Thermo ebook on eQTL - 7

analyses. Microarray solutions from Thermo Fisher
Scientific enable genome- and transcriptome-wide
analyses with simple workflows and data analysis
packages. The Axiom Precision Medicine Research
Array (PMRA) offers a genome-wide imputation
grid from phase III of the 1000 Genomes Project and
from the NHGRI-EBI GWAS catalog published in May
2016, offering the most up-to-date content, broad
coverage, and high accuracy for disease association studies across populations.4 The Clariom D Assays provide the most intricate transcriptome-wide
gene- and exon-level expression profiles and can
detect alternative splicing events of coding and
long noncoding RNA (lncRNA).5 And to verify and
extend the results, probes on both the Axiom PMRA
and Clariom D Assays are mapped to predesigned
TaqMan Genotyping and TaqMan Gene Expression
Assays, respectively, thus streamlining the process
of RT-qPCR verification of microarray data.

ples. Functionality of these eQTLs was further verified by TaqMan Genotyping and Gene Expression
Assays.9 This complete workflow for eQTL discovery
and verification is depicted in Figure 1.

Methods
Genomic DNA (gDNA) and total RNA was extracted
using previously described procedures8 from non-involved, apparently normal lung tissue of 93 lung adenocarcinoma research samples from patients who underwent lobectomy. Following extraction, gDNA and
RNA were processed on the Axiom PMRA and Clariom D Assays, respectively, at the Microarray Research
Services Laboratory (Thermo Fisher Scientific, Santa
Clara, CA). Samples were prepared and hybridized on
the arrays according to standard protocols.
Briefly, 100 ng of total double-stranded DNA from
each sample was prepared using the Applied Biosystems™ Axiom™ 2.0 Reagent Kit; arrays were hybridized and imaged on an Applied Biosystems™
GeneTitan™ MC Instrument. Approximately 500 ng of
total RNA was prepared for hybridization on Clariom
D Assays using the Applied Biosystems™ GeneChip™
WT PLUS Reagent Kit; arrays were then hybridized
with biotinylated cRNA for 16-18 hrs at 45°C. Standard post-hybridization washing and staining were
performed on the Applied Biosystems™ GeneChip™
Fluidics Station 450, followed by scanning on the
Applied Biosystems™ GeneChip™ Scanner 3000 7G.

eQTLs have been mapped in many tumor types,
such as breast, lung, and prostate cancer.6 Lung cancer is the most frequently diagnosed cancer and the
leading cause of mortality worldwide. One of the
subtypes of this disease is adenocarcinoma, which
accounts for about 40% of all lung cancers.7 Among
other factors, heritability is considered to play a significant role in the development of lung adenocarcinoma. Although previous GWAS have identified
several lung cancer susceptibility loci, the functionality of most of these loci still remains unexplained.8
Studying eQTLs associated with lung adenocarcinoma could help us understand the function of these
loci and provide further insights into the molecular
mechanisms of this disease.

A CHP file is a probe array results file; it contains
probe set analysis results generated by the software.
CHP files from the Axiom PMRA were analyzed on
Applied Biosystems™ Axiom™ Analysis Suite, and
from Clariom D Assays on Transcriptome Analysis
Console (TAC) 4.0. eQTL analysis was carried out using the MatrixEQTL R package.10

In this study, we used the Axiom PMRA and Clariom
D Assays to identify eQTLs associated with lung adenocarcinoma in a cohort of 93 patient research sam-

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Thermo ebook on eQTL

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