High-density genome array is superior to fluorescence in-situ hybridization analysis of monosomy 3 in choroidal melanoma fine needle aspiration biopsy.
OBJECTIVE
Using fluorescence in situ hybridization (FISH) and high-density single nucleotide polymorphism (SNP) mapping genome array, we comparatively evaluated chromosome 3 status and other chromosomal aberrations within a series of choroidal melanomas biopsied by fine needle aspiration (FNAB).


METHODS
Transscleral FNAB was performed in 59 patients (59 eyes) who had a clinical diagnosis of choroidal melanoma. Biopsies were processed for chromosome 3 status by centromeric interphase FISH, cytopathology, cell culture, and simultaneous genomic DNA and RNA mapping 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 43 of 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 in 13 of the 15 cases. Furthermore, high-density SNP mapping array revealed five additional cases of significant chromosome 3 aberration not detected by FISH. High-density genomic mapping also provided detailed patterns of chromosomal gain and loss on chromosomes 1, 6, 8, and 9 which segregated into two groups characterized by either monosomy 3 or chromosome 6p gain.


CONCLUSIONS
High-density SNP mapping array was better than FISH in detecting chromosome 3 aberrations and monosomy in our melanoma samples. More importantly, the mapping arrays detected additional patterns of chromosomal aberration, which suggest specific pathways for cytogenetic rearrangements in choroidal melanoma and may improve prognostic testing.
Young
Tara A
TA
Department of Ophthalmology and Jules Stein Eye Institute, Los Angeles, CA 90095-7000, USA. young@jsei.ucla.edu
Burgess
Barry L
BL
Rao
Nagesh P
NP
Gorin
Michael B
MB
Straatsma
Bradley R
BR
D044963:Biopsy, Fine-Needle; D002830:Choroid Neoplasms / Q000235:genetics* / Q000473:pathology; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics / Q000648:ultrastructure; D002893:Chromosomes, Human, Pair 3 / Q000235:genetics* / Q000648:ultrastructure; D002896:Chromosomes, Human, Pair 6 / Q000235:genetics / Q000648:ultrastructure; D002897:Chromosomes, Human, Pair 7 / Q000235:genetics / Q000648:ultrastructure; D002899:Chromosomes, Human, Pair 9 / Q000235:genetics / Q000648:ultrastructure; D020732:Cytogenetic Analysis / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D007621:Karyotyping / Q000379:methods; D008545:Melanoma / Q000235:genetics* / Q000473:pathology; D009006:Monosomy / Q000175:diagnosis*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity