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A genome-wide association study for late-onset Alzheimer's disease using DNA pooling.

Abraham R, Moskvina V, Sims R, Hollingworth P, Morgan A, Georgieva L, Dowzell K, Cichon S, Hillmer AM, O'Donovan MC, Williams J, Owen MJ, Kirov G - BMC Med Genomics (2008)

Bottom Line: Five of seven tag SNPs chosen to cover LRAT showed significant association with LOAD with a SNP in intron 2 of LRAT, showing greatest evidence of association (rs201825, p-value = 6.1 x 10-7).We provide evidence for LRAT as a novel candidate gene for LOAD.LRAT plays a prominent role in the Vitamin A cascade, a system that has been previously implicated in LOAD.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Psychological Medicine, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK. AbrahamRA@Cardiff.ac.uk

ABSTRACT

Background: Late-onset Alzheimer's disease (LOAD) is an age related neurodegenerative disease with a high prevalence that places major demands on healthcare resources in societies with increasingly aged populations. The only extensively replicable genetic risk factor for LOAD is the apolipoprotein E gene. In order to identify additional genetic risk loci we have conducted a genome-wide association (GWA) study in a large LOAD case - control sample, reducing costs through the use of DNA pooling.

Methods: DNA samples were collected from 1,082 individuals with LOAD and 1,239 control subjects. Age at onset ranged from 60 to 95 and Controls were matched for age (mean = 76.53 years, SD = 33), gender and ethnicity. Equimolar amounts of each DNA sample were added to either a case or control pool. The pools were genotyped using Illumina HumanHap300 and Illumina Sentrix HumanHap240S arrays testing 561,494 SNPs. 114 of our best hit SNPs from the pooling data were identified and then individually genotyped in the case - control sample used to construct the pools.

Results: Highly significant association with LOAD was observed at the APOE locus confirming the validity of the pooled genotyping approach.For 109 SNPs outside the APOE locus, we obtained uncorrected p-values

Conclusion: We have validated the pooling method for GWA studies by both identifying the APOE locus and by observing a strong enrichment for significantly associated SNPs. We provide evidence for LRAT as a novel candidate gene for LOAD. LRAT plays a prominent role in the Vitamin A cascade, a system that has been previously implicated in LOAD.

No MeSH data available.


Related in: MedlinePlus

Plot of combined Z-test p-values against chromosomal location for pooled data. Out of 561,494 SNPs that were genotyped in our case – control pools, only 3 would have remained significant after Bonferroni correction for multiple testing, two of these SNPs are near the APOE gene on Chromosome 19. For a genome-wide association study on 500,000 markers (assuming that markers are independent) the significance level is 10-7. The line of genome-wide significance is plotted therefore at this level, although the combined Z-statistic provides only an approximation of the p-values produced from individual genotyping.
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Figure 3: Plot of combined Z-test p-values against chromosomal location for pooled data. Out of 561,494 SNPs that were genotyped in our case – control pools, only 3 would have remained significant after Bonferroni correction for multiple testing, two of these SNPs are near the APOE gene on Chromosome 19. For a genome-wide association study on 500,000 markers (assuming that markers are independent) the significance level is 10-7. The line of genome-wide significance is plotted therefore at this level, although the combined Z-statistic provides only an approximation of the p-values produced from individual genotyping.

Mentions: Figure 3 shows the combined Z-test p-value results for the whole genome. On the X-axis we have plotted the position in the genome by chromosome, and on the Y-axis the negative logarithm of the p-value. The strongest evidence for association with LOAD was observed with SNPs on chromosome 19 surrounding the APOE gene. In all, 7 SNPs within 71 kb were predicted by the pools to have allele frequency differences between 6% – 14% and "combined" p-values ranging from 9.0 × 10-5 to 3.6 × 10-22. No other region of the genome showed such a large number of significant markers over a relatively small region. Five of the seven SNPs were individually genotyped and were confirmed to be highly significant (p-value range 2.08 × 10-9 – 8.24 × 10-11, Table 1). All are in high linkage disequilibrium (LD) with the SNPs that define the APOE genotypes which are not themselves typed on the Illumina platform (Figure 4). The distributions of APOE alleles in this population are as follows:


A genome-wide association study for late-onset Alzheimer's disease using DNA pooling.

