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Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE.

Wijsman EM, Pankratz ND, Choi Y, Rothstein JH, Faber KM, Cheng R, Lee JH, Bird TD, Bennett DA, Diaz-Arrastia R, Goate AM, Farlow M, Ghetti B, Sweet RA, Foroud TM, Mayeux R, NIA-LOAD/NCRAD Family Study Gro - PLoS Genet. (2011)

Bottom Line: Late-onset Alzheimer's disease (LOAD) is the most common form of dementia in the elderly.Association in this gene was replicated in an independent sample consisting of three cohorts.We suggest that similar adjustments may also be needed for many other large multi-site studies.

View Article: PubMed Central - PubMed

Affiliation: Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America.

ABSTRACT
Late-onset Alzheimer's disease (LOAD) is the most common form of dementia in the elderly. The National Institute of Aging-Late Onset Alzheimer's Disease Family Study and the National Cell Repository for Alzheimer's Disease conducted a joint genome-wide association study (GWAS) of multiplex LOAD families (3,839 affected and unaffected individuals from 992 families plus additional unrelated neurologically evaluated normal subjects) using the 610 IlluminaQuad panel. This cohort represents the largest family-based GWAS of LOAD to date, with analyses limited here to the European-American subjects. SNPs near APOE gave highly significant results (e.g., rs2075650, p = 3.2×10(-81)), but no other genome-wide significant evidence for association was obtained in the full sample. Analyses that stratified on APOE genotypes identified SNPs on chromosome 10p14 in CUGBP2 with genome-wide significant evidence for association within APOE ε4 homozygotes (e.g., rs201119, p = 1.5×10(-8)). Association in this gene was replicated in an independent sample consisting of three cohorts. There was evidence of association for recently-reported LOAD risk loci, including BIN1 (rs7561528, p = 0.009 with, and p = 0.03 without, APOE adjustment) and CLU (rs11136000, p = 0.023 with, and p = 0.008 without, APOE adjustment), with weaker support for CR1. However, our results provide strong evidence that association with PICALM (rs3851179, p = 0.69 with, and p = 0.039 without, APOE adjustment) and EXOC3L2 is affected by correlation with APOE, and thus may represent spurious association. Our results indicate that genetic structure coupled with ascertainment bias resulting from the strong APOE association affect genome-wide results and interpretation of some recently reported associations. We show that a locus such as APOE, with large effects and strong association with disease, can lead to samples that require appropriate adjustment for this locus to avoid both false positive and false negative evidence of association. We suggest that similar adjustments may also be needed for many other large multi-site studies.

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Quality control evaluation of association tests in the CCun and CCall samples.Panels A, B: Quantile difference plots for association tests excluding SNPs in the APOE region; and panel C: −log10(p) for the same analyses for the 95 SNPs in the APOE region. For panels A and B, results are shown, for N tests, as the difference of the ith of N ordered observed (−log10(pi)) and expected (−log10(i/N)) quantiles plotted against the expected quantiles. A: results for the CCun sample, with grey: PCA adjusted; magenta: unadjusted analysis; cyan: ε4 adjustment; black: full adjustment. B: results for the sample containing related individuals; grey: unadjusted analysis of NW subgroup; magenta: unadjusted analysis of CCall; cyan: ε4-stratified analysis of CCall; black: full adjustment. C: UN depicts results for analysis of CCun; REL depicts results for analysis of the larger sample, in both cases for the same four conditions and colors as in panels A and B.
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pgen-1001308-g006: Quality control evaluation of association tests in the CCun and CCall samples.Panels A, B: Quantile difference plots for association tests excluding SNPs in the APOE region; and panel C: −log10(p) for the same analyses for the 95 SNPs in the APOE region. For panels A and B, results are shown, for N tests, as the difference of the ith of N ordered observed (−log10(pi)) and expected (−log10(i/N)) quantiles plotted against the expected quantiles. A: results for the CCun sample, with grey: PCA adjusted; magenta: unadjusted analysis; cyan: ε4 adjustment; black: full adjustment. B: results for the sample containing related individuals; grey: unadjusted analysis of NW subgroup; magenta: unadjusted analysis of CCall; cyan: ε4-stratified analysis of CCall; black: full adjustment. C: UN depicts results for analysis of CCun; REL depicts results for analysis of the larger sample, in both cases for the same four conditions and colors as in panels A and B.

