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Detection of a Distinctive Genomic Signature in Rhabdoid Glioblastoma, A Rare Disease Entity Identified by Whole Exome Sequencing and Whole Transcriptome Sequencing.

Koh Y, Park I, Sun CH, Lee S, Yun H, Park CK, Park SH, Park JK, Lee SH - Transl Oncol (2015)

Bottom Line: We found loss of heterozygosity and focal homozygous deletion on 9q21, which includes CDKN2A and CDKN2B.These simultaneous alterations are very rarely found in GBM.We observed a unique genomic signature in R-GBM compared to conventional GBM, which may provide insight regarding R-GBM as a distinct disease entity among the larger group of GBMs.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea; Cancer Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-799, Korea.

No MeSH data available.


Related in: MedlinePlus

Expression status of selected genetic changes found in the R-GBM sample in comparison with normal brain. (A) genetic changes with copy number alteration, (B) genetic changes with single nucleotide variation, and (C) genetic changes with gene fusion (y axis shows the log2 ratio of the expression level (value in RPKM) in our patient over the mean expression level (value in RPKM) in normal brain (http://www.brainspan.org)).
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f0015: Expression status of selected genetic changes found in the R-GBM sample in comparison with normal brain. (A) genetic changes with copy number alteration, (B) genetic changes with single nucleotide variation, and (C) genetic changes with gene fusion (y axis shows the log2 ratio of the expression level (value in RPKM) in our patient over the mean expression level (value in RPKM) in normal brain (http://www.brainspan.org)).

Mentions: We used WTS data to investigate functional genetic changes in R-GBM, and the public database was used as a reference. First, we compared the RPKM values of specific genetic changes found between tumor and normal brain tissue (Figure 3). We focused on affected genes with more than a 4-fold change in expression and integrated the results among WES, WTS, and array-CGH. Several genes had significant SNVs, CNAs, or fusions. Among genes with SNVs, NDRG2, NKAIN2, CER1, and ISL1 were downregulated, whereas PARP9 was upregulated in the tumor sample of the study patient compared to normal brain tissue. Among genes with CNAs, NOTCH1, EGFR, CDK6, EZH2, and MET were upregulated, whereas CDKN2A and 2B were downregulated in the tumor sample of the study patient compared to normal brain tissue. These results are summarized in Table 3.


Detection of a Distinctive Genomic Signature in Rhabdoid Glioblastoma, A Rare Disease Entity Identified by Whole Exome Sequencing and Whole Transcriptome Sequencing.

Koh Y, Park I, Sun CH, Lee S, Yun H, Park CK, Park SH, Park JK, Lee SH - Transl Oncol (2015)

Expression status of selected genetic changes found in the R-GBM sample in comparison with normal brain. (A) genetic changes with copy number alteration, (B) genetic changes with single nucleotide variation, and (C) genetic changes with gene fusion (y axis shows the log2 ratio of the expression level (value in RPKM) in our patient over the mean expression level (value in RPKM) in normal brain (http://www.brainspan.org)).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4562980&req=5

f0015: Expression status of selected genetic changes found in the R-GBM sample in comparison with normal brain. (A) genetic changes with copy number alteration, (B) genetic changes with single nucleotide variation, and (C) genetic changes with gene fusion (y axis shows the log2 ratio of the expression level (value in RPKM) in our patient over the mean expression level (value in RPKM) in normal brain (http://www.brainspan.org)).
Mentions: We used WTS data to investigate functional genetic changes in R-GBM, and the public database was used as a reference. First, we compared the RPKM values of specific genetic changes found between tumor and normal brain tissue (Figure 3). We focused on affected genes with more than a 4-fold change in expression and integrated the results among WES, WTS, and array-CGH. Several genes had significant SNVs, CNAs, or fusions. Among genes with SNVs, NDRG2, NKAIN2, CER1, and ISL1 were downregulated, whereas PARP9 was upregulated in the tumor sample of the study patient compared to normal brain tissue. Among genes with CNAs, NOTCH1, EGFR, CDK6, EZH2, and MET were upregulated, whereas CDKN2A and 2B were downregulated in the tumor sample of the study patient compared to normal brain tissue. These results are summarized in Table 3.

Bottom Line: We found loss of heterozygosity and focal homozygous deletion on 9q21, which includes CDKN2A and CDKN2B.These simultaneous alterations are very rarely found in GBM.We observed a unique genomic signature in R-GBM compared to conventional GBM, which may provide insight regarding R-GBM as a distinct disease entity among the larger group of GBMs.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 110-744, Korea; Cancer Research Institute, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 110-799, Korea.

No MeSH data available.


Related in: MedlinePlus