Comments (3)
What's the fusion partner gene of this TCF3 fusion?
Please note that, GeneFuse only detects gene fusions that both two fusion genes are listed in the CSV file.
from genefuse.
Hi, the fusion partners were HLF in one sample and PBX1 in the other, these fusions were experimentally confirmed by FISH. Both HLF and PBX1 were included in the fusion file along with TCF3, with the transcripts covering expected fusion junctions:
grep HLF test_fusions.csv
HLF_NM_002126,chr17:55264959-55325187
grep PBX1 test_fusions.csv
PBX1_NM_002585,chr1:164559183-164851831
grep TCF3 test_fusions.csv
TCF3_NM_003200,chr19:1609291-1652615
And these are the expected breakpoints:
sample 1:
chr19:1617928 - chr1:164683443, 59 supporting reads, TCF3-PBX1
sample 2:
chr19:1617921 - chr17:55318881, 77 supporting reads, TCF3-HLF
chr19:1617932 - chr17:55318898, 66 supporting reads, TCF3-HLF
Is there any other reason why this may be happening? Any hard coded filters on the reads/regions? Many thanks in advance!
from genefuse.
Maybe reads contained breakpoint were filtered. In such a scenario which a mismatch occurred beside the breakpoint, all kmer contained the mismatch and the breakpoint would not be traced back to a genomic position and thus caused more mismatch and be filtered eventually.
from genefuse.
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from genefuse.