Concordance Testing of Replicate
Preparing sample replicates is a
common practice in clinical research,
wild and domesticated animal genetic
profiling, and ecology/environmental
research. Typically samples are amplified
using a kit or
custom chemistry and the products
then undergo capillary electrophoresis
on an ABI®PRISM,
instrument, or another CE system.
This technique lessens the impact
of allele dropout and other common
artifacts, and allows the analyst
to confidently deduce a consensus
genotype. GeneMarker® software,
already preloaded with Fragile
Testing, and AFLP
applications, is now equipped with
the Replicate Comparison Tool, which
allows researchers to quickly check
replicates for differences and determine
the resulting consensus genotype.
Replicates may be compared based solely
on allele calls, or by peak height,
size, and/or area. GeneMarker software
supports several digital and hard
copy reporting formats, including
text, excel, and customizable print
Concordance of Sample Replicates in
Comparison Tool - Main View
In the replicate comparison tool,
different replicates of the same sample
are grouped together and then compared.
The results are displayed in the report
table, and the alignment of the replicates
is displayed in the electropherogram.
The comparison settings are flexible:
replicates can be compared simply
by the allele call at a given marker,
or by additional parameters, such
as peak size, height, and/or area.
Use the Replicate Comparison Settings
window to choose which parameters
to compare for each replicate. For
some parameters (size, area, height,
and score) the user may set a range
of allowable values.
The report table displays the allele
call for each replicate at a given
marker, the results of the comparison
of those calls (concordant, discordant,
or null), and the consensus genotype
at the specified marker. This table
can be exported as a tab-delimited
The informative report table displays
the allele calls for each replicate
at the specified marker, the “status”
of that marker, (described below),
and the Final Genotype at that locus.
The status column for a specified
marker will display a C for Concordant
if the replicates have the same call,
a D for Discordant, if the call is
different, and N, for Null, if only
one replicate has allele calls (i.e.
the other replicates failed). The
report table is linked with the electropherogram;
simply click on an allele or the corresponding
status to be taken to that locus in
For markers with C and N calls, the
final genotype column is automatically
filled with the available genotype.
In cases where the status is D, the
user may manually select the genotype
of that locus from a dropdown menu.
The final report may then be exported
as a tab-delimited text file.
For discordant (conflicting) replicates,
the user may manually select the genotype
of the specified locus.
The replicate comparison tool can
comfortably accommodate more than
two replicates in each group. Shown
above is a project in which four replicates
were processed for each sample.
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Research use only (RUO)