To estimate algorithm performance on novel samples, we performed leave-one-out cross-validation (LOOCV), in which the top-scoring pair as determined by N-1 samples is used to predict the left-out sample class.
For the HD samples, we performed a small-pool PCR as described in37 (Supplementary Fig. S7).
To further identify genome-wide H3.3 distribution changes after DAXX inhibition in PTEN-null/GBM-PDX samples, we performed unbiased chromatin immunoprecipitation sequencing (ChIP-seq) (Supplementary Fig. 9a).
Due to the strong cytoplasmic signal observed by immunostaining in the angiosarcoma samples, we performed a western blot on tissue sections from an angiosarcoma patient and confirmed that two bands could be detected by western blotting analysis, with the lower band matching the molecular weight reported for Myc-nick (Supplementary Fig. 7b).
Because of the predefined number of available biobank samples, we performed post hoc power calculations and included confidence intervals for MAF differences (according to [19]) (Additional file 1: Figure S1 and Table 1).
Results were expressed as area under the curve (AUC) of luminescence during the 20 min. For some samples, we performed several measurements to test reproducibility of the luminometric analysis under different conditions that might be encountered in clinical practice.
In addition to the comparison between the entire Argentinian and North American samples, we performed a more specific comparison between only the subgroups with early onset, defined as occurring at less than or equal to 21 years of age.
Since we compared distribution-free small-size samples, we performed non-parametric tests and reported median and quartiles data.
In an attempt to detect intact bacilli in these PCR-positive samples, we performed Ziehl-Nielsen staining.
To gain an overview of differential gene expression between the epicardial and muscle control samples, we performed an unsupervised analysis of the gene array data (SOM 2×2).
To examine whether this correlation held true in our HNSCC patient samples, we performed a global LOH analysis using 10K SNPChip data.
