https://ogma.newcastle.edu.au/vital/access/ /manager/Index ${session.getAttribute("locale")} 5 Choosing between per-genotype, per-allele, and trend approaches for initial detection of gene-disease association https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:7642 Sat 24 Mar 2018 08:36:03 AEDT ]]> The quality of meta-analyses of Genetic Association Studies: a review with recommendations https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:7108 Sat 24 Mar 2018 08:34:12 AEDT ]]> Shared genetic susceptibility to ischemic stroke and coronary artery disease : a genome-wide analysis of common variants https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:21442 x10^-8) for the combined phenotype of IS or CAD and 17 loci passed genome-wide significance for LAS or CAD. Because these loci had prior evidence for genome-wide significance for CAD, we specifically analyzed the respective signals for IS and LAS and found evidence for association at chr12q24/SH2B3 (P_IS=1.62x10^-7) and ABO (P_IS=2.6x10^-4), as well as at HDAC9 (P_LAS=2.32x10-12), 9p21 (P_LAS=3.70x10^-6), RAI1-PEMT-RASD1 (P_LAS=2.69x10^-5), EDNRA (P_LAS=7.29x10^-4), and CYP17A1-CNNM2-NT5C2 (P_LAS=4.9x10^-4). Conclusions-Our results demonstrate substantial overlap in the genetic risk of IS and particularly the LAS subtype with CAD.]]> Sat 24 Mar 2018 08:05:46 AEDT ]]> SNP prioritization using a Bayesian probability of association https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:19473 P-values alone, but researchers sometimes take account of external annotation information about the SNPs such as whether the SNP lies close to a good candidate gene. Using external information in this way is inherently subjective and is often not formalized, making the analysis difficult to reproduce. Building on previous work that has identified 14 important types of external information, we present an approximate Bayesian analysis that produces an estimate of the probability of association. The calculation combines four sources of information: the genome-wide data, SNP information derived from bioinformatics databases, empirical SNP weights, and the researchers’ subjective prior opinions. The calculation is fast enough that it can be applied to millions of SNPS and although it does rely on subjective judgments, those judgments are made explicit so that the final SNP selection can be reproduced. We show that the resulting probability of association is intuitively more appealing than the P-value because it is easier to interpret and it makes allowance for the power of the study. We illustrate the use of the probability of association for SNP prioritization by applying it to a meta-analysis of kidney function genome-wide association studies and demonstrate that SNP selection performs better using the probability of association compared with P-values alone.]]> Sat 24 Mar 2018 08:02:21 AEDT ]]> The meta-analysis of genome-wide association studies https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:17898 Sat 24 Mar 2018 07:56:18 AEDT ]]> Methods for meta-analyses of genome-wide association studies: critical assessment of empirical evidence https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:19432 Sat 24 Mar 2018 07:51:57 AEDT ]]> How should we use information about HWE in the meta-analyses of genetic association studies? https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:4619 Sat 24 Mar 2018 07:21:53 AEDT ]]> Importance of different types of prior knowledge in selecting genome-wide findings for follow-up https://ogma.newcastle.edu.au/vital/access/ /manager/Repository/uon:19470 Fri 22 May 2020 16:37:38 AEST ]]>