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All candidate variables for histologic marker analysis were p53, Ki67, TS, BAX, HIF1α, ALDH1, CD166, p21, EpCAM, CD44, CD133, which were selected due to potential candidates for cancer stem cell markers or histologic prognostic factors according to recent research on rectal cancer, with consideration of and technical availability [ 7, 11- 17].
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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).
Additional marker analysis is needed to confirm if this holds true also for the nasotemporal axis of the eye.
Therefore, the initial single marker analysis was used to identify SNPs with suggestive effects on the CM phenotype and the subsequent analysis was pursued in the context of haplotype association using corrected P values (see methods section).
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.
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.
SRAP marker analysis was conducted according to [ 82].
The SSR marker analysis was conducted as previously described [ 19].
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