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Background marker analysis was also done for the promising variants.
A trait-based marker analysis was used to identify QTLs for validation in BC2F5 generation.
GS3 marker analysis was carried out according to the protocol described by Fan et al. (2009) using primers SF28-U and SF28-L.
qSW5/GW5 marker analysis was conducted according to the method presented in Weng et al. (2008) using primers Indel2-F and Indel2-R, and GW8 marker analysis was carried out using indel markers to detect a 10-bp deletion in the promoter region (Additional file 8: Table S3).
The results for the third in silico QTL at rs3698264 (chromosome 1, 79.9 Mb, index 575, p-value 0.000034) appeared to be an isolated signal when only single marker analysis was considered.
Only the combinatory analysis of the CD8α and CD8β chain along with CD45RA, CCR7+, CD27 and CD28 marker analysis was able to segregate CD8 phenotypes in patients with MS from CD8+T-cells from healthy blood donors.
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Additional marker analysis is needed to confirm if this holds true also for the nasotemporal axis of the eye.
An alternative to single marker analysis is haplotype-based association analysis.
Single marker analysis is a useful tool for genetic association studies.
The LOD score curves obtained by single marker analysis are depicted in Figure 1.
Further research aimed at finding other sensitive biological markers in PE and for defining the best combination for marker analysis is warranted as well.
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