Abraham R, Moskvina V, Sims R, Hollingworth P, Morgan A, Georgieva L, Dowzell K, Cichon S, Hillmer AM, O'Donovan MC, Williams J, Owen MJ, Kirov G - BMC Med Genomics (2008)

Plot of combined Z-test p-values against chromosomal location for pooled data. Out of 561,494 SNPs that were genotyped in our case – control pools, only 3 would have remained significant after Bonferroni correction for multiple testing, two of these SNPs are near the APOE gene on Chromosome 19. For a genome-wide association study on 500,000 markers (assuming that markers are independent) the significance level is 10-7. The line of genome-wide significance is plotted therefore at this level, although the combined Z-statistic provides only an approximation of the p-values produced from individual genotyping.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570675&req=5

Figure 3: Plot of combined Z-test p-values against chromosomal location for pooled data. Out of 561,494 SNPs that were genotyped in our case – control pools, only 3 would have remained significant after Bonferroni correction for multiple testing, two of these SNPs are near the APOE gene on Chromosome 19. For a genome-wide association study on 500,000 markers (assuming that markers are independent) the significance level is 10-7. The line of genome-wide significance is plotted therefore at this level, although the combined Z-statistic provides only an approximation of the p-values produced from individual genotyping.
Mentions: Figure 3 shows the combined Z-test p-value results for the whole genome. On the X-axis we have plotted the position in the genome by chromosome, and on the Y-axis the negative logarithm of the p-value. The strongest evidence for association with LOAD was observed with SNPs on chromosome 19 surrounding the APOE gene. In all, 7 SNPs within 71 kb were predicted by the pools to have allele frequency differences between 6% – 14% and "combined" p-values ranging from 9.0 × 10-5 to 3.6 × 10-22. No other region of the genome showed such a large number of significant markers over a relatively small region. Five of the seven SNPs were individually genotyped and were confirmed to be highly significant (p-value range 2.08 × 10-9 – 8.24 × 10-11, Table 1). All are in high linkage disequilibrium (LD) with the SNPs that define the APOE genotypes which are not themselves typed on the Illumina platform (Figure 4). The distributions of APOE alleles in this population are as follows:

Bottom Line: Five of seven tag SNPs chosen to cover LRAT showed significant association with LOAD with a SNP in intron 2 of LRAT, showing greatest evidence of association (rs201825, p-value = 6.1 x 10-7).We provide evidence for LRAT as a novel candidate gene for LOAD.LRAT plays a prominent role in the Vitamin A cascade, a system that has been previously implicated in LOAD.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Psychological Medicine, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK. AbrahamRA@Cardiff.ac.uk

ABSTRACT

Background: Late-onset Alzheimer's disease (LOAD) is an age related neurodegenerative disease with a high prevalence that places major demands on healthcare resources in societies with increasingly aged populations. The only extensively replicable genetic risk factor for LOAD is the apolipoprotein E gene. In order to identify additional genetic risk loci we have conducted a genome-wide association (GWA) study in a large LOAD case - control sample, reducing costs through the use of DNA pooling.

Methods: DNA samples were collected from 1,082 individuals with LOAD and 1,239 control subjects. Age at onset ranged from 60 to 95 and Controls were matched for age (mean = 76.53 years, SD = 33), gender and ethnicity. Equimolar amounts of each DNA sample were added to either a case or control pool. The pools were genotyped using Illumina HumanHap300 and Illumina Sentrix HumanHap240S arrays testing 561,494 SNPs. 114 of our best hit SNPs from the pooling data were identified and then individually genotyped in the case - control sample used to construct the pools.

Results: Highly significant association with LOAD was observed at the APOE locus confirming the validity of the pooled genotyping approach.For 109 SNPs outside the APOE locus, we obtained uncorrected p-values

Conclusion: We have validated the pooling method for GWA studies by both identifying the APOE locus and by observing a strong enrichment for significantly associated SNPs. We provide evidence for LRAT as a novel candidate gene for LOAD. LRAT plays a prominent role in the Vitamin A cascade, a system that has been previously implicated in LOAD.

No MeSH data available.


Related in: MedlinePlus