Thermo ebook on eQTL - 10

cance of the eQTLs detected was
first determined by the software
using the t-statistic and then adjusted for multiple testing using
the Benjamini-Hochberg procedure to obtain the false discovery rate (FDR) of each eQTL. The
threshold significance level was
set at FDR < 0.05. For demonstration of this workflow, we selected the most significant eQTL for
each autosomal chromosome.
This screening data revealed 22
statistically significant eQTLs associated with lung adenocarcinoma in a sample set of 93 individuals (Table 1 and Figure 3).

Confirming results using
TaqMan Assays
Results obtained using wholegenome or whole-transcriptome
discovery-level techniques are
usually verified using orthogonal technologies and more samples. We used TaqMan Assays to
confirm the results found with
the microarray studies. Finding
TaqMan Gene Expression Assays
is simple, since they are mapped
to probes on Clariom arrays, and
these assays can be searched by
probe or transcript cluster ID on
thermofisher.com/taqman using the online search tool. Probe
IDs on Axiom arrays are mapped
to rsIDs on Axiom Analysis
Suite, which, in turn, are linked
to TaqMan Genotyping Assays

Figure 3. eQTL analysis on MatrixEQTL R package software. Effect of genotype on gene expression of GBP3, XRRA1, LRRC37A17P, and RBM12 in lung
adenocarcinoma disease research. Box plot shows differential expression of
respective genes by genotype. Number in parentheses corresponds to number of samples for each of the genotypes. Y-axis is the expression signal intensity from Clariom D Assays and X-axis is clustering of samples by genotype as
identified by Axiom Analysis Suite.
that can be selected for verification studies.
Our results confirmed the 22
eQTLs from the discovery-based
microarray analysis. For the purpose of demonstrating a complete workflow, we used qPCR to

confirm the genotype and gene
expression levels of 15 of these
targets. An example of genotype calls using TaqMan Genotyping Assays on the GT app on
Thermo Fisher Connect is shown
in Figure 4. Four of the 15 SNPs

http://www.thermofisher.com/taqman

Thermo ebook on eQTL

Table of Contents for the Digital Edition of Thermo ebook on eQTL