These subpopulations (Tables 1 and 2; column 2) were chosen based on previous reports of markers expressed by human breast stem/progenitors, mouse mammary epithelial stem cells, and human breast tumor-initiating cells [ 10, 11].
The sample size estimate of seventeen subjects per group was based on previous data on oxidation and inflammation markers (markers of primary outcome) and subjected to a probability of error (α = 5%%) and to a test power (1 − β = 80%%).
The rationale for using selected markers was based on previous studies in human cartilage and the correlation analysis between markers of catabolism and anabolism for each disease.
The hypothesized groupings of Ag1, Ag4, As1, As8 and As9 were based on previous studies that used molecular markers to evaluate the genetic variation [ 17, 18, 20, 23, 52].
Based on previous results, deregulation of cell cycle markers can elicit apoptosis in post mitotic neurons, which is one of the primary mechanisms leading to cell death in degenerating neurons, including DArgic neurons [23].
Reliability from 3,000 markers is based on previous studies of actual genotypes [ 29, 30].
Lengths are based on previous estimation using highly scrutinized SSR markers [ 38] taking into consideration only the segregating part of these SSR maps, and on current observations using filtered but otherwise non-scrutinized SNP markers.
The selection of transcriptomic markers was based on previous findings from whole genome analyses and known mechanisms of the inflammatory response, and comprised various mediators of inflammation (cytokines, complement system), Danger-Associated Molecular Patterns (DAMPs) and Pattern Recognition Receptors (PRRs), and the heme degradation pathway.
The selection of these potential marker compounds was based on previous studies on COPD, i.e. either non-hypothesis/proteomics (SP-A) or hypothesis driven (SP-D, MMP-9) studies, which have indicated that especially these markers may predict COPD, its development and/or progression [ 4- 9].
Covariates were selected a priori based on previous research and included characteristics associated with inflammatory markers and LTL in previous research.
