Centro de Investigación en Biología Celular y Molecular, Ciudad de la Investigación, Universidad de Costa Rica, San José, Costa Rica.
BMC Genet. 2005 Dec 30;6 Suppl 1(Suppl 1):S86. doi: 10.1186/1471-2156-6-S1-S86.
Linkage disequilibrium (LD) content was calculated for the Genetic Analysis Workshop 14 Affymetrix and Illumina single-nucleotide polymorphism (SNP) genome scans of the Collaborative Study on the Genetics of Alcoholism samples. Pair-wise LD was measured as both D' and r2 on 505 pedigree founder individuals. The r2 estimates were then used to correct the multipoint identity by descent matrix (MIBD) calculation to account for LD and LOD scores on chromosomes 3 and 18 were calculated for COGA's ttdt3 electrophysiological trait using those MIBDs. Extensive LD was observed throughout both marker sets, and it was higher in Affymetrix's more dense SNP map. However, SNP density did not solely account for Affymetrix's higher LD. MIBD estimation procedures assume linkage equilibrium to construct genotypes of non-genotyped pedigree founder individuals, and dense SNP genotyping maps are likely to contain moderate to high LD between markers. LOD score plots calculated after correction for LD followed the same general pattern as uncorrected ones. Since in our study almost half of the pedigree founders were genotyped, it is possible that LD had a minor impact on the LOD scores. Caution should probably be taken when using high density SNP maps when many non-genotyped founders are present in the study pedigrees.
连锁不平衡（LD）含量的计算是基于遗传分析研讨会 14 阿菲米亚和因美纳单核苷酸多态性（SNP）基因组扫描的酒精中毒协作研究样本。在 505 个系谱创始人个体上，通过 D'和 r2 来测量成对 LD。然后使用 r2 估计值来校正多点同源关系矩阵（MIBD）的计算，以解释 LD，并用这些 MIBDs 计算 COGA 的 ttdt3 电生理特征的染色体 3 和 18 的 LOD 得分。在两个标记组中都观察到了广泛的 LD，并且在 Affymetrix 的更密集的 SNP 图谱中更高。然而，SNP 密度并不能完全解释 Affymetrix 更高的 LD。MIBD 估计程序假设连锁平衡，以构建未分型系谱创始人个体的基因型，并且密集的 SNP 基因分型图谱中标记之间可能存在中度到高度的 LD。在 LD 校正后计算的 LOD 得分图遵循与未校正的相同的总体模式。由于在我们的研究中，几乎一半的系谱创始人被分型，因此 LD 可能对 LOD 得分有较小的影响。当研究谱系中有许多未分型的创始人时，使用高密度 SNP 图谱时应谨慎。
