Recent publications have shown that
a substantial portion of cell lines
much as 36% - are either contaminated
or misidentified entirely. In response,
has understandably re-emphasized
the need for Cell Line Authentication.
Several commercial PCR kits are now
available for this purpose, including
systems, as well as Life Technologies
To assist with the analysis of such
kits and custom chemistries, GeneMarker®
HID software is now equipped with
a Cell Line Authentication application.
The user may compare their sample's
STR profile against a database of
reference genotypes using a percent
match calculation. The tool is built
into the program - the user can simply
upload their raw data from any ABI
instrument, genotype their samples,
and then proceed directly to Cell
Line Authentication. No additional
data transfer is required. GeneMarker
HID software also comes pre-loaded
with additional analysis tools including
search, and mixture
Cell Line Authentication Application
Cell Line Authentication Main
Window. Samples are automatically
imported from the user's current project
- no manual entry required. Select
a sample from the sample dropdown
menu to search the database. Results
are displayed in the table to the
Building Your Database
The Cell Line authentication application
is equipped with a built in database
function. This database is seeded
with 60+ common cells lines, but can
be easily and rapidly expanded to
include thousands of references.
Uploading a database of cell lines
into GeneMarker HID software. These
samples will be saved to the database,
where they can be reviewed,
deleted, or modified using GeneMarker
HID software's database management
To run a new project, simply load
your raw data files, and use GeneMarker
HID software's Run Wizard to perform
size and allele calling. Settings
can be saved as templates, greatly
simplifying the analysis.
Processing raw data using the
After data processing, allele calls
will be displayed in the electropherogram
and the allele report table. Allele
calls can be saved using GeneMarker
HID software's many exporting and
Completed genotyping results
Query the Database
After genotyping, proceed directly
to the Cell Line Authentication application.
Sample genotypes obtained from your
current project will be imported directly
into the Cell Line window (no manual
Simply select a sample from the sample
dropdown menu to query the database.
You may also set the minimum percent
match threshold for the search. Results
are displayed in the report table
to the right.
Samples from your project are
automatically imported into the application.
Select a sample from the Sample dropdown
menu to search it against the database.
Clicking on a result will display
that reference's genotype in the References
Table, allowing side-by-side comparison
with the sample genotype. Differences
are flagged for easy identification.
For more information, please email:
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