Thermo ebook on eQTL - 27

Figure 7. Example of how to use the GTEx database to link possible eQTLs to GWAS. (A) The IGV browser indicates
six locations that are significant in GWAS studies (circled) that fall within the SERPINH1 gene. There is potential
overlap with three eQTLs in mammary tissue. (B) Entering SERPINH1 in the "GTEx IGV eQTL Browser" confirms that
two eQTLs have been mapped to mammary tissue but not to whole blood. (C) Clicking on the bars in (B) brings up
violin plots showing the relationship between genotype and expression levels. Note that neither of these SNPs has
very large effects on expression levels. (D) TaqMan Assays can be used to confirm and extend these results. TaqMan
Gene Expression Assays can measure the expression levels of SERPINH1, and can be used to identify SNP genotypes
of individuals at the putative eQTL.
4.

Joehanes et al. (2017) Integrated genome-wide analysis
of expression quantitative trait loci aids interpretation
of genomic association studies. Genome Biol 18:16.

GTEx Consortium (2013) The Genotype-Tissue
Expression (GTEx) Project. Nat Genet 45:580-585.

He X et al. (2013) Sherlock: detecting gene-disease
associations by matching patterns of expression QTL
and GWAS. Am J Hum Genet 92:667-680.

Thorvaldsdóttir H et al. (2013) Integrative Genomics
Viewer (IGV): high-performance genomics data
visualization and exploration. Brief Bioinform
14:178-192.

Zhu et al. (2015) Chaperone Hsp47 drives malignant
growth and invasion by modulating an ECM gene
network. Cancer Res 75:1580-1591.

Steve Jackson has over 10 years of experience in
genetic analysis technologies. As a senior member
of the R&D team at Thermo Fisher Scientific, he helps
develop solutions for the research and healthcare
markets, leveraging varied technologies such as
capillary electrophoresis, digital PCR, next-generation
sequencing, and microarray analysis. Before Thermo
Fisher Scientific, he was at Nanostring Technologies
running the Field Applications Specialist (FAS) team.
He was also an Acting Assistant Professor at University
of Washington, Department of Genome Sciences,
investigating developmental genetics of Drosophila.

Thermo ebook on eQTL

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