while i am reading a paper name "An algorithm for Gene Fusion Discovery in Tumor RNA-Seq DATA" related to Gene fusion discovery , I have a trouble with its context.
below is my difficult paragraph from paper and I need someone to understand the fuzzy concept.
I displayed in bold text which I cannot understand.
Previous work on gene fusion detection from RNA-Seq
FusionSeq has been used to identify
fusions in prostate tumor samples and cell lines [10,11]. While the
methods used for these studies are capable of identifying genuine
gene fusions, many challenges and limitations remain in the
analysis of RNA-Seq data. For example, the aforementioned
studies only considered reads that align uniquely to the genome.
However, errors in next generation sequencing together with
homologous and repetitive sequences shared between genes often
produce ambiguous alignments of the short reads generated in
RNA-Seq experiments. While resolving the ‘correct’ placement of
these reads is often not possible, we propose that ambiguously
aligning reads provide important evidence of real gene fusions,
and therefore should be leveraged by analysis methods
Firstly I am so confused about the homologous.
I already know the concept of the homologous, but I can't connect the concept into sequencing field.
also why not het instaed of homo? because i think , homologous is always same DNA in chromosome pair.
Secondly, What is the meaning of shared between genes?
I hope you understand because I am very beginner in this field.
anyway I am looking forward to your reply.