I don't think the difference would be material as all molecular tests require small percentage of tumor cells in the specimen in comparison to histology diagnoses. Problems with RT PCR may be quantity and quality of RNA that can be isolated from archival tissue and while FISH detects any rearrangement involving ALK, including potentially rare uncharacterized rearrangements, RT PCR detects different breakpoints in EML4 or ALK but novel ALK fusion partners will probably not detected.
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