Archer has provided information to guide the detection of fusions and variations. However, every sample is different. Each lab must interpret the results, and take into consideration any information known about their particular samples. Read statistics and the visualization tools can assist in making proper calls. Some things to consider include:
Does the fusion appear in the strong evidence tab?
Are there several reads supporting the fusion call? 5 is the MINIMUM recommended number of unique reads to call a fusion.
Are there enough reads supporting the fusion transcript(s) as compared to the wild-type transcript(s)?
Is the expression level of the target gene normally high or low?
How does the expression level of the target in the analyzed sample compare to expression in a normal (control) sample?
Is the fusion known in the literature?
When visualizing the data, are there any insertions or deletions present in more than a few of the reads near the breakpoint? This may indicate a mapping error.
Watch the video below to learn more about visualizing reads and fusions in JBrowse:
For Research Use Only. Not for use in diagnostic procedures.
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