Urrence of the genomic breakpoints was analyzed in both groups. In

Urrence of the genomic breakpoints was analyzed in both groups. In

Urrence of the genomic breakpoints was analyzed in both groups. In the 1p/19q-co-deleted tumors, by definition, the chromosome 1 and 19 centromeric breakpoints were observed simultaneously within all of the tumors (Figure S1, Panel A). In the non-1p/19q-co-deleted tumors, the most common co-occurrence of genomic breakpoints involved chromosome 9 (44683090) and chromosome 19 (32455280) in 6/15 cases (Figure S1, Panel B).Copy Neutral LOH in Anaplastic OligodendrogliomasFigure 2. Frequency of genomic alterations in the 1p/19q-co-deleted anaplastic oligodendrogliomas on the top part of the panel and non-1p/19q-co-deleted anaplastic oligodendrogliomas on the bottom part. Panel A. Genomic gain, genomic loss and uniparental disomy are indicated in red, green and blue, respectively. Panel B. High-level amplification and homozygous deletion are indicated in red and green, respectively. Panel C. Genomic breakpoints are indicated with a black dot across the genome. 22948146 doi:10.1371/journal.pone.0045950.gTable 1. Genomic alterations BTZ-043 web containing candidate genes in 1p/19q co-deleted anaplastic oligodendrogliomas in at least two tumors (as TA01 custom synthesis identified by genoCN).Chromosome region Homozygous deletion chr19_32455280_32670285 chr19_32679064_32877033 chr9_44683090_44770712 chr4_69097539_69135491 chr9_44779627_45338079 chr4_69139402_69258302 chr6_67075448_67105019 chr9_21963422_22123716 High-level amplification chr21_46815526_46935542 chr11_133914145_134445626 chr21_46746267_46812570 chr8_39350791_39457081 chr11_133844842_133909403 chr12_21054_213172 chr3_38411_267992 chr8_146163558_146264218 doi:10.1371/journal.pone.0045950.tN 6 5 5 3 3 2 2 2 4 3 3 3 2 2 2GenesZNFTMPRSS11B FAM27C YTHDCCDKN2B-AS1-CDKN2A-CDKN2B-C9orf53 NCRNA00175-SLC19A1-COL18A1 VPS26B-GLB1L3-NCAPD3-ACAD8-B3GAT1-LOC283177-THYN1-JAM3-GLB1LADAM3A-ADAM18 LOC100128239 LOC100288778-IQSEC3-FAM138D CHL1 ZNF252-TMED10P1-C8orf77-ZNFCopy Neutral LOH in Anaplastic OligodendrogliomasTable 2. Genomic alterations containing candidate genes in non 1p/19q co-deleted anaplastic oligodendrogliomas in at least two tumors (as identified by genoCN).Chromosome region Homozygous deletion chr9_22534004_22615342 chr9_21413394_21951866 chr9_21998026_22531137 chr9_22617742_23432605 High-level amplification chr7_54622953_55307516 chr12_56366092_56463559 chr3_38411_267992 chr7_54577787_54620005 chr7_55312776_55466552 chr7_61504406_62203847 chr8_121235610_121468055 doi:10.1371/journal.pone.0045950.tN 3 2 2 2 3 2 2 2 2 2GenesIFNE-IFNA1-MIR31-MTAP-LOC554202 CDKN2B-AS1-CDKN2B-DMRTAEGFR-VSTM2A-SEC61G CDK2-RAB5B-RPS26-IKZF4-SUOX CHL1 VSTM2A LANCLMTBP-MRPL13-COL14AClinico-molecular correlationsNo statistically significant difference was observed between the cohort of patients with 1p/19q-co-deleted tumors versus the cohort of patients with non-1p/19q-co-deleted tumors in terms of: (i) sexratio (1.3 versus 1.5, p = 0.9), (ii) median age at diagnosis (50.0 versus 49.9 years, p = 0.9) and (iii) median KPS at diagnosis (90 versus 90 , p = 0.9).Figure 3. An anaplastic oligodendroglioma with CDKN2A expression and normal CDKN2A gene copy number and allelic statuses. Panel A. Top part: Genomic profile with the copy number status. Middle part: Genomic profile with the allelic frequencies. Bottom part: The genomic profile including genomic loss (in green), normal copy number status (light blue) and copy neutral loss of heterozygosity (dark blue). Panel B. Chromosome 9 and the allelic