Thermo ebook on eQTL - 13

verification of eQTLs. Use of microarrays for discovery and screening where a large cohort of samples
are required to be tested can also prove to be a relatively economical solution compared to other technologies used for similar studies.

thermofisher.com/ClariomDdatasheet
6.

Acids Res 46:D971-D976.
7.

heterogeneity in genetic susceptibility across
histological subtypes. Nat Genet 49(7):1126-1132.
8.

Van der Sijde et al. (2014) Systems genetics: From GWAS to
disease pathways. Biochim Biophys Acta 1842:1903-1909.

Nica et al. (2013) Expression quantitative trait loci:
present and future. Philos Trans R Soc Lond B Biol Sci
6;368(1620):20120362.

Axiom Precision Medicine Research Array.
thermofisher.com/PMRAdatasheet

Pintarelli et al. (2017) Genetic susceptibility variants
for lung cancer: replication study and assessment
as expression quantitative trait loci. Nat Sci Reports
7:42185

Thermo Fisher Scientific. Gene expression and
Genotyping analysis using TaqMan Assays,
thermofisher.com/qpcr

10. Shabalin, A.A. Matrix (2012) eQTL: Ultra fast eQTL
analysis via large matrix operations. Bioinformatics
(28)10:1353-1358.
11. GTEx Portal, https://www.gtexportal.org

Harita Veereshlingam is a Senior Product Application
Scientist in the Genetic Sciences Division at Thermo
Fisher Scientific. She has over 10 years of experience in
product development with an emphasis on real time
PCR assays for gene expression and miRNA analysis.
In her current role, Harita is responsible for product
portfolio growth through the development of novel
applications, customer collaborations, technical notes,
and webinars. She lives by and is a strong proponent of
sustainable living. She has a PhD in Molecular Biology
from the University of North Texas.

References

McKay et al. (2017) Large-scale association analysis
identifies new lung cancer susceptibility loci and

The workflow presented in this paper can be effectively used to identify and confirm eQTLs associated
with any disease or trait, and it may facilitate the identification of new biomarkers that could help understand the basis of specific pathologies or phenotypes.

Cookson et al. (2009) Mapping complex disease traits
with global gene expression. Nat Rev Genet 10:184-194.

Gong et al. (2018) PancanQTL: Systematic identification
of cis-eQTLs and trans-eQTLs in 33 cancer types. Nucleic

Total gDNA and RNA samples were conveniently
processed on Axiom PMRA arrays and Clariom D Assays at the Microarray Research Services Laboratory,
a high-throughput genotyping and expression analysis facility that enables partners to complete their
proof-of-principle studies quickly. Data analysis on
MatrixEQTL R package revealed 22 statistically significant eQTLs. Of these, 15 were verified using real
time PCR for this proof-of-principle study. In our
small sample size, we confirmed the presence of four
eQTLs using TaqMan Assays. Analysis of more (several hundred) samples may confirm a larger number of eQTLs using this orthogonal technique. Since
probes on both Axiom PMRA and Clariom D Assays
are pre-mapped to TaqMan Assays, selecting assays
for verification was simple and efficient.

Clariom D solution for human, mouse and rat.

http://www.thermofisher.com/ClariomDdatasheet http://www.thermofisher.com/qpcr https://www.gtexportal.org http://www.thermofisher.com/PMRAdatasheet

Thermo ebook on eQTL

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