STAR-Fusion/STAR-Fusion

BCL2:IGH fusion not reported

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asaki1986 commented

Hi all,

I am using STAR-Fusion-v1.12.0 to analyze the target RNA sequencing data.

The sample we tested had been already proved positive by both FISH and DNA sequencing data. Results from delly showed that the sample had a structural variant BCL2:IGHJ6 as follows,

18 60793522 BCL2:EXON_3(UTR3) + 14 106329453 IGHJ6:EXON_1 - 5to3 166 84 0.664 BND

However, this fusion was not reported by star-fusion.

I carefully review the intermediate file, and found that there were ~100 lines, containing both BCL2 and IGH-ext in star-fusion.junction_breakpts_to_genes.txt, which was list as follows,

chr18 60793595 - chr14 106204153 - 2 1 3 E150003903L1C002R0361269800 60793596 24S106M 106204129 24M106S 2 130 105 125 125 1 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"sense","pt_align":"60793596","delta":3017,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":106}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106204152,"delta":1079128,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":24},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106204152,"delta":1079128,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":24}]

chr18 60793595 - chr14 106232305 - 2 1 3 E150003903L1C002R0361269800 60793596 24S106M 106232281 24M106S 2 130 105 125 125 1 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"sense","pt_align":"60793596","delta":3017,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":106}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106232304,"delta":1050976,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":24},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106232304,"delta":1050976,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":24}]

chr18 60985923 + chr14 106778833 + 0 0 5 E150003903L1C008R0082564542 60985781 142M23S 106778834 142S23M 3 165 145 158 158 1 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"antisense","pt_align":60985922,"delta":123,"exon":{"rend":"60986045","orient":"-","lend":"60985135","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60985135^60986045^-"},"pt_exon":"60986045","anchor_length":142}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":"106778834","delta":725608,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"106053226","anchor_length":23},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":"106778834","delta":725608,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"106053226","anchor_length":23}]

chr18 60985928 + chr14 106476387 + 0 0 0 E150003903L1C008R0082564542 60985781 147M18S 106476388 147S18M 3 165 145 158 158 1 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"antisense","pt_align":60985927,"delta":118,"exon":{"rend":"60986045","orient":"-","lend":"60985135","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60985135^60986045^-"},"pt_exon":"60986045","anchor_length":147}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":"106476388","delta":423162,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"106053226","anchor_length":18},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":"106476388","delta":423162,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"106053226","anchor_length":18}]

chr18 60986406 - chr14 106209408 - 1 0 0 E150003903L1C008R0092273363 60986407 57S176M 106209351 57M176S 1 233 172 228 228 1 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"sense","pt_align":"60986407","delta":0,"exon":{"rend":"60987019","orient":"-","lend":"60986407","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60986407^60987019^-"},"pt_exon":"60986407","anchor_length":176}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106209407,"delta":1073873,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":57},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106209407,"delta":1073873,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":57}]

chr18 60793595 - chr14 106209411 - -1 0 0 E150003903L1C009R0142976594 60793596 150M 106209264 147M3S 1 300 148 291 291 0 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"sense","pt_align":"60793596","delta":3017,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":150}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106209410,"delta":1073870,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":147},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106209410,"delta":1073870,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":147}]

chr14 106329441 + chr18 60793777 + 0 0 1 E150003903L1C009R0144125528 106329361 80M54S 60793778 80S54M 1 134 79 127 127 1 GRPundef [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106329440,"delta":953840,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":80},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106329440,"delta":953840,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":80}] [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"antisense","pt_align":"60793778","delta":3199,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":54}]

chr18 60793544 - chr14 106209237 - 2 0 0 E150003903L1C018R0130175686 60793545 93S42M 106209144 93M42S 1 135 87 126 126 1 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"sense","pt_align":"60793545","delta":2966,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":42}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106209236,"delta":1074044,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":93},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106209236,"delta":1074044,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":93}]

chr14 106329442 + chr18 60793547 + -1 0 0 E150003903L1C018R0101049175 106329292 150M 60793548 150M 1 300 148 294 294 0 GRPundef [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106329441,"delta":953839,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":150},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106329441,"delta":953839,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":150}] [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"antisense","pt_align":"60793548","delta":2969,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":150}]

chr18 60793566 - chr14 106329454 - -1 0 0 E150003903L1C019R0254011815 60793567 150M 106237643 100M91665N46M4S 1 300 148 282 282 0 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"sense","pt_align":"60793567","delta":2988,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":150}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106329453,"delta":953827,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":46},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106329453,"delta":953827,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":46}]

chr18 60793543 - chr14 106329454 - -1 0 0 E150003903L1C020R0364208122 60793544 150M 106237643 100M91665N46M4S 1 300 148 282 282 0 GRPundef [{"gene_id":"BCL2^ENSG00000171791.10","chr":"chr18","sense_or_antisense":"sense","pt_align":"60793544","delta":2965,"exon":{"rend":"60795992","orient":"-","lend":"60790579","chr":"chr18","gene":"BCL2^ENSG00000171791.10","token":"BCL2^ENSG00000171791.10^60790579^60795992^-"},"pt_exon":"60790579","anchor_length":150}] [{"gene_id":"IGH-@-ext^IGH-.g@-ext","chr":"chr14","sense_or_antisense":"antisense","pt_align":106329453,"delta":953827,"exon":{"rend":"107283280","orient":"+","lend":"106053226","chr":"chr14","gene":"IGH-@-ext^IGH-.g@-ext","token":"IGH-@-ext^IGH-.g@-ext^106053226^107283280^+"},"pt_exon":"107283280","anchor_length":46},{"gene_id":"IGH@-ext^IGH.g@-ext","chr":"chr14","sense_or_antisense":"sense","pt_align":106329453,"delta":953827,"exon":{"rend":"107283280","orient":"-","lend":"106053226","chr":"chr14","gene":"IGH@-ext^IGH.g@-ext","token":"IGH@-ext^IGH.g@-ext^106053226^107283280^-"},"pt_exon":"107283280","anchor_length":46}]

However, the BCL2:IGH fusion was not reported in the final result.

