PMID- 37635381
OWN - NLM
STAT- MEDLINE
DCOM- 20230925
LR  - 20230925
IS  - 1477-4054 (Electronic)
IS  - 1467-5463 (Print)
IS  - 1467-5463 (Linking)
VI  - 24
IP  - 5
DP  - 2023 Sep 20
TI  - Systematic investigation of the homology sequences around the human fusion gene 
      breakpoints in pan-cancer - bioinformatics study for a potential link to MMEJ.
LID - 10.1093/bib/bbad314 [doi]
LID - bbad314
AB  - Microhomology-mediated end joining (MMEJ), an error-prone DNA damage repair 
      mechanism, frequently leads to chromosomal rearrangements due to its ability to 
      engage in promiscuous end joining of genomic instability and also leads to 
      increasing mutational load at the sequences flanking the breakpoints (BPs). In 
      this study, we systematically investigated the homology sequences around the 
      genomic breakpoint area of human fusion genes, which were formed by the 
      chromosomal rearrangements initiated by DNA double-strand breakage. Since the 
      RNA-seq data is the typical data set to check the fusion genes, for the known 
      exon junction fusion breakpoints identified from RNA-seq data, we have to infer 
      the high chance of genomic breakpoint regions. For this, we utilized the high 
      feature importance score area calculated from our recently developed fusion BP 
      prediction model, FusionAI and identified 151 K microhomologies among ~24 K 
      fusion BPs in 20 K fusion genes. From our multiple bioinformatics studies, we 
      found a relationship between sequence homologies and the immune system. This 
      in-silico study will provide novel knowledge on the sequence homologies around 
      the coded structural variants.
CI  - (c) The Author(s) 2023. Published by Oxford University Press.
FAU - Kim, Pora
AU  - Kim P
AUID- ORCID: 0000-0002-8321-6864
AD  - School of Biomedical Informatics, The University of Texas Health Science Center 
      at Houston, Houston, TX 77030, USA.
FAU - Kumar, Himansu
AU  - Kumar H
AUID- ORCID: 0000-0002-4335-4517
AD  - School of Biomedical Informatics, The University of Texas Health Science Center 
      at Houston, Houston, TX 77030, USA.
FAU - Yang, Chengyuan
AU  - Yang C
AD  - School of Public Health Informatics, The University of Texas Health Science 
      Center at Houston, Houston, TX 77030, USA.
FAU - Luo, Ruihan
AU  - Luo R
AD  - School of Biomedical Informatics, The University of Texas Health Science Center 
      at Houston, Houston, TX 77030, USA.
FAU - Liu, Jiajia
AU  - Liu J
AD  - School of Biomedical Informatics, The University of Texas Health Science Center 
      at Houston, Houston, TX 77030, USA.
FAU - Zhou, Xiaobo
AU  - Zhou X
AD  - School of Biomedical Informatics, The University of Texas Health Science Center 
      at Houston, Houston, TX 77030, USA.
LA  - eng
GR  - R35 GM138184/GM/NIGMS NIH HHS/United States
GR  - R01 CA241930/CA/NCI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PL  - England
TA  - Brief Bioinform
JT  - Briefings in bioinformatics
JID - 100912837
SB  - IM
MH  - Humans
MH  - *Computational Biology
MH  - Genomics
MH  - *Neoplasms/genetics
MH  - Exons
MH  - Genomic Instability
PMC - PMC10516359
OTO - NOTNLM
OT  - DNA damage repair
OT  - MMEJ
OT  - fusion gene breakpoint
OT  - fusion neoantigen
OT  - fusionAI
OT  - microhomology
EDAT- 2023/08/28 06:42
MHDA- 2023/09/25 06:42
PMCR- 2023/08/26
CRDT- 2023/08/28 02:02
PHST- 2023/05/01 00:00 [received]
PHST- 2023/07/10 00:00 [revised]
PHST- 2023/08/10 00:00 [accepted]
PHST- 2023/09/25 06:42 [medline]
PHST- 2023/08/28 06:42 [pubmed]
PHST- 2023/08/28 02:02 [entrez]
PHST- 2023/08/26 00:00 [pmc-release]
AID - 7252294 [pii]
AID - bbad314 [pii]
AID - 10.1093/bib/bbad314 [doi]
PST - ppublish
SO  - Brief Bioinform. 2023 Sep 20;24(5):bbad314. doi: 10.1093/bib/bbad314.