Identification of genomic aberrations in hemangioblastoma by droplet digital PCR and SNP microarray highlights novel candidate genes and pathways for pathogenesis

BMC Genomics
Ruty Mehrian-ShaiAmos Toren

Abstract

The genetic mechanisms underlying hemangioblastoma development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays and droplet digital PCR analysis to detect copy number variations (CNVs) in total of 45 hemangioblastoma tumors. We identified 94 CNVs with a median of 18 CNVs per sample. The most frequently gained regions were on chromosomes 1 (p36.32) and 7 (p11.2). These regions contain the EGFR and PRDM16 genes. Recurrent losses were located at chromosome 12 (q24.13), which includes the gene PTPN11. Our findings provide the first high-resolution genome-wide view of chromosomal changes in hemangioblastoma and identify 23 candidate genes: EGFR, PRDM16, PTPN11, HOXD11, HOXD13, FLT3, PTCH, FGFR1, FOXP1, GPC3, HOXC13, HOXC11, MKL1, CHEK2, IRF4, GPHN, IKZF1, RB1, HOXA9, and micro RNA, such as hsa-mir-196a-2 for hemangioblastoma pathogenesis. Furthermore, our data implicate that cell proliferation and angiogenesis promoting pathways may be involved in the molecular pathogenesis of hemangioblastoma.

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Citations

Jul 2, 2020·Molecular Cytogenetics·Jéssica Almeida Batista-GomesAndré Salim Khayat
Apr 16, 2020·International Journal of Molecular Sciences·Amelia CasamassimiCiro Abbondanza
May 16, 2019·Familial Cancer·Anouk N A van der Horst-SchriversThera P Links
Oct 24, 2021·World Neurosurgery·Dragan JankovicKenan I Arnautovic

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Methods Mentioned

BETA
ubiquitination
PCR
chip
chromosomal aberrations
biopsies

Software Mentioned

Chromosome Analysis Suite ( ChAS )
Primer Express BLAST
Quantasoft

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