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Article

Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades

1
Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia
2
Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
3
Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb, School of Medicine and University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
4
Genom Ltd., Ilica 190, 10000 Zagreb, Croatia
5
Exaltum ultra Ltd.; Vrbik 13, 10000 Zagreb, Croatia
6
Department of Neurology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(5), 1251; https://doi.org/10.3390/ijms20051251
Received: 13 February 2019 / Revised: 4 March 2019 / Accepted: 6 March 2019 / Published: 12 March 2019
A collection of intracranial astrocytomas of different malignancy grades was analyzed for copy number aberrations (CNA) in order to identify regions that are driving cancer pathogenesis. Astrocytomas were analyzed by Array Comparative Genomic Hybridization (aCGH) and bioinformatics utilizing a Bioconductor package, Genomic Identification of Significant Targets in Cancer (GISTIC) 2.0.23 and DAVID software. Altogether, 1438 CNA were found of which losses prevailed. On our total sample, significant deletions affected 14 chromosomal regions, out of which deletions at 17p13.2, 9p21.3, 13q12.11, 22q12.3 remained significant even at 0.05 q-value. When divided into malignancy groups, the regions identified as significantly deleted in high grades were: 9p21.3; 17p13.2; 10q24.2; 14q21.3; 1p36.11 and 13q12.11, while amplified were: 3q28; 12q13.3 and 21q22.3. Low grades comprised significant deletions at 3p14.3; 11p15.4; 15q15.1; 16q22.1; 20q11.22 and 22q12.3 indicating their involvement in early stages of tumorigenesis. Significantly enriched pathways were: PI3K-Akt, Cytokine-cytokine receptor, the nucleotide-binding oligomerization domain (NOD)–like receptor, Jak-STAT, retinoic acid-inducible gene (RIG)-I-like receptor and Toll-like receptor pathways. HPV and herpex simplex infection and inflammation pathways were also represented. The present study brings new data to astrocytoma research amplifying the wide spectrum of changes that could help us identify the regions critical for tumorigenesis. View Full-Text
Keywords: astrocytoma; aCGH; comparative genomic hybridization; copy number aberrations; GISTIC2.0.23 astrocytoma; aCGH; comparative genomic hybridization; copy number aberrations; GISTIC2.0.23
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MDPI and ACS Style

Pećina-Šlaus, N.; Kafka, A.; Gotovac Jerčić, K.; Logara, M.; Bukovac, A.; Bakarić, R.; Borovečki, F. Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades. Int. J. Mol. Sci. 2019, 20, 1251. https://doi.org/10.3390/ijms20051251

AMA Style

Pećina-Šlaus N, Kafka A, Gotovac Jerčić K, Logara M, Bukovac A, Bakarić R, Borovečki F. Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades. International Journal of Molecular Sciences. 2019; 20(5):1251. https://doi.org/10.3390/ijms20051251

Chicago/Turabian Style

Pećina-Šlaus, Nives, Anja Kafka, Kristina Gotovac Jerčić, Monika Logara, Anja Bukovac, Robert Bakarić, and Fran Borovečki. 2019. "Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades" International Journal of Molecular Sciences 20, no. 5: 1251. https://doi.org/10.3390/ijms20051251

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