Identification of novel candidate oncogenes in chromosomal region 17p11.2-p12 in human osteosarcoma
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE32964 | GEO | 2013/04/15
SECONDARY ACCESSION(S): PRJNA146523
REPOSITORIES: GEO
Similar Datasets
Project description:in 25% - 30% of all OS cases the chromosome region 17p11.2-p12 is aberrant. Using SNP array in conjunction with expression microarrays we try to identify genes which can be classified as oncogens or are in someway benificial to the survival of the tumor. To identify minimal significant amplified region(s) that is(are) aberrant in osteosarcoma tumorigenesis, with a special emphasis on but not limitied to chromosome region 17p11.2-p12
2013-04-15 | E-GEOD-32964 | biostudies-arrayexpress
Project description:Osteosarcoma is the most common primary malignancy of bone. The tumours are characterized by high genomic instability, including the occurrence of multiple regions of amplifications and deletions. Chromosome region 17p11.2-p12 is amplified in about 25% of cases. In previous studies, COPS3 and PMP22 have been identified as candidate oncogenes in this region. Considering the complexity and variation of the amplification profiles for this segment, the involvement of additional causative oncogenes is to be expected. The aim of the present investigation is to identify novel candidate oncogenes in 17p11.2-p12. We selected 26 of in total 85 osteosarcoma samples (31%) with amplification events in 17p11.2-p12, using quantitative PCR for 8 marker genes. These were subjected to high-resolution SNP array analysis and subsequent GISTIC analysis to identify the most significantly amplified regions. Two major amplification peaks were found in the 17p11.2-p12 region. Overexpression as a consequence of gene amplification is a major mechanism for oncogene activation in tumours. Therefore, to identify the causative oncogenes, we next determined expression levels of all genes within the two segments using expression array data that could be generated for 20 of the selected samples. We identified 11 genes that were overexpressed through amplification in at least 50% of cases. Nine of these, c17orf39, RICH2, c17orf45, TOP3A, COPS3, SHMT1, PRPSAP2, PMP22, and RASD1, demonstrated a significant association between copy number and expression level. We conclude that these genes, including COPS3 and PMP22, are candidate oncogenes in 17p11.2-p12 of importance in osteosarcoma tumourigenesis.
| S-EPMC3266911 | biostudies-literature
Project description:Background: Osteosarcoma (OS) tumors and derived cell lines are characterized by complex chromosomal abnormalities. The availability of molecular genome profiling techniques such as array CGH have markedly enabled the high-resolution genome analysis of tumor genomes, as well as helped elucidate the mechanisms leading to their complexity. The identification of tumor-specific genomic profiles is currently the focus of many array CGH studies, but there have been no analyses to date documenting the genomic signatures consistent with chromosomal instability mechanisms in OS. Results: In this study we utilized high-resolution oligonucleotide array CGH to interrogate recurrent signatures of genomic imbalance in 10 OS tumors that were consistent with the breakage fusion bridge(BFB) mechanism. Comparative analysis of the tumors showed that they exhibited varying levels of genomic imbalance. The analysis also highlighted three chromosomal regions (6p21 ~ p22, 8q24 and 17p11.2 ~ p12) that were consistently involved in high level gain or amplification events. These three regions have been previously shown by us to be not only involved in high-level imbalance in OS-derived cell lines, but also to exhibit similar imbalance profiles consistent with BFB-related events. Karyotype and dual-color FISH analysis showed that repeated rearrangements of these unstable chromosomes through BFB cycles may create a heterogeneous pattern of copy number alterations. Conclusions: This genome-wide analysis is the first to utilize oligonucleotide array CGH and FISH analysis to derive possible genomic signatures of chromosomal instability in OS tumors. Perpetuation of the BFB cycle will create a heterogeneous pattern of copy number alterations by repeated rearrangement of the unstable tumor genome., thereby generating diverse phenotypes The resulting phenotypic diversity can generate tumors with a propensity for an aggressive disease course. A better understanding of the underlying mechanisms events leading to tumor development could result in the identification of prognostic markers and therapeutic targets. Experiment Overall Design: 10 OS tumor samples were used; fluor-flip was performed with normal human DNA as control
2008-06-16 | E-GEOD-9654 | biostudies-arrayexpress
