Interpret 3'/5' Imbalance scores for assay calls
3'/5' Imbalance values are reported in the 3'/5' Imbalance column. The 3'/5' Imbalance score for an assay applies to all fusion calls with the driver gene that is reported in the Genes (Exons) column.
-
Find the driver gene for the fusion, which
is the second gene listed in the
Genes (Exons)
column.
- Find the ASSAYS_5P_3P entry that reports that driver gene in its Genes (Exons) field.
-
Use the Imbalance value for that
ASSAYS_5P_3P entry to interpret the fusion calls for all fusions whose driver
gene matches the ASSAYS_5P_3P's
Genes (Exons)
field.
An Imbalance value is calculated by subtracting the number of 5' reads from the number of 3' reads, and dividing the result by the sum of all EXPR_CONTROL reads:
-
(3' reads - 5' reads) / (sum of all EXPR_CONTROL reads)
Note: The column heading 3'/5' Imbalance in the Analysis Results table implies that the imbalance value is a direct ratio of the 3' and 5' reads. The value is not a direct ratio of 3' and 5' reads.
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Imbalance values are interpreted as follows:
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Higher Imbalance values (0.025 or greater) indicate a greater likelihood that the fusion is present in your sample.
-
Lower Imbalance values (either close to zero or negative) indicate a greater likelihood that the fusion is not present in your sample.
Note: Imbalance values provide information that is supplementary to the detection calls of Present or Absent. If a fusion call is Absent, then it is recommended that you check the imbalance value to see if there is supplemental evidence of the presence of a fusion.
-
-
For the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel and similar panels from AmpliSeq.com, the following table lists the imbalance score thresholds.
Gene
No evidence of a fusion
Uncertain
Strong evidence of a fusion
ALK
≤0.001
0.001—0.015
≥0.015
RET
0.03
0.03—0.55
≥0.55
ROS1
≤0.2
0.2—0.5
≥0.5
-
For the Oncomine™ Focus Assay, the following table lists the imbalance score thresholds:
Gene
No evidence of a fusion
Uncertain
Strong evidence of a fusion
ALK
≤0.001
0.001—0.0015
≥0.0015
RET
0.3
0.3—0.55
≥0.55
ROS1
≤2.1
2.1—2.1
≥2.1