High-density genome array is superior to fluorescence in-situhybridization analysis of monosomy 3 in choroidal melanoma fine needleaspiration biopsy

[摘要] Purpose: Using fluorescence in situ hybridization (FISH) andhigh-density single nucleotide polymorphism (SNP) mapping genome array,we comparatively evaluated chromosome 3 status and other chromosomalaberrations within a series of choroidal melanomas biopsied by fineneedle aspiration (FNAB).Methods: Transscleral FNAB was performed in 59 patients (59 eyes)who had a clinical diagnosis of choroidal melanoma. Biopsies wereprocessed for chromosome 3 status by centromeric interphase FISH,cytopathology, cell culture, and simultaneous genomic DNA and RNAmapping array analysis.Results: FISH yielded chromosome 3 status in 38 of 59 (64%) eyes,while high-density SNP mapping array yielded chromosome 3 status in 43of 59 (73%) eyes. Monosomy 3 was detected by FISH in 15 of 38 (39%)cases, and high-density SNP mapping array data confirmed the finding in13 of the 15 cases. Furthermore, high-density SNP mapping array revealedfive additional cases of significant chromosome 3 aberration notdetected by FISH. High-density genomic mapping also provided detailedpatterns of chromosomal gain and loss on chromosomes 1, 6, 8, and 9which segregated into two groups characterized by either monosomy 3 orchromosome 6p gain.Conclusions: High-density SNP mapping array was better than FISH indetecting chromosome 3 aberrations and monosomy in our melanoma samples.More importantly, the mapping arrays detected additional patterns ofchromosomal aberration, which suggest specific pathways for cytogeneticrearrangements in choroidal melanoma and may improve prognostictesting.

[学科分类] 生物化学/生物物理