Project description:Background: Osteosarcoma (OS) tumors and derived cell lines are characterized by complex chromosomal abnormalities. The availability of molecular genome profiling techniques such as array CGH have markedly enabled the high-resolution genome analysis of tumor genomes, as well as helped elucidate the mechanisms leading to their complexity. The identification of tumor-specific genomic profiles is currently the focus of many array CGH studies, but there have been no analyses to date documenting the genomic signatures consistent with chromosomal instability mechanisms in OS. Results: In this study we utilized high-resolution oligonucleotide array CGH to interrogate recurrent signatures of genomic imbalance in 10 OS tumors that were consistent with the breakage fusion bridge(BFB) mechanism. Comparative analysis of the tumors showed that they exhibited varying levels of genomic imbalance. The analysis also highlighted three chromosomal regions (6p21 ~ p22, 8q24 and 17p11.2 ~ p12) that were consistently involved in high level gain or amplification events. These three regions have been previously shown by us to be not only involved in high-level imbalance in OS-derived cell lines, but also to exhibit similar imbalance profiles consistent with BFB-related events. Karyotype and dual-color FISH analysis showed that repeated rearrangements of these unstable chromosomes through BFB cycles may create a heterogeneous pattern of copy number alterations. Conclusions: This genome-wide analysis is the first to utilize oligonucleotide array CGH and FISH analysis to derive possible genomic signatures of chromosomal instability in OS tumors. Perpetuation of the BFB cycle will create a heterogeneous pattern of copy number alterations by repeated rearrangement of the unstable tumor genome., thereby generating diverse phenotypes The resulting phenotypic diversity can generate tumors with a propensity for an aggressive disease course. A better understanding of the underlying mechanisms events leading to tumor development could result in the identification of prognostic markers and therapeutic targets. Keywords: osteosarcoma, chromosomal instability, gene amplification, breakage-fusion-bridge cycle, oligonucleotide array comparative genomic hybridization
2007-11-21 | GSE9654 | GEO
Project description:We describe a 6-year-old girl with a T118M PMP22 mutation and heterozygous deletion of PMP22 on chromosome 17 (17p11.2-p12) resulting in a severe sensorimotor polyneuropathy.This study is a case report in which the relevant mutations are described.Foot pain, cavovarus feet, tibialis anterior atrophy, absent reflexes, and inability to walk were found when the patient was age 6 years. Nerve conduction studies showed evidence of a sensorimotor polyneuropathy and compressive mononeuropathies of bilateral median nerves at the wrist and ulnar nerves at the elbow. Genetic testing revealed deletion of a PMP22 allele and T118M PMP22 mutation in the remaining allele.The severe sensorimotor polyneuropathy and hereditary neuropathy with liability to pressure palsies (HNPP) in this patient was likely a consequence of both decreased expression of PMP22 causing features consistent with HNPP and unopposed expression of the T118M mutant form of PMP22 that is relatively benign in the heterozygous state. The T118M mutant form of PMP22 can be disease-modifying in the appropriate circumstances.
| S-EPMC4596757 | biostudies-literature
Project description:Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. Our data indicate an increased rate of clustered single nucleotide variant mutation in cis that is not present with recurrent rearrangement of the genome at the same locus. Indel and single nucleotide mutations are associated with both copy number gains and losses of 17p11.2, occur up to ~1 Mb away from the breakpoint junctions, and favor C>G transversion substitutions; results suggesting that single stranded DNA is formed during the genesis of the SV and providing compelling support for a microhomology-mediated break-induced replication mechanism for SV formation.
2019-01-17 | GSE125209 | GEO
Project description:Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. Our data indicate an increased rate of clustered single nucleotide variant mutation in cis that is not present with recurrent rearrangement of the genome at the same locus. Indel and single nucleotide mutations are associated with both copy number gains and losses of 17p11.2, occur up to ~1 Mb away from the breakpoint junctions, and favor C>G transversion substitutions; results suggesting that single stranded DNA is formed during the genesis of the SV and providing compelling support for a microhomology-mediated break-induced replication mechanism for SV formation.
2019-01-17 | GSE125208 | GEO
Project description:Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. Our data indicate an increased rate of clustered single nucleotide variant mutation in cis that is not present with recurrent rearrangement of the genome at the same locus. Indel and single nucleotide mutations are associated with both copy number gains and losses of 17p11.2, occur up to ~1 Mb away from the breakpoint junctions, and favor C>G transversion substitutions; results suggesting that single stranded DNA is formed during the genesis of the SV and providing compelling support for a microhomology-mediated break-induced replication mechanism for SV formation.
2019-01-17 | GSE125207 | GEO
Project description:Transcriptome data of Glaciozyma antarctica P12
| PRJNA509767 | ENA
Project description:Transcriptome analysis of AGS cells infected with Helicobacter pylori P12
2018-09-17 | GSE73226 | GEO