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Empirical characteristics of family-based linkage to a complex trait: the ADIPOQ region and adiponectin levels.

Abstract：

:We previously identified a low-frequency (1.1 %) coding variant (G45R; rs200573126) in the adiponectin gene (ADIPOQ) which was the basis for a multipoint microsatellite linkage signal (LOD = 8.2) for plasma adiponectin levels in Hispanic families. We have empirically evaluated the ability of data from targeted common variants, exome chip genotyping, and genome-wide association study data to detect linkage and association to adiponectin protein levels at this locus. Simple two-point linkage and association analyses were performed in 88 Hispanic families (1,150 individuals) using 10,958 SNPs on chromosome 3. Approaches were compared for their ability to map the functional variant, G45R, which was strongly linked (two-point LOD = 20.98) and powerfully associated (p value = 8.1 × 10(-50)). Over 450 SNPs within a broad 61 Mb interval around rs200573126 showed nominal evidence of linkage (LOD > 3) but only four other SNPs in this region were associated with p values < 1.0 × 10(-4). When G45R was accounted for, the maximum LOD score across the interval dropped to 4.39 and the best p value was 1.1 × 10(-5). Linked and/or associated variants ranged in frequency (0.0018-0.50) and type (coding, non-coding) and had little detectable linkage disequilibrium with rs200573126 (r (2) < 0.20). In addition, the two-point linkage approach empirically outperformed multipoint microsatellite and multipoint SNP analysis. In the absence of data for rs200573126, family-based linkage analysis using a moderately dense SNP dataset, including both common and low-frequency variants, resulted in stronger evidence for an adiponectin locus than association data alone. Thus, linkage analysis can be a useful tool to facilitate identification of high-impact genetic variants.

journal_name

Hum Genet

journal_title

Human genetics

authors

Hellwege JN,Palmer ND,Mark Brown W,Ziegler JT,Sandy An S,Guo X,Ida Chen YD,Taylor K,Hawkins GA,Ng MC,Speliotes EK,Lorenzo C,Norris JM,Rotter JI,Wagenknecht LE,Langefeld CD,Bowden DW

doi

10.1007/s00439-014-1511-8

subject

Has Abstract

pub_date

2015-02-01 00:00:00

pages

203-13

issue

2

eissn

0340-6717

issn

1432-1203

journal_volume

134

pub_type

临床试验,杂志文章

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