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Article: Current limitations of SNP data from the public domain for studies of complex disorders: A test for ten candidate genes for obesity and osteoporosis

TitleCurrent limitations of SNP data from the public domain for studies of complex disorders: A test for ten candidate genes for obesity and osteoporosis
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: Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. Results: To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. Conclusion: A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups. ©2004 Dvornyk et al; licensee BioMed Central Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/178902
ISSN
2015 Impact Factor: 2.152
2015 SCImago Journal Rankings: 1.185
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorDvornyk, Ven_US
dc.contributor.authorLong, JRen_US
dc.contributor.authorXiong, DHen_US
dc.contributor.authorLiu, PYen_US
dc.contributor.authorZhao, LJen_US
dc.contributor.authorShen, Hen_US
dc.contributor.authorZhang, YYen_US
dc.contributor.authorLiu, YJen_US
dc.contributor.authorRochaSanchez, Sen_US
dc.contributor.authorXiao, Pen_US
dc.contributor.authorRecker, RRen_US
dc.contributor.authorDeng, HWen_US
dc.date.accessioned2012-12-19T09:50:36Z-
dc.date.available2012-12-19T09:50:36Z-
dc.date.issued2004en_US
dc.identifier.citationBmc Genetics, 2004, v. 5en_US
dc.identifier.issn1471-2156en_US
dc.identifier.urihttp://hdl.handle.net/10722/178902-
dc.description.abstractBackground: Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. Results: To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. Conclusion: A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups. ©2004 Dvornyk 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.titleCurrent limitations of SNP data from the public domain for studies of complex disorders: A test for ten candidate genes for obesity and osteoporosisen_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.doi10.1186/1471-2156-5-4en_US
dc.identifier.pmid15113403-
dc.identifier.scopuseid_2-s2.0-2442684156en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-2442684156&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume5en_US
dc.identifier.isiWOS:000221187100001-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridDvornyk, V=6701789786en_US
dc.identifier.scopusauthoridLong, JR=36120777800en_US
dc.identifier.scopusauthoridXiong, DH=7007033697en_US
dc.identifier.scopusauthoridLiu, PY=7404618030en_US
dc.identifier.scopusauthoridZhao, LJ=7404455505en_US
dc.identifier.scopusauthoridShen, H=36126870600en_US
dc.identifier.scopusauthoridZhang, YY=12781205700en_US
dc.identifier.scopusauthoridLiu, YJ=36065513000en_US
dc.identifier.scopusauthoridRochaSanchez, S=6508079951en_US
dc.identifier.scopusauthoridXiao, P=34573749200en_US
dc.identifier.scopusauthoridRecker, RR=7007086875en_US
dc.identifier.scopusauthoridDeng, HW=34568563000en_US
dc.identifier.citeulike11225864-

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