It will be great if you can tale a look.

Best,
Junfeng

brianjohnhaas commented
asaki1986 commented

Hi brain,

I've sent the files via mail. Plz take a look at your convenience.

Best,
Junfeng

brianjohnhaas commented
asaki1986 commented

promiscuous

Hi Brain,

Thanks for reply.

It indeed find several other parteners for BCL2 in STAR-Fusion, which exceed max promiscuity.

We also found another BCL2 FISH positive sample encountered the same issue, while FusionCather reported these two fusions (both Arriba and JAFFA did not).

We extracted the reads covering the breakpoint, which are listed as follows,

E150003903L1C001R0023300833/1/1
TTTGACCTTTAGAGAGTTGCTTTACGTGGCCTGTTTCAACACAGACCCACCCAGAGCCCTCCTGCCCTCCTTCCGCGGGGGCTTTCTCATGGCTGCCCTGAGGTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGC
E150003903L1C001R0051737469/1/1
GGGGGAAGACCGATGGGCCCTTGGTGGAGGCTGAGGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTACCTCAGGGCAGCCATGAGAAAGCCCCCGCGGAAGGAGGGCAGGAGGGCTCTGGGTGGGTCTGTGTTGAAACAGG
E150003903L1C001R0072448096/1/1
TGGTCCCTTTGCCCCAGACGTCCATGTACCTCAGGGCAGCCATGAGAAAGCCCCCGCGGAAGGAGGGCAGGAGGGCTCTGGGTGGGTCTGTGTTGAAACAGGCCACGTAAAGCAACTCTCTAAAGGTCAAACCACCATAGATTTGAATCT
E150003903L1C001R0093511907/2/2
TCCTGCCCTCCTTCCGCGGGGGCTTTCTCATGGCTGCCCTGAGGTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGGTAAGAATGGCCACTCTAGGGCCTTTGTTTTCTGCTACTGCCTGTGGGGTTTCCTGAGCA
E150003903L1C001R0100377918/1/1
TGGAGGAGGGTGCCAGGGGGAAGACCGATGGGCCCTTGGTGGAGGCTGAGGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTACCTCAGGGCAGCCATGAGAAAGCCCCCGCGGAAGGAGGGCAGGAGGGCTCTGGGTGGGT
E150003903L1C001R0100432518/1/1
GCCAGGGGGAAGACCGATGGGCCCTTGGTGGAGGCTGAGGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTACCTCAGGGCAGCCATGAGAAAGCCCCCGCGGAAGGAGGGCAGGAGGGCTCTGGGTGGGTCTGTGTTGAAA
E150003903L1C001R0104297198/2/2
AGAGCCCTCCTGCCCTCCTTCCGCGGGGGCTTTCTCATGGCTGCCCTGAGGTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACC
E150003903L1C001R0111569028/1/1
CTTGGAGGAGGGTGCCAGGGGGAAGACCGATGGGCCCTTGGTGGAGGCTGAGGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTACCTCAGGGCAGCCATGAGAAAGCCCCCGCGGAAGGAGGGCAGGAGGGCTCTGAGATC
E150003903L1C001R0111771499/1/1
GTTGCTTTACGTGGCCTGTTTCAACACAGACCCACCCAGAGCCCTCCTGCCCTCCTTCCGCGGGGGCTTTCTCATGGCTGCCCTGAGGTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCC
E150003903L1C001R0112736145/1/1
CCCAGAGCCCTCCTGCCCTCCTTCCGCGGGGGCTTTCTCATGGCTGCCCTGAGGTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGTAGAGATCTCGT
E150003903L1C001R0112736145/2/2
CCTGAGGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTACCTCAGGGCAGCCATGAGAAAGCCCCCGCGGAAGGAGGGCAGGAGGGCTCTGGGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTCAGTCGATGTGTAGAT
E150003903L1C001R0113400740/1/1
GACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTACCTCAGGGCAGCCATGAGAAAGCCCCCGCGGAAGGAGGGCAGGAGGGCTCTGGGTGGGTCTGTGTTGAAACAGGCCACGTAAAGCAACTCTCTAAAGGTCAAACCACCATA
E150003903L1C001R0113875283/1/1
CTTTACGTGGCCTGTTTCAACACAGACCCACCCAGAGCCCTCCTGCCCTCCTTCCGCGGGGGCTTTCTCATGGCTGCCCTGAGGTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAGCCTCCACCAAGGGCCCATCG

We also crudely blast these sequences to the genome and found most of them were mapped to BCL2-IGH genes.
Meanwhile, in these sequences, we found a random 6-9bp sequences that could not mapped to the genome.

I was wondering whether did these random sequences contributed to the promiscuity, while FusionCathcer might neglect?

By the way, we also verified BCL6 and MYC -IGH fusion positive samples, and STAR-Fusion reported quite well.

Hope you can explore a bit.

Best,
Junfeng

asaki1986 commented

Quick update,

I added --max_promiscuity 1000000 option in the command line to seek this variant, but still failed.

For fusioncatcher:
image

Any other parameter that I can tune to recover this fusion, since STAR-Fusion is one of the best among others in other fusion positive samples.

Junfeng

brianjohnhaas commented
brianjohnhaas commented
asaki1986 commented

Hi brian

I've sent the data file via mail

Junfeng