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The chapter is divided into two principal sections: (1) a summary of factors that affect the quality of individual array results; and (2) a discussion of experimental design features and replication criteria that enable researchers to gain confidence in their findings.
With more stringent replication criteria, that requires LO D = 3 and maximum QTL LOD position in the 30–40 cM interval, 929 (59%) eQTL replicate.
The replication criteria used in our study were particularly strict and required a significant p-value in both, the family-based and the case-control association test in two different populations.
While only these six SNPs were found to be nominally significant in both, the TDT and the case-control analysis, and therefore fulfilled the formal replication criteria, 47 SNPs were significant in only one test, including two more SNPs in the 5p13.1 region (#79, #105), one in NELL1 (#116), and one in the IBD5 region (#191).
Three of these 49 loci were already known to be associated with AMD and the SNPs meeting our replication criteria (Table 1) from the remaining 46 loci were genotyped in a second, independent group of subjects with and without AMD from the Mayo Clinic.
Strict replication criteria were used in the single-marker analyses (Konig 2011).
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This replication criterion of at least one SNP with a 'meta- P' ≤ 0.05 is equivalent to the unadjusted minimum P-value approach.
For the gene-based analyses, a robust permutation-based approach, which accounts for LD structure and SNP number, was used to select genes for replication, the criteria for which were subsequently relaxed to avoid over-penalizing the larger, more relevant genes.
Second, the majority of studies described their procedures with sufficient detail for replication of criterion 8 - 'Was the executive of the index test described in sufficient detail to permit replication of the test?' (30/31, 97%) [6,7,17 22,24 44,64], enabling future comparison of newer screening tools to already evaluated tools.
Moreover, replication of psychometric criteria in follow-up studies is considered important since the validity and the usefulness of self-report instruments are empirical issues that depend on a growing body of evidence [ 18].
For a replication, the rejection criterion of the null hypothesis (β k =0) was a p v a l u e less than 0.05.
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