Mentions: The distribution of p-values obtained from the unadjusted genome scans deviated from a uniform distribution, suggesting the presence of uncorrected confounding. This effect was mild near the median test value (λ = 0.97 for CCun, λ = 1.02 for CCall) but more apparent in the tails of the distribution, providing evidence for potential confounding in analysis of both samples (Figure 6A, 6B; magenta points; Figure S2). Some of the deviation from the distribution is likely to be attributable to the greater sensitivity to HWD for the allele-based tests than for logistic regression in CCun (Figures S2, S3, CCun results). However, deviation from the distribution in the direction of an increased type I error over the nominal level was especially marked in the upper 0.1% of the tail of the distribution for the unadjusted analysis of the CCun sample even under analysis with logistic regression (Figure S4), and in the upper 1% for the CCall sample (Figure 6A, 6B, magenta points). The excess fraction of small p-values was not explained by SNPs in the APOE region (Figure 6C), some of which had, as expected, much more extreme p-values. This deviation from the distribution was not explained by inadequate correction for relationships in the CCall sample since the same excess pattern of extreme p-values occurred in the analysis of both the CCun and CCall samples, and over a wider range of p-values when the CCun sample was analyzed with a chi-square test instead of with logistic regression (Figure S2). Control for test statistic inflation was also not achieved by incorporation of the first four principal components as covariates [64] (Figure 6A, grey points; Figure S3), or by restricting analysis to the more uniform NW group (Figure 6B, grey points).


Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE.

Wijsman EM, Pankratz ND, Choi Y, Rothstein JH, Faber KM, Cheng R, Lee JH, Bird TD, Bennett DA, Diaz-Arrastia R, Goate AM, Farlow M, Ghetti B, Sweet RA, Foroud TM, Mayeux R, NIA-LOAD/NCRAD Family Study Gro - PLoS Genet. (2011)

Quality control evaluation of association tests in the CCun and CCall samples.Panels A, B: Quantile difference plots for association tests excluding SNPs in the APOE region; and panel C: −log10(p) for the same analyses for the 95 SNPs in the APOE region. For panels A and B, results are shown, for N tests, as the difference of the ith of N ordered observed (−log10(pi)) and expected (−log10(i/N)) quantiles plotted against the expected quantiles. A: results for the CCun sample, with grey: PCA adjusted; magenta: unadjusted analysis; cyan: ε4 adjustment; black: full adjustment. B: results for the sample containing related individuals; grey: unadjusted analysis of NW subgroup; magenta: unadjusted analysis of CCall; cyan: ε4-stratified analysis of CCall; black: full adjustment. C: UN depicts results for analysis of CCun; REL depicts results for analysis of the larger sample, in both cases for the same four conditions and colors as in panels A and B.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3040659&req=5

