It has approximately 1,500 mapped DNA markers comprised of approximately 700 mapped unigenes with the remainder amplified fragment length polymorphisms (AFLPs), restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs) [ 14].
The sizes of the bands resolved by T-RFLP were determined by comparing their relative position with known size markers, comprised of bands equivalent to 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900 and 1000 bases of single-stranded DNA (microSTEP 15a [700 nm], Microzone, Lewes, UK).
Products from endotracheal tube extract PCRs were run alongside a marker comprising of an equal mixture of PCR products from the three known bacterial stains.
Moreover, the number of markers comprising bins of common frequency (6,894,397 markers with MAF > 0.05) is much lower than the number of markers comprising bins of low frequency (23,178,341 markers with MAF < 0.05), which usually have low imputation quality.
Altogether, genotyping data was obtained for a total of 169 markers, comprising 148 gene fragments (of which 139 developed using ICCARE) and 21 microsatellites from the GGA5 genetic map.
The 24 consensus LGs covered a distance of 1,320 cM, with a length ranging from 78 to 145 cM, and the distance between adjacent markers (comprising all types of markers without accessory markers) averaging 4 cM.
As an additional validation step we examined the expression profiles of a panel of 39 known cell-specific markers, comprised predominantly of CD antigens [see Additional file 1].
A panel of markers comprising KLK5, KLK6, KLK7 and B7-H4 baselevelsevels (c0) resulted in an improved AUC of 0.77 for predicting response to chemotherapy.
Promoter methylation was evaluated for the CIMP panel of markers comprising CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1, where PMR (percentage methylated reference) values were derived using the ALU normalisation control reaction (Weisenberger et al, 2006).
The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF atpH, and psbK psbI) loci.
