clarification about FusionInspector manuscript

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filippo martignano

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Jun 9, 2025, 1:35:49 PM6/9/25

to Trinity_CTAT_users

Dear Brian,

I was looking at supplementary table 6 from "Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector", the tab "TARGET_fusion_results".
I'm particularly interested in the TARGET pediatric AML cohort.

In TARGET there are 199 patients with available RNAseq data. I was wondering if all available Diagnosis/Relapse samples from these patients have been analyzed.

I explain why i'm asking: I noticed that for some patients either the Diagnosis or Relapse sample is missing from table 6, while both appear to be available on TARGET

I assume it's because it hasn't been found any fusion in the "missing" samples, but i just wanted to be sure they haven't been excluded from the analysis because of some reasons i might have missed out.

Since i'm doing some Diagnosis Vs Relapse comparison, this detail is pretty crucial.

Thanks a lot in advance for the help!
Filippo

Brian Haas

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Jun 9, 2025, 2:37:39 PM6/9/25

to filippo martignano, Trinity_CTAT_users

Hi Filippo,

The full list of TARGET samples we examined are listed here:
https://github.com/broadinstitute/FusionInspectorPaper/blob/main/data/TARGETdb.sample_info.tsv

If there are any in particular you'd like me to explore a bit further, I should be able to explore files I might have archived from that study. Feel free to write me directly at

bhaas at broadinstitute dot org

best,

Brian

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