Validation of gene panels Sample Clauses

Validation of gene panels. To illustrate that our reference panel is capable of imputing and the panel is tissue- specific, we calculated the “distance” between each new “unknown” sample with all of our reference panels. In this study, the panel is constructed using GTEx data on 30 tissues. We then go through each individual TCGA sample, impute the variance for all genes in the human genome using their corresponding panel. We pretend to have no information about the source for TCGA samples and use the distance between each new sample and reference panel to determine the source for TCGA sample. Figure 26(a) - (d) shows the results for TCGA-LUAD (lung), TCGA-KIRC (kidney), TCGA-LIHC (liver), TCGA-BRCA (breast) samples, respectively. In general, all results indicate that the reference panel is informative to “predict” the unknown sample’s source. Figure 26 Predict new “unknown” samples. For any new samples, distance between the new sample and predefined panels are calculated. The panel with smallest distance can used to predict the source of the new sample In Figure 27 (a) – (c), we show the landscape of imputation scores for kidney, liver and lung. The 90% and 95% quantile red lines shows that most genes have well imputed variances. Figure 27 (d) shows a Venn diagram for outliers for different tissues. The Venn diagram demonstrates that the outliers are tissue-specific, which indicates that panels could be defined by tissue sources.
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