A novel intronic polymorphism of ABCA1 gene reveals risk for sporadic Alzheimer's disease in Chinese
Identifieur interne : 001133 ( Main/Exploration ); précédent : 001132; suivant : 001134A novel intronic polymorphism of ABCA1 gene reveals risk for sporadic Alzheimer's disease in Chinese
Auteurs : Leung Wing Chu [Hong Kong] ; Yan Li [Hong Kong] ; Zhong Li [Hong Kong, République populaire de Chine] ; Alan Yb Tang [Hong Kong] ; Bernard My Cheung [Hong Kong] ; Raymond Yh Leung [Hong Kong] ; Ping-Yiu Yik [Hong Kong] ; Dong-Yan Jin [Hong Kong] ; You-Qiang Song [Hong Kong]Source :
- American Journal of Medical Genetics Part B: Neuropsychiatric Genetics [ 1552-4841 ] ; 2007-12-05.
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Abstract
Recent genetic studies have shown that variants of the ATP‐binding cassette transporter A1, ABCA1, may be implicated in the pathogenesis of Alzheimer's disease (AD). In this case‐control study, a panel of 19 single nucleotide polymorphisms (SNP) (including three amino‐acid‐coding SNPs used for replication of previous work, and 16 newly selected intronic tag SNPs) was genotyped. Nominally significant single marker P‐values were observed in four SNPs, with the highest score of 0.003 for rs2297404 (OR = 1.88, 95%CI 1.23–2.87). In addition, six distinct linkage disequilibrium (LD) blocks were detected. LD block1 harbored three nominally significant SNPs (rs2297404, rs2230808, and rs2020927), and showed a different haplotype structure in the affected and unaffected groups. Of the four haplotypes identified, haplotype2 (CAC) was more prevalent in the disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over‐represented in the healthy controls (0.595 in control vs. 0.493 in AD), indicating disease risk conferring possibility of haplotype2. After doubling the sample size, the three nominally significant SNPs were still significantly associated with AD. Although coding SNP (rs2230808) was confirmed to have a significant association with AD, prediction of the effects of an amino acid substitution SNP rs2230808 (R1587K) on the three‐dimensional structure and function of the ABCA1 protein using PolyPhen program revealed that it is unlikely to be functionally significant. However, the adjacent rs2297404 in the same LD block is potentially functionally significant because of its position in the immediate vicinity of a splicing branch site. Further functional analysis of this polymorphism should be a high priority. © 2007 Wiley‐Liss, Inc.
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DOI: 10.1002/ajmg.b.30525
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Genet.</title><idno type="ISSN">1552-4841</idno><idno type="eISSN">1552-485X</idno><imprint><publisher>Wiley Subscription Services, Inc., A Wiley Company</publisher><pubPlace>Hoboken</pubPlace><date type="published" when="2007-12-05">2007-12-05</date><biblScope unit="volume">144B</biblScope><biblScope unit="issue">8</biblScope><biblScope unit="page" from="1007">1007</biblScope><biblScope unit="page" to="1013">1013</biblScope></imprint><idno type="ISSN">1552-4841</idno></series><idno type="istex">F110B2CE3F40DA62FB8E93CD9CE523A9E28CE616</idno><idno type="DOI">10.1002/ajmg.b.30525</idno><idno type="ArticleID">AJMG30525</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1552-4841</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>ABCA1</term><term>Alzheimer's disease</term><term>association</term><term>case‐control</term><term>haplotype</term><term>single nucleotide polymorphisms (SNP)</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recent genetic studies have shown that variants of the ATP‐binding cassette transporter A1, ABCA1, may be implicated in the pathogenesis of Alzheimer's disease (AD). In this case‐control study, a panel of 19 single nucleotide polymorphisms (SNP) (including three amino‐acid‐coding SNPs used for replication of previous work, and 16 newly selected intronic tag SNPs) was genotyped. Nominally significant single marker P‐values were observed in four SNPs, with the highest score of 0.003 for rs2297404 (OR = 1.88, 95%CI 1.23–2.87). In addition, six distinct linkage disequilibrium (LD) blocks were detected. LD block1 harbored three nominally significant SNPs (rs2297404, rs2230808, and rs2020927), and showed a different haplotype structure in the affected and unaffected groups. Of the four haplotypes identified, haplotype2 (CAC) was more prevalent in the disease group (0.323 in AD vs. 0.202 in control); while haplotype1 (TGG) was over‐represented in the healthy controls (0.595 in control vs. 0.493 in AD), indicating disease risk conferring possibility of haplotype2. After doubling the sample size, the three nominally significant SNPs were still significantly associated with AD. Although coding SNP (rs2230808) was confirmed to have a significant association with AD, prediction of the effects of an amino acid substitution SNP rs2230808 (R1587K) on the three‐dimensional structure and function of the ABCA1 protein using PolyPhen program revealed that it is unlikely to be functionally significant. However, the adjacent rs2297404 in the same LD block is potentially functionally significant because of its position in the immediate vicinity of a splicing branch site. Further functional analysis of this polymorphism should be a high priority. © 2007 Wiley‐Liss, Inc.</div></front></TEI><affiliations><list><country><li>Hong Kong</li><li>République populaire de Chine</li></country><region><li>Guangdong</li></region><settlement><li>Jiangmen</li></settlement></list><tree><country name="Hong Kong"><noRegion><name sortKey="Chu, Leung Wing" sort="Chu, Leung Wing" uniqKey="Chu L" first="Leung Wing" last="Chu">Leung Wing Chu</name></noRegion><name sortKey="Cheung, Bernard My" sort="Cheung, Bernard My" uniqKey="Cheung B" first="Bernard My" last="Cheung">Bernard My Cheung</name><name sortKey="Jin, Dong An" sort="Jin, Dong An" uniqKey="Jin D" first="Dong-Yan" last="Jin">Dong-Yan Jin</name><name sortKey="Leung, Raymond Yh" sort="Leung, Raymond Yh" uniqKey="Leung R" first="Raymond Yh" last="Leung">Raymond Yh Leung</name><name sortKey="Li, Yan" sort="Li, Yan" uniqKey="Li Y" first="Yan" last="Li">Yan Li</name><name sortKey="Li, Zhong" sort="Li, Zhong" uniqKey="Li Z" first="Zhong" last="Li">Zhong Li</name><name sortKey="Song, You Iang" sort="Song, You Iang" uniqKey="Song Y" first="You-Qiang" last="Song">You-Qiang Song</name><name sortKey="Song, You Iang" sort="Song, You Iang" uniqKey="Song Y" first="You-Qiang" last="Song">You-Qiang Song</name><name sortKey="Song, You Iang" sort="Song, You Iang" uniqKey="Song Y" first="You-Qiang" last="Song">You-Qiang Song</name><name sortKey="Tang, Alan Yb" sort="Tang, Alan Yb" uniqKey="Tang A" first="Alan Yb" last="Tang">Alan Yb Tang</name><name sortKey="Yik, Ping Iu" sort="Yik, Ping Iu" uniqKey="Yik P" first="Ping-Yiu" last="Yik">Ping-Yiu Yik</name></country><country name="République populaire de Chine"><region name="Guangdong"><name sortKey="Li, Zhong" sort="Li, Zhong" uniqKey="Li Z" first="Zhong" last="Li">Zhong Li</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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