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Heterogeneity in uveal melanoma assessed by multiplex ligation‐dependent probe amplification (MLPA)
Author(s) -
DOPIERALA J,
COUPLAND SE,
DAMATO B
Publication year - 2009
Publication title -
acta ophthalmologica
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.534
H-Index - 87
eISSN - 1755-3768
pISSN - 1755-375X
DOI - 10.1111/j.1755-3768.2009.3263.x
Subject(s) - multiplex ligation dependent probe amplification , multiplex , locus (genetics) , microbiology and biotechnology , pathology , monosomy , genetic heterogeneity , biology , cancer research , genetics , medicine , gene , chromosome , karyotype , phenotype , exon
Purpose To study intratumour heterogeneity in primary uveal melanoma (UM) by MLPA in microdissected formalin‐fixed, paraffin‐embedded (FFPE) tissues. Methods DNA was extracted from 2‐9 areas microdissected from 32 FFPE UMs. Thirty‐one loci on chromosomes 1p, 3, 6 and 8 were tested for copy number changes using the SALSA MLPA P027.B1 assay (MRC Holland). MLPA data were displayed as dosage quotients (DQs), which were classified to 5 ranges (0.35‐0.64 deleted; 0.65‐0.84 equivocal deletion; 0.85‐1.14 normal; 1.15‐1.35 equivocal amplification; >1.35 amplified). The tumour was considered heterogeneous at a locus, if a) the difference in DQs of any two areas was higher than 0.2 (value determined by ROC analysis), and b) the DQs of the areas belonged to different ranges. Results Genetic abnormalities were detected in all 32 UMs. Monosomy 3, the most significant metastasis predictor, and gain of 8q genes MYC or DDEF1 were detected in at least 1 microdissected area of 22 (69%) and 28 (87%) of the tumours, respectively. The comparison of MLPA data obtained from different areas of UMs showed heterogeneity in 1‐24 loci across chromosomes 1p, 3, 6 and 8 in 26 (81%) tumours. Interestingly, trisomy 3 was observed in 3 (9%) UMs and these tumours showed the highest degree of heterogeneity (>23 heterogeneous loci). Intratumour heterogeneity of 3p12.2 (ROBO1) and 6p21.2 (CDKN1A) were most common and present in more than 35% of the tumours. Conclusion Heterogeneity of chromosomal abnormalities of 1p, 3, 6 and 8 is present in many UM. Taking one random tumour sample for prognostic testing, therefore, may not be representative of the whole tumour.