Thermo ebook on eQTL - 21

played in their respective columns. In addition, links
to graphical displays (violin plot, the Integrative Genomics Viewer [IGV] browser described below, and
a representation across multiple tissues) are shown.

The eQTL database can be queried by entering the
rsID (rs9787897) in the Browse "By variant or rsID"
field on the landing page. A page similar to Figure
3 will appear, highlighting the tissue(s) where the
SNP has been shown to be an eQTL, the P value, and
the NES. In addition, genes with which the eQTL has
been shown to have a significant association are also
shown in the "Gene Symbol" column. As above, clicking on any of the hyperlinks will provide more visual
information or link out to other pages. Batch queries
for eQTLs by tissue or gene can be made in the "eQTL
Dashboard" section of the landing page.

You can find the Applied Biosystems™ TaqMan®
SNP Genotyping Assay that corresponds to each
SNP from the "Search Applied Biosystems TaqMan
Assays" page (thermofisher.com/taqman). Simply choose "SNP Genotyping" from the assay type
box, enter the rsID number for the SNP of interest,
and click the magnifying glass icon. A page with
the TaqMan Assay will appear; from here, the assay
can be added to the cart. Multiple assays for different eQTLs can also be easily ordered: From the GTEx
page, click the "CSV" button to export the eQTL table
in readable Microsoft™ Excel™ format. The CSV document can then be opened in Excel software and the
column with all the rsIDs can be copied and pasted
in the rsID entry box on the TaqMan ordering page.
The search results will appear as a list of assays that
can then be added individually or as a group to the
cart. The TaqMan SNP Genotyping Assays might display as mapping to different genes than the GTEx
database; this does not mean that the SNP associated with the rsID is not an eQTL for your gene of interest. In instances where no existing TaqMan Assay
exists for a SNP, a custom genotyping assay can be
designed (go to the Custom TaqMan Assay Design
Tool at thermofisher.com/cadt). Once obtained,
these TaqMan Assays can be used to confirm or determine the genotypes of other samples.

However, if the SNP has not been mapped to an
eQTL, then the page will state "No variant with ID
rsXXXXXXX found." This does not mean the SNP
could not be an eQTL. It only means that an eQTL
has not been found to act as one in the tissues that
are in the GTEx database.
To find the right TaqMan Genotyping Assays corresponding to the SNP, simply enter the rsID in the
TaqMan Assay ordering page as described above.
Additionally, the goal of the study might be to examine expression levels of the gene(s) associated
with the eQTL. Once the genes that will be tested
have been identified, ordering the Applied Biosystem™ TaqMan® Gene Expression Assays is very easy:
enter the gene symbol in the query box, choose
"Gene Expression" from the TaqMan Assays box,
and click the magnifying glass. Note that to order
a TaqMan Gene Expression Assay, the gene symbol
and not the rsID must be used. A page will appear
that lists all available gene expression assays for the
gene, with the assay that has the best coverage appearing at the top of the list. From here, the assays
can be added to the cart and ordered when convenient. These assays can be used to further analyze mRNA expression characteristics of a gene that
might be linked to an eQTL.

Example 2: Identifying genes that are associated with a putative eQTL
Second, a SNP identified in a GWAS or other study
can be analyzed whether or not it is an eQTL, and
linked genes for which the SNP has eQTL data can be
found. For example, assume that a study identifies
the SNP rs9787897 as genetically linked to a trait.

http://www.thermofisher.com/taqman http://www.thermofisher.com/cadt

Thermo ebook on eQTL

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