Journal article
Whole exome sequencing of a single osteosarcoma case—integrative analysis with whole transcriptome RNA-seq data
Human Genomics, Vol.8(1)
2014
Abstract
Background
Osteosarcoma (OS) is a prevalent primary malignant bone tumour with unknown etiology. These highly metastasizing tumours are among the most frequent causes of cancer-related deaths. Thus, there is an urgent need for different markers, and with our study, we were aiming towards finding novel biomarkers for OS.
Methods
For that, we analysed the whole exome of the tumorous and non-tumour bone tissue from the same patient with OS applying next-generation sequencing. For data analysis, we used several softwares and combined the exome data with RNA-seq data from our previous study.
Results
In the tumour exome, we found wide genomic rearrangements, which should qualify as chromotripsis—we detected almost 3,000 somatic single nucleotide variants (SNVs) and small indels and more than 2,000 copy number variants (CNVs) in different chromosomes. Furthermore, the somatic changes seem to be associated to bone tumours, whereas germline mutations to cancer in general. We confirmed the previous findings that the most significant pathway involved in OS pathogenesis is probably the WNT/β-catenin signalling pathway. Also, the IGF1/IGF2 and IGF1R homodimer signalling and TP53 (including downstream tumour suppressor gene EI24) pathways may have a role. Additionally, the mucin family genes, especially MUC4 and cell cycle controlling gene CDC27 may be considered as potential biomarkers for OS.
Conclusions
The genes, in which the mutations were detected, may be considered as targets for finding biomarkers for OS. As the study is based on a single case and only DNA and RNA analysis, further confirmative studies are required.
Details
- Title
- Whole exome sequencing of a single osteosarcoma case—integrative analysis with whole transcriptome RNA-seq data
- Authors/Creators
- E. Reimann (Author/Creator)S. Kõks (Author/Creator)X.D. Ho (Author/Creator)K. Maasalu (Author/Creator)A. Märtson (Author/Creator)
- Publication Details
- Human Genomics, Vol.8(1)
- Publisher
- BioMed Central
- Identifiers
- 991005545016807891
- Copyright
- © 2014 Reimann et al.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
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- Citation topics
- 1 Clinical & Life Sciences
- 1.118 Soft Tissue, Bone & Nerve Cancers
- 1.118.300 Sarcoma Research
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics