HST -values are below the diagonal; TRANSMIT -values are above; estimated minor allele frequencies are on the left margin

<p><b>Copyright information:</b></p><p>Taken from "Identification of polymorphisms explaining a linkage signal: application to the GAW14 simulated data"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S88-S88.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866692.</p><p></p> The square identified by "i" represents the imost significant (by both HST and TRANSMIT) SNP pair ranked by the sum of the TRANSMIT and HST -values. For example, in the top panel, "3" (in the first row) means that HST and TRANSMIT -values for pair B8321–B8341 are both significant and the sum of their -values is the third most significant. Hj and Tj represent the jsignificant SNP pair by HST and TRANSMIT, respectively. Note, on the top panel, "2"-H2, "3"-H3 coincide; only "2" and "3" are identified. Similarly for the bottom panel, "4"-T5, "6"-H4 coincide and only "4" and "6" are identified

Identification of polymorphisms explaining a linkage signal: application to the GAW14 simulated data-0

<p><b>Copyright information:</b></p><p>Taken from "Identification of polymorphisms explaining a linkage signal: application to the GAW14 simulated data"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S88-S88.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866692.</p><p></p>l dotted line (-log0.05)

Sample characteristics of Alzheimer disease, fibrinogen, HDL and uric acid data in the genotyped and imputed sample.

<p>For continuous variables, mean value and standard deviation (in parenthesis) are presented, while for binary variables, the number of cases and its proportion (in parenthesis) are presented.</p

Results of top SNPs (p-value <1.25E-7) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using 550K genotype data and incorporated genotype data.

<p>Results of top SNPs (p-value <1.25E-7) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using 550K genotype data and incorporated genotype data.</p

Scatter plots of –log₁₀(p-value) from 550K GWAS and GWAS using incorporated genotype data.

<p>Scatter plots of –log₁₀(p-value) from 550K GWAS and GWAS using incorporated genotype data.</p

Example for pedigree splitting and trimming.

<p>Example for pedigree splitting and trimming.</p

Number of genome-wide significant SNPs (p-value <1.25E-7) with improved statistical significance (smaller p-value) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using incorporated genotype data (new GWAS).

<p>Number of genome-wide significant SNPs (p-value <1.25E-7) with improved statistical significance (smaller p-value) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using incorporated genotype data (new GWAS).</p

Scatter plot of MAF in well-genotyped sample and filtered (person_specific imputation certainty greater than 50%) imputed sample.

<p>Scatter plot of MAF in well-genotyped sample and filtered (person_specific imputation certainty greater than 50%) imputed sample.</p

Mean imputation certainty of the top SNPs in the entire 3121 imputed sample and in the person-specific certainty >0.5, SNP-specific certainty >0.6 and phenotyped sample.

†<p><b><i>N</i></b>: the number of phenotyped and imputed individuals with person-specific certainty >0.5 and SNP-specific certainty >0.6.</p

Top SNPs (p-value <1.25E-7) from GWAS of Alzheimer disease, fibrinogen, HDL and uric acid using 550K genotype data.

†<p>Position in base pairs, based on NCBI build 36.1 (hg18).</p>*<p>MAF is computed in genotyped and phenotyped sample.</p>††<p>rs4420638 is a marker of the APOE haplotype.</p