The correlation was significantly improved from r = 0.47 using the single markers PRO-C3 to r = 0.62 for model A. A multiple marker approach combining the MELD score for liver function and the two novel ECM serological markers for fibrosis, model B, increased the correlation with HVPG to a higher level than observed for MELD alone (r = 0.75).
We used the single marker analysis function of NEO (LEO.NB.SingleMarker) score, which is the log10 probability of this model divided by the log10 probability of the next best fitting alternative model [ 34].
To scan phenotypes against the genome-wide SNP genotype data for association between trait and SNP, we used the single-marker mixed model [ 12] (Methods).
PLINK was used in the single marker GWAS, and INTERSNP was used to perform the two-marker GWIS, focusing only on SNPs with p ≤ 0.01 for the GWAS analysis.
To correct for multiple testing, Bonferroni correction for the number of studied SNPs (n = 10) was used in the single marker analysis and permutation (10 000 permutations) was used in the sliding window analyses.
Young bulls were selected using strategies based on 1) the single marker with greatest contrast (BEST1), 2) the sum of n greatest contrasts (BESTn), 3) the best n contrasts, limited to one per chromosome (LIMn), 4) the sum of all contrasts exceeding a given threshold n (THRESn), and 5) the sum of contrasts exceeding a threshold, but limited to one per chromosome (LIMT).
The low expression group was used as a reference in the single marker analyses.
(Studies that would use deletion of RD711 as the single marker to define M. africanum West Aftican-1 strains may therefore risk mis-categorizing some isolates).
In the OSNA assay, which used the CK19 single marker, it was reported that in an examination of 346 ALNs from 32 patients, sensitivity was 96.3%, specificity was 94.7% and the concordance rate was 94.8% (Visser et al, 2008).
