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Identification of Gene Fusions in Sarcomas through RNA Sequencing

Hofvander, Jakob (2014) MOBT19 20131
Degree Projects in Molecular Biology
Abstract
Popular science summary:

Cancer is genetic disease arising due to mutations in our genome. Gene fusions are one type of mutation that has a strong impact on tumor development. They are often characteristic for specific tumor types and can therefore be used a diagnostic tool. The identification of new gene fusions have, in the recent years, been highly successful using a newly developed technique called RNA-sequencing.

Double stranded breaks in the DNA causing incorrect rejoining of the DNA molecules can fuse two previously separate genes resulting in the formation of a fusion gene. Gene fusions can be found in all malignancies and are often associated with structural rearrangements visible at the chromosome level.

RNA sequencing... (More)
Popular science summary:

Cancer is genetic disease arising due to mutations in our genome. Gene fusions are one type of mutation that has a strong impact on tumor development. They are often characteristic for specific tumor types and can therefore be used a diagnostic tool. The identification of new gene fusions have, in the recent years, been highly successful using a newly developed technique called RNA-sequencing.

Double stranded breaks in the DNA causing incorrect rejoining of the DNA molecules can fuse two previously separate genes resulting in the formation of a fusion gene. Gene fusions can be found in all malignancies and are often associated with structural rearrangements visible at the chromosome level.

RNA sequencing (RNA-seq) is a newly developed technique that already has contributed substantially to the detection of new gene fusions. It aims to sequence cells complete set of mRNA transcripts, generating millions of short sequences called reads. Advanced bioinformatical softwares can use the information from these reads to detect gene fusions.

Sarcomas are rare malignant tumors of unknown cellular origin arising in bone or soft tissues. There are more than 50 different subtypes and diagnosis can be very challenging due to their morphological similarities and the rarity of the tumors. New biological markers are therefore needed to help differentiate between the tumor subtypes.

Ten sarcoma samples were picked on the basis of their simple karyotypes, having only one or a few structural chromosome aberrations. The samples were subjected to RNA-seq in order to identify new gene fusions and to evaluate to what extent chromosome rearrangements are associated with the generation of gene fusions. Three different gene fusion detecting softwares were used to identify potential fusion transcripts from the RNA-seq data.

We were, in this study, able to verify five novel fusions and one previously known fusion using different molecular genetic techniques. However, deeper analysis at the protein level is needed to evaluate their effect on tumor development.

This study has shown that RNA-Seq is a powerful tool to detect new gene fusions in sarcomas. Karyotypes are a helpful tool when analyzing potential fusion transcripts as all of the six fusions confirmed in this study had connections with the reported structural rearrangements. There still seems to be bioinformatical limitations when handling RNA-seq data since none of the softwares used in this study was able to identify all confirmed fusions. It is therefore advisable to use more than one software to detect fusion genes in sarcomas and, reasonably, in other solid tumors. (Less)
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author
Hofvander, Jakob
supervisor
organization
course
MOBT19 20131
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
4467853
date added to LUP
2014-06-17 12:24:08
date last changed
2014-06-17 12:24:08
@misc{4467853,
  abstract     = {Popular science summary:

Cancer is genetic disease arising due to mutations in our genome. Gene fusions are one type of mutation that has a strong impact on tumor development. They are often characteristic for specific tumor types and can therefore be used a diagnostic tool. The identification of new gene fusions have, in the recent years, been highly successful using a newly developed technique called RNA-sequencing.

Double stranded breaks in the DNA causing incorrect rejoining of the DNA molecules can fuse two previously separate genes resulting in the formation of a fusion gene. Gene fusions can be found in all malignancies and are often associated with structural rearrangements visible at the chromosome level.

RNA sequencing (RNA-seq) is a newly developed technique that already has contributed substantially to the detection of new gene fusions. It aims to sequence cells complete set of mRNA transcripts, generating millions of short sequences called reads. Advanced bioinformatical softwares can use the information from these reads to detect gene fusions. 

Sarcomas are rare malignant tumors of unknown cellular origin arising in bone or soft tissues. There are more than 50 different subtypes and diagnosis can be very challenging due to their morphological similarities and the rarity of the tumors. New biological markers are therefore needed to help differentiate between the tumor subtypes.

Ten sarcoma samples were picked on the basis of their simple karyotypes, having only one or a few structural chromosome aberrations. The samples were subjected to RNA-seq in order to identify new gene fusions and to evaluate to what extent chromosome rearrangements are associated with the generation of gene fusions. Three different gene fusion detecting softwares were used to identify potential fusion transcripts from the RNA-seq data. 

We were, in this study, able to verify five novel fusions and one previously known fusion using different molecular genetic techniques. However, deeper analysis at the protein level is needed to evaluate their effect on tumor development. 

This study has shown that RNA-Seq is a powerful tool to detect new gene fusions in sarcomas. Karyotypes are a helpful tool when analyzing potential fusion transcripts as all of the six fusions confirmed in this study had connections with the reported structural rearrangements. There still seems to be bioinformatical limitations when handling RNA-seq data since none of the softwares used in this study was able to identify all confirmed fusions. It is therefore advisable to use more than one software to detect fusion genes in sarcomas and, reasonably, in other solid tumors.},
  author       = {Hofvander, Jakob},
  language     = {eng},
  note         = {Student Paper},
  title        = {Identification of Gene Fusions in Sarcomas through RNA Sequencing},
  year         = {2014},
}