frequencies (the arrow indicates the CDKNA locus). Panel C.Urrence of the genomic breakpoints was analyzed in both groups. In the 1p/19q-co-deleted tumors, by definition, the chromosome 1 and 19 centromeric breakpoints were observed simultaneously within all of the tumors (Figure S1, Panel A). In the non-1p/19q-co-deleted tumors, the most common co-occurrence of genomic breakpoints involved chromosome 9 (44683090) and chromosome 19 (32455280) in 6/15 cases (Figure S1, Panel B).Copy Neutral LOH in Anaplastic OligodendrogliomasFigure 2. Frequency of genomic alterations in the 1p/19q-co-deleted anaplastic oligodendrogliomas on the top part of the panel and non-1p/19q-co-deleted anaplastic oligodendrogliomas on the bottom part. Panel A. Genomic gain, genomic loss and uniparental disomy are indicated in red, green and blue, respectively. Panel B. High-level amplification and homozygous deletion are indicated in red and green, respectively. Panel C. Genomic breakpoints are indicated with a black dot across the genome. 22948146 doi:10.1371/journal.pone.0045950.gTable 1. Genomic alterations containing candidate genes in 1p/19q co-deleted anaplastic oligodendrogliomas in at least two tumors (as identified by genoCN).Chromosome region Homozygous deletion chr19_32455280_32670285 chr19_32679064_32877033 chr9_44683090_44770712 chr4_69097539_69135491 chr9_44779627_45338079 chr4_69139402_69258302 chr6_67075448_67105019 chr9_21963422_22123716 High-level amplification chr21_46815526_46935542 chr11_133914145_134445626 chr21_46746267_46812570 chr8_39350791_39457081 chr11_133844842_133909403 chr12_21054_213172 chr3_38411_267992 chr8_146163558_146264218 doi:10.1371/journal.pone.0045950.tN 6 5 5 3 3 2 2 2 4 3 3 3 2 2 2GenesZNFTMPRSS11B FAM27C YTHDCCDKN2B-AS1-CDKN2A-CDKN2B-C9orf53 NCRNA00175-SLC19A1-COL18A1 VPS26B-GLB1L3-NCAPD3-ACAD8-B3GAT1-LOC283177-THYN1-JAM3-GLB1LADAM3A-ADAM18 LOC100128239 LOC100288778-IQSEC3-FAM138D CHL1 ZNF252-TMED10P1-C8orf77-ZNFCopy Neutral LOH in Anaplastic OligodendrogliomasTable 2. Genomic alterations containing candidate genes in non 1p/19q co-deleted anaplastic oligodendrogliomas in at least two tumors (as identified by genoCN).Chromosome region Homozygous deletion chr9_22534004_22615342 chr9_21413394_21951866 chr9_21998026_22531137 chr9_22617742_23432605 High-level amplification chr7_54622953_55307516 chr12_56366092_56463559 chr3_38411_267992 chr7_54577787_54620005 chr7_55312776_55466552 chr7_61504406_62203847 chr8_121235610_121468055 doi:10.1371/journal.pone.0045950.tN 3 2 2 2 3 2 2 2 2 2GenesIFNE-IFNA1-MIR31-MTAP-LOC554202 CDKN2B-AS1-CDKN2B-DMRTAEGFR-VSTM2A-SEC61G CDK2-RAB5B-RPS26-IKZF4-SUOX CHL1 VSTM2A LANCLMTBP-MRPL13-COL14AClinico-molecular correlationsNo statistically significant difference was observed between the cohort of patients with 1p/19q-co-deleted tumors versus the cohort of patients with non-1p/19q-co-deleted tumors in terms of: (i) sexratio (1.3 versus 1.5, p = 0.9), (ii) median age at diagnosis (50.0 versus 49.9 years, p = 0.9) and (iii) median KPS at diagnosis (90 versus 90 , p = 0.9).Figure 3. An anaplastic oligodendroglioma with CDKN2A expression and normal CDKN2A gene copy number and allelic statuses. Panel A. Top part: Genomic profile with the copy number status. Middle part: Genomic profile with the allelic frequencies. Bottom part: The genomic profile including genomic loss (in green), normal copy number status (light blue) and copy neutral loss of heterozygosity (dark blue). Panel B. Chromosome 9 and the allelic frequencies (the arrow indicates the CDKNA locus). Panel C.

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