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STR
Expansion Analysis
NextGENe®LR software can be used
for STR Expansion analysis from long
read sequencing data such as< data from Pacific BioSciences systems.
This provides an accurate reporting
of STR lengths to identify STR loci with lengths associated with
disease.
NextGENeLR aligns the long sequence
reads to the reference sequence using
a specialized alignment algorithm. Alignment results are saved
to a BAM file which can be loaded
in the built-in Alignment
Viewer for visualization and reporting.
When the STR Expansion Report is opened,
the STR regions to be
evaluated are defined. A default list
of STR regions associated with disease
is provided. This list of
regions can be modified by removing
regions, adding regions, editing regions,
or uploading a text file
containing a list of regions to be
added. For the STR regions of interest,
the number of reads with each
repeat length is counted.
Figure
1: STR Expansion Regions of Interest
can be defined. The default list can
be used as is, regions can be removed
and/or added, or a custom list of
regions can be loaded..
Repeat lengths for all included regions
of interest are displayed in the graphical
STR Expansion Report.
The normal range for the repeat length
is displayed with green. Gray denotes
the premutation range
and red indicates the repeat length
associated with disease. Blue boxes
are placed at the repeat
length(s) detected for the sample.
The top number for each blue box indicates
the repeat length and
the bottom number indicates the number
of reads with this length.
Figure
2: The NextGENeLR STR Expansion Report
displays the repeat lengths detected
for all STR regions of interest. Green
indicates the normal STR length range,
gray for premutation, and red for
affected. In this case, the ATXN2
STR region shows some reads in the
premutation range.
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