1. Integrative statistical analysis pipeline for RNA-seq and NanoString with application to gene expression data of cancer patients
Jeea Choi, Catarina D. Campbell, Xiaoshan Wang, Wei He, Leary Rebecca, Venkatesan Kavitha, Doug Robinson, Stephane Wong, Bin Fu, Ying A. Wang
July 31, 2018

2. RNAexpressionToolbox
Motivation
Gene expression profiling enables a wide variety of basic research, translational medicine, and in vitro diagnostics applications
Many variations of statistical methods for RNA-seq and NanoString have been published with application to cancer genomics
RNAexpressionToolbox
We implemented comprehensive analyses steps for both RNA- seq and NanoString analysis into a R package
We applied the pipeline to both RNA-seq and NanoString expression data from commercial samples of 38 melanoma cancer patients and 28 non-small cell lung cancer (NSCLC) patients
Business Use Only

3. Application to Melanoma, NSCLC
Figure 1: Concordance between RNA-seq and NanoString of one sample (left) and distribution of correlation coefficient (right) displayed. Melanoma data
Normalization
RNA-seq normalization by TMM (Robinson, et al.,2010)
NanoString normalization by NanoStringNorm (Waggott et al., 2012)
High concordance between assays (Fig. 1)
Sensitive Detection of Expressed Genes (Fig. 2)
Similar proportion of genes had detectable expression with low level threshold cutoff 34
(4.5%)
684 (90.8%) 22
(2.9%)
13 (1.7%) not detected by either
Detection threshold ≥ 1 counts (mean)
123
(18.8%)
448 (59.5%) 46
(6.1%)
136 (18.1%) not detected by either
Detection threshold ≥ 50 counts (mean)
RNA-seq
NanoString
RNA-seq
NanoString
Figure 2: Genes detected by RNA-seq and NanoString Panels
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4. Application to Melanoma, NSCLC
Lung
Figure 3: Top 50 DE genes in immune response genes (GO: ) are shown in RNA-seq panel
DE analysis (edgeR) has performed using RNA-seq between Melanoma and NSCLC samples
Total 5,666 DE genes were identified (FDR 1%)
Out of 495 genes in immune response GO term (GO: ), 72 (41) % are contained in the RNA-seq (NanoString) panel
Top DE genes in immune response GO term are shown in both panels
Melanoma
Lung
Figure 4: Top 24 out of 50 DE genes found in NanoString panel are shown
Business Use Only