Research article
Data mining of high density genomic variant data for prediction of Alzheimer's disease risk
1 Computational Biosciences Program, School of Mathematics and Statistical Sciences, Arizona State University, 1711 South Rural Road, Tempe, Arizona, 85287-1804, USA
2 Department of Biomedical Informatics, Arizona State University, Mayo Clinic, Samuel C. Johnson Research Bldg. 13212 East Shea Boulevard, Scottsdale, Arizona 85259, USA
BMC Medical Genetics 2012, 13:7 doi:10.1186/1471-2350-13-7
Published: 25 January 2012Additional files
Additional file 1:
Table SA. Complete list of 199 SNPs from logistic regression approach I with corresponding pathway, disease or biological function information which may be pertinent to AD.
Format: XLSX Size: 81KB Download file
Additional file 2:
Figure S1. LD display for SNPs across the 300 kb region surrounding the ST5 locus. Top: Entrez gene track overlaid with Hapmap genotyped SNPs across a 300 kb pairs interval surrounding the ST5 locus. Bottom: zoomed LD SNP region. The SNPs identified, rs4910068 and rs10743089, were found to be in significant LD with a D' value of 0.83. Standard color scheme for Haploview: D' < 1 and LOD < 2 are white, D' = 1 and LOD < 2 are blue, D' < 1 and LOD ≥ 2 are shades of pink/red, D' = 1 and LOD ≥ 2 are bright red. LOD = log of the odds.
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Additional file 3:
Figure S2. LD display for SNPs across the 300 kb region surrounding the TRPC1 locus. Top: Entrez gene track overlaid with Hapmap genotyped SNPs across a 300 kb region surrounding the TRPC1 locus. Bottom two: zoomed LD SNP region. The SNPs identified, rs4259003, rs9784320, and rs2033912, were found to be in significant LD; rs4259003 and rs9784320, rs4259003 and rs2033912, and rs9784320 and rs2033912 with D' values of 1.0. Standard color scheme for Haploview: D' < 1 and LOD < 2 are white, D' = 1 and LOD < 2 are blue, D' < 1 and LOD ≥ 2 are shades of pink/red, D' = 1 and LOD ≥ 2 are bright red. LOD = log of the odds.
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Additional file 4:
Figure S3. LD display for SNPs across the 300 kb region surrounding the ATG10 locus. Top: Entrez gene track overlaid with Hapmap genotyped SNPs across a 300 kb region surrounding the ATG10 locus. Bottom three: zoomed LD SNP region. The SNPs identified, rs891159, rs1485587, and rs4703879, were found to be in significant LD; rs891159 and rs1485587, rs891159 and rs4703879, and rs1485587 and rs4703879 with D' = 1. Standard color scheme for Haploview: D' < 1 and LOD < 2 are white, D' = 1 and LOD < 2 are blue, D' < 1 and LOD ≥ 2 are shades of pink/red, D' = 1 and LOD ≥ 2 are bright red. LOD = log of the odds.
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Additional file 5:
Figure S4. LD display for SNPs across the 300 kb region surrounding the ANO3 locus. Top: Entrez gene track overlaid with Hapmap genotyped SNPs across a 300 kb region surrounding the ANO3 locus. Bottom two: zoomed LD SNP region. The SNPs identified, rs1389421, rs10834774, and rs11028909, were found to be in significant LD; rs1389421 and rs10834774, rs1389421 and rs10834774, and rs11028909 and rs10834774 with D' = 1. Standard color scheme for Haploview: D' < 1 and LOD < 2 are white, D' = 1 and LOD < 2 are blue, D' < 1 and LOD ≥ 2 are shades of pink/red, D' = 1 and LOD ≥ 2 are bright red. LOD = log of the odds.
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Additional file 6:
Figure S5. LD display for SNPs across the 300 kb region surrounding the NDUFA12 locus. Top: Entrez gene track overlaid with Hapmap genotyped SNPs across a 300 kb pairs interval surrounding the NDUFA12 locus. Bottom: zoomed LD SNP region. The SNPs identified, rs249153 and rs249154, were found to be in significant LD with D' = 1. Standard color scheme for Haploview: D' < 1 and LOD < 2 are white, D' = 1 and LOD < 2 are blue, D' < 1 and LOD ≥ 2 are shades of pink/red, D' = 1 and LOD ≥ 2 are bright red. LOD = log of the odds.
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Additional file 7:
Figure S6. LD display for SNPs across the 300 kb region surrounding the NISCH locus. Top: Entrez gene track overlaid with Hapmap genotyped SNPs across a 300 kb region surrounding the NISCH locus. Bottom: zoomed LD SNP region. The SNPs identified, rs6784615, rs9855470, rs6445486, rs10865972, rs4687619, and rs6810027, were found to be in significant LD; rs6784615 and rs9855470, rs6784615 and rs6445486, rs6784615 and rs10865972, rs6784615 and rs4687619, rs6784615 and rs6810027, rs9855470 and rs6445486, rs9855470 and rs10865972, rs9855470 and rs4687619, rs9855470 and rs6810027, rs6445486 and rs10865972, rs6445486 and rs4687619, rs6445486 and rs6810027, rs10865972 and rs4687619, rs10865972 and rs6810027, and rs4687619 and rs6810027 with D' values of 1. Standard color scheme for Haploview: D' < 1 and LOD < 2 are white, D' = 1 and LOD < 2 are blue, D' < 1 and LOD ≥ 2 are shades of pink/red, D' = 1 and LOD ≥ 2 are bright red. LOD = log of the odds.
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