CTAT_HumanFusionLib construction to detect target gene fusion

[Bole Pan]

Hello,

We had a question about how to construct the CTAT_HumanFusionLib in our use case. Our target, Gene X, is randomly inserted into the genome and can form fusions with various partner genes. While we don’t know all possible fusion partners in advance, our goal is to detect any fusion involving Gene X.

Given that, how should we modify the fusion lib? Should we simply add Gene X as a candidate gene, or do we need to explicitly list potential fusion pairs (e.g., GeneX--BCR, GeneX--ABL1, etc.)? I couldn’t find detailed documentation on this particular use case—though it’s possible I missed it.

Thank you in advance for your guidance!

[Brian Haas]

Hi,

If GeneX is something that's not a normal part of the human genome, then you'd need to create a new ctat genome lib that includes it somehow - even if it's as its own mini-chromsome.   Otherwise, you could just run STAR-Fusion (assuming STAR-Fusion here) in max sensitivity mode (options below) and filter based on your target GeneX.

#    --max_sensitivity                     includes options: --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --min_spanning_frags_only 1 --min_novel_junction_support 1 --skip_FFPM --no_single_fusion_per_breakpoint --skip_EM
#
#    --full_Monty                          includes max sensitivity and disables filters via: --max_promiscuity 1000000 --min_pct_dom_promiscuity 1 --min_alt_pct_junction 1e-3 --no_annotation_filter --no_RT_artifact_filter
#

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas