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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

Scatter plot of pooled genotype data. Predicted allele frequencies of ~31,000 randomly selected SNPs in LOAD case and control DNA pools predicted by the Illumina HumanHap300 array. Averaging three case and four control arrays, we obtain a correlation r = 0.998.
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Figure 1: Scatter plot of pooled genotype data. Predicted allele frequencies of ~31,000 randomly selected SNPs in LOAD case and control DNA pools predicted by the Illumina HumanHap300 array. Averaging three case and four control arrays, we obtain a correlation r = 0.998.

Mentions: Genome-wide pooled genotyping was carried out on the Illumina HumanHap300 and Illumina Sentrix HumanHap240S arrays assaying 561,494 SNPs. Frequencies for each SNP were averaged over four replicate case and three replicate control arrays for the Illumina HumanHap300 and eight each for the Sentrix HumanHap240S arrays. The predicted averaged patient and control allele frequencies showed as expected a very high Pearson correlation with each other of r = 0.998, indicating a low technical variability of the method. Figure 1 shows predicted allele frequencies in case and control pools determined using the Illumina HumanHap300 platform. Data from the Illumina Sentrix HumanHap240S arrays showed similarly high correlations (r = 0.997). Predicted allele frequencies were compared with actual population allele frequencies (1958 Birth Cohort controls genotyped with the same HumanHap300) and gave a very good correlation of 0.969 (Figure 2). This indicates that even uncorrected data from pooling on this platform predict fairly well the true absolute allele frequencies of SNPs.


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)

Scatter plot of pooled genotype data. Predicted allele frequencies of ~31,000 randomly selected SNPs in LOAD case and control DNA pools predicted by the Illumina HumanHap300 array. Averaging three case and four control arrays, we obtain a correlation r = 0.998.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Scatter plot of pooled genotype data. Predicted allele frequencies of ~31,000 randomly selected SNPs in LOAD case and control DNA pools predicted by the Illumina HumanHap300 array. Averaging three case and four control arrays, we obtain a correlation r = 0.998.
Mentions: Genome-wide pooled genotyping was carried out on the Illumina HumanHap300 and Illumina Sentrix HumanHap240S arrays assaying 561,494 SNPs. Frequencies for each SNP were averaged over four replicate case and three replicate control arrays for the Illumina HumanHap300 and eight each for the Sentrix HumanHap240S arrays. The predicted averaged patient and control allele frequencies showed as expected a very high Pearson correlation with each other of r = 0.998, indicating a low technical variability of the method. Figure 1 shows predicted allele frequencies in case and control pools determined using the Illumina HumanHap300 platform. Data from the Illumina Sentrix HumanHap240S arrays showed similarly high correlations (r = 0.997). Predicted allele frequencies were compared with actual population allele frequencies (1958 Birth Cohort controls genotyped with the same HumanHap300) and gave a very good correlation of 0.969 (Figure 2). This indicates that even uncorrected data from pooling on this platform predict fairly well the true absolute allele frequencies of SNPs.

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