157284-
dc.identifier.scopuseid_2-s2.0-25444510847en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-25444510847&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume5en_US
dc.identifier.isiWOS:000222343100001-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridLong, JR=36120777800en_US
dc.identifier.scopusauthoridZhao, LJ=7404455505en_US
dc.identifier.scopusauthoridLiu, PY=7404618030en_US
dc.identifier.scopusauthoridLu, Y=26321148700en_US
dc.identifier.scopusauthoridDvornyk, V=6701789786en_US
dc.identifier.scopusauthoridShen, H=36126870600en_US
dc.identifier.scopusauthoridLiu, YJ=36065513000en_US
dc.identifier.scopusauthoridZhang, YY=12781205700en_US
dc.identifier.scopusauthoridXiong, DH=7007033697en_US
dc.identifier.scopusauthoridXiao, P=34573749200en_US
dc.identifier.scopusauthoridDeng, HW=34568563000en_US

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