Wrong amino acid sequence for fusion protein

[pmrotem]

Hi Daniel,

We noted an an instance in which FusionCatcher reported a long sequence of Ks in the predicted fusion protein. When we tried to reconstruct the protein sequence we got a different protein.

This is the sequence of the fusion protein that Fusion Catcher predicts:

KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKCGHCKRLAPEYEAAATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSHLTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWRNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALERFLQDYFDGNLKRYLKASGGDRAGARAAPADRVAERPALGTGTGSLLGLPALGADTV

And this is the line from the final-list_candidate-fusion-genes_sequences.txt file:

Gene_1_symbol(5end_fusion_partner)      Gene_2_symbol(3end_fusion_partner)      Fusion_description      Counts_of_common_mapping_reads  Spanning_pairs  Spanning_unique_reads     Longest_anchor_found    Fusion_finding_method   Fusion_point_for_gene_1(5end_fusion_partner)    Fusion_point_for_gene_2(3end_fusion_partner)    Gene_1_id(5end_fusion_partner)    Gene_2_id(3end_fusion_partner)  Exon_1_id(5end_fusion_partner)  Exon_2_id(3end_fusion_partner)  Fusion_sequence Predicted_effect Predicted_fused_transcripts      Predicted_fused_proteins
PDIA3   APOE    m3      0       4       6       40      BOWTIE+BLAT;BOWTIE+STAR 15:43768557:+   19:44907778:+   ENSG00000167004 ENSG00000130203                 GAGAGGTTCCTGCAGGATTACTTTGATGGCAATCTGAAGAGATACCTGAA*AGCAAGCGGTGGAGACAGAGCCGGAGCCCGAGCTGCGCCAGCAGACCGAG     out-of-frame    ENST00000300289:1245/ENST00000252486:173;ENST00000300289:1245/ENST00000434152:197;ENST00000300289:1245/ENST00000446996:151;ENST00000300289:1245/ENST00000425718:327       KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKCGHCKRLAPEYEAAATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSHLTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWRNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALERFLQDYFDGNLKRYLKASGGDRAGARAAPADRVAERPALGTGTGSLLGLPALGADTV;KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKCGHCKRLAPEYEAAATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSHLTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWRNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALERFLQDYFDGNLKRYLKASGGDRAGARAAPADRVAERPALGTGTGSLLGLPALGADTV;KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKCGHCKRLAPEYEAAATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSHLTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWRNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALERFLQDYFDGNLKRYLKASGGDRAGARAAPADRVAERPALGTGTGSLLGLPALGADTV;KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKCGHCKRLAPEYEAAATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSHLTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWRNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALERFLQDYFDGNLKRYLKASGGDRAGARAAPADRVAERPALGTGTGSLLGLPALGADTV

Here is a link to the output dir of fusion catcher:

https://owncloud.incpm.weizmann.ac.il/owncloud/index.php/s/GnMFv4lELikNByb

Thank you,

Gil & Rotem

[ndaniel]

Thanks for the bug report! I will take a look!

When you reconstructed the protein sequence did you use the gene annotation from Ensembl release 90 (which is used by FusionCatcher v1.00) or something else?

Cheers, Daniel

[pmrotem]

We took notice to use the same Ensembl release as FusionCatcher.

[ndaniel]

ok. Thanks!

[ndaniel]

So, finally I have had some time for looking into this but now the link above is broken. I am not sure if this can be fixed without it.