Supplementary Figures 1 - 11 from Expression Profiling of Archival Tumors for Long-term Health Studies

PDF file - 1787K, Supplemental Figure S1: Immunohistochemistry for selected proteins. Supplemental Figure S2: Pairwise scatterplots of technical variables for 1,003 DASL arrays from the NHS/HPFS study, including median value of Illumina control probes, sample age, RNA concentration, fraction of probes called present (p<0.05), and Interquartile Range (IQR). Supplemental Figure S3: Spatial distribution of sample-independent positive control probes (CY3_HYB) across the 12 96-well plates of the NHS/HPFS experiment. Supplemental Figure S4: Spearman correlation of expression profiles of individual technical replicates to the median pseudochip decreases with Interquartile Range (IQR), particularly for samples with IQR less than 1. Supplemental Figure S5: CAT-boxplots for six covariates available in the NHS/HPFS study, showing reproducibility of ranked lists of differentially expressed between two independent samples by plotting fractional concordance of the top n genes in each list on the y-axis, against n on the x-axis. Supplemental Figure S6: Examples of two of the "best" (0.1% and 0.2% quantile) and "worst" (99.8% and 99.9% quantile) probes for reproducibility as assessed by Spearman correlation, Euclidian Distance, and Manhattan Distance. Supplemental Figure S7: Reproducibility of individual probe intensity measurements. For samples passing quality control in the BC/A experiment, Spearman correlation between technical replicates was calculated for each probe, as a function of four different measures of probe activity. Supplemental Figure S8: Analysis of probe reproducibility measured by Euclidian distance, and relationships between different probe filtering criteria. Supplemental Figure S9: t-statistics using samples passing strict QC and permissive QC for the molecular markers considered in Supplemental Table 1. Supplemental Figure S10: validation of MSI-associated mRNA transcripts previously reported from fresh-frozen tissues(24). Supplemental Figure S11: Distribution of presence calls (fraction of samples in which a probe is called present, p<0.01) for all 24,526 probes on the DASL assay, and for probes involved in validation of previously identified MSI-associated gene transcripts(24).