Barry, et al., “Micro RNA Expression Profiles as Adjunctive Data to Assess the Risk of Hepatocellular Carcinoma Recurrence after Liver Transplantation” AJT 2012, 12(2):428-437.

 

Figure S1

Figure S1. Representative electrophoresis gel showing consistently high yields of miRNA (pink arrows) from FFPE tumor blocks using the Roche High Pure miRNA kit.

Figure S2

Figure S2. Representative scatter plot of microarray hybridization results comparing miRNA purified from freshly frozen cells (x-axis) and identical cells that were first fixed with formalin and paraffin embedded (FFPE, y-axis) prior to miRNA purification. Cells used were from the OE-19 esophageal cancer cell line, harvested during exponential growth phase. Purified miRNA was labelled and hybridized to Affymetrix GeneChip miRNA 1.0 microarrays as described in the text.

 

 

Table S1

 

 

 

Table S2

Table S2. MiRNAs present in our univariate analysis with preexisting literature evidence for relevance to HCC (highlighted in red).

 

Figure S3

Figure S3. Principal component analysis of recurrence (red points) and nonrecurrence (black points) samples. The first principal component (x-axis) accounts for most of the variability in the data and separates recurrence from nonrecurrence similarly to the hierarchical clustering analysis (Figures 1A-C).

 

Figure S4

Figure S4. Box plots of sensitivity of mean miRNA expression probe reduction versus min/max reduction.

 

Table S3

 

Probe Feature Proportion of CV fits
hsa-miR-454-star_st_MAX

1.000

hsa-miR-885-5p_st_MAX

0.994

hsa-miR-501-5p_st_MIN

0.992

hsa-miR-454-star_st_MIN

0.982

hsa-miR-501-5p_st_MAX

0.978

hsa-miR-365_st_MIN

0.976

hsa-miR-1273_st_MIN

0.962

hsa-miR-365_st_MAX

0.960

hsa-miR-1274b_st_MIN

0.948

hsa-miR-194_st_MIN

0.936

hsa-miR-125b-2-star_st_MIN

0.926

hsa-miR-610_st_MAX

0.890

hsa-miR-592_st_MIN

0.850

hsa-miR-137_st_MIN

0.848

hsa-miR-193b_st_MIN

0.798

hsa-miR-545_st_MAX

0.786

hsa-miR-146b-3p_st_MAX

0.770

hsa-miR-20a-star_st_MIN

0.768

hsa-miR-1293_st_MAX

0.756

hsa-miR-424_st_MIN

0.744

hsa-miR-671-3p_st_MAX

0.736

hsa-miR-377-star_st_MAX

0.732

hsa-miR-937_st_MIN

0.724

hsa-miR-548c-3p_st_MIN

0.706

hsa-miR-576-3p_st_MIN

0.704

hsa-miR-146b-3p_st_MIN

0.700

hsa-miR-513a-3p_st_MIN

0.692

hsa-miR-137_st_MAX

0.688

hsa-miR-630_st_MIN

0.664

hsa-miR-671-3p_st_MIN

0.644

hsa-miR-1274b_st_MAX

0.630

hsa-miR-1180_st_MIN

0.590

hsa-miR-505_st_MAX

0.578

hsa-miR-424_st_MAX

0.558

hsa-miR-15a-star_st_MAX

0.544

hsa-miR-485-3p_st_MAX

0.538

hsa-miR-182_st_MIN

0.538

hsa-miR-610_st_MIN

0.536

hsa-miR-937_st_MAX

0.526

hsa-miR-1260_st_MIN

0.524

hsa-miR-1179_st_MIN

0.524

hsa-miR-99a-star_st_MIN

0.518

hsa-miR-491-3p_st_MIN

0.508

hsa-miR-145_st_MIN

0.504

Table S3. All probe features appearing in at least 50% of biomarkers fit in the CV for the MIN-MAX model with Milan incorporated.

 

Figure S5

Figure S5. R squared values (y-axis) versus number of probes (x-axis) showing performance of Min-Max versus mean miRNA expression probe reduction with and without the addition of Milan criteria.

 

Figure S6

Figure S6. Cross validation procedures as a function of maximum number of probe features (M). AUC statistics for Min-Max with Milan (____), Min-Max alone (—-), mean of multifocal expression values with Milan (….), and mean alone (.-.-).

 

Figure S7

Figure S7. Plots showing expression of three representative miRNAs comprising the biomarker: 497, 194, and 125b-2-star with relative expression on the y axis and individual patients on the x axis. Boxes show the spread of expression values for that miRNA in patients with multifocal disease.

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