pgen-1001308-g006: Quality control evaluation of association tests in the CCun and CCall samples.Panels A, B: Quantile difference plots for association tests excluding SNPs in the APOE region; and panel C: −log10(p) for the same analyses for the 95 SNPs in the APOE region. For panels A and B, results are shown, for N tests, as the difference of the ith of N ordered observed (−log10(pi)) and expected (−log10(i/N)) quantiles plotted against the expected quantiles. A: results for the CCun sample, with grey: PCA adjusted; magenta: unadjusted analysis; cyan: ε4 adjustment; black: full adjustment. B: results for the sample containing related individuals; grey: unadjusted analysis of NW subgroup; magenta: unadjusted analysis of CCall; cyan: ε4-stratified analysis of CCall; black: full adjustment. C: UN depicts results for analysis of CCun; REL depicts results for analysis of the larger sample, in both cases for the same four conditions and colors as in panels A and B.
Mentions: The distribution of p-values obtained from the unadjusted genome scans deviated from a uniform distribution, suggesting the presence of uncorrected confounding. This effect was mild near the median test value (λ = 0.97 for CCun, λ = 1.02 for CCall) but more apparent in the tails of the distribution, providing evidence for potential confounding in analysis of both samples (Figure 6A, 6B; magenta points; Figure S2). Some of the deviation from the distribution is likely to be attributable to the greater sensitivity to HWD for the allele-based tests than for logistic regression in CCun (Figures S2, S3, CCun results). However, deviation from the distribution in the direction of an increased type I error over the nominal level was especially marked in the upper 0.1% of the tail of the distribution for the unadjusted analysis of the CCun sample even under analysis with logistic regression (Figure S4), and in the upper 1% for the CCall sample (Figure 6A, 6B, magenta points). The excess fraction of small p-values was not explained by SNPs in the APOE region (Figure 6C), some of which had, as expected, much more extreme p-values. This deviation from the distribution was not explained by inadequate correction for relationships in the CCall sample since the same excess pattern of extreme p-values occurred in the analysis of both the CCun and CCall samples, and over a wider range of p-values when the CCun sample was analyzed with a chi-square test instead of with logistic regression (Figure S2). Control for test statistic inflation was also not achieved by incorporation of the first four principal components as covariates [64] (Figure 6A, grey points; Figure S3), or by restricting analysis to the more uniform NW group (Figure 6B, grey points).

Bottom Line: Late-onset Alzheimer's disease (LOAD) is the most common form of dementia in the elderly.Association in this gene was replicated in an independent sample consisting of three cohorts.We suggest that similar adjustments may also be needed for many other large multi-site studies.

View Article: PubMed Central - PubMed

Affiliation: Division of Medical Genetics, University of Washington, Seattle, Washington, United States of America.

ABSTRACT
Late-onset Alzheimer's disease (LOAD) is the most common form of dementia in the elderly. The National Institute of Aging-Late Onset Alzheimer's Disease Family Study and the National Cell Repository for Alzheimer's Disease conducted a joint genome-wide association study (GWAS) of multiplex LOAD families (3,839 affected and unaffected individuals from 992 families plus additional unrelated neurologically evaluated normal subjects) using the 610 IlluminaQuad panel. This cohort represents the largest family-based GWAS of LOAD to date, with analyses limited here to the European-American subjects. SNPs near APOE gave highly significant results (e.g., rs2075650, p = 3.2×10(-81)), but no other genome-wide significant evidence for association was obtained in the full sample. Analyses that stratified on APOE genotypes identified SNPs on chromosome 10p14 in CUGBP2 with genome-wide significant evidence for association within APOE ε4 homozygotes (e.g., rs201119, p = 1.5×10(-8)). Association in this gene was replicated in an independent sample consisting of three cohorts. There was evidence of association for recently-reported LOAD risk loci, including BIN1 (rs7561528, p = 0.009 with, and p = 0.03 without, APOE adjustment) and CLU (rs11136000, p = 0.023 with, and p = 0.008 without, APOE adjustment), with weaker support for CR1. However, our results provide strong evidence that association with PICALM (rs3851179, p = 0.69 with, and p = 0.039 without, APOE adjustment) and EXOC3L2 is affected by correlation with APOE, and thus may represent spurious association. Our results indicate that genetic structure coupled with ascertainment bias resulting from the strong APOE association affect genome-wide results and interpretation of some recently reported associations. We show that a locus such as APOE, with large effects and strong association with disease, can lead to samples that require appropriate adjustment for this locus to avoid both false positive and false negative evidence of association. We suggest that similar adjustments may also be needed for many other large multi-site studies.

Show MeSH
Related in: MedlinePlus