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J. Dopierala, B. E. Damato, S. E. Coupland; Gains in Chromosome 3 Detected by MLPA in Uveal Melanoma. Invest. Ophthalmol. Vis. Sci. 2010;51(13):856.
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© ARVO (1962-2015); The Authors (2016-present)
To investigate gains in chromosome 3 in uveal melanomas (UM) using Multiplex Ligation-Dependent Probe Amplification (MLPA).
Using MLPA, we examined 371 UMs collected between 1999 and 2008. The DNA was extracted from 104 frozen specimens using a salt/ethanol precipitation method; 259 fresh specimens using the EZ1 BioRobot (Qiagen); and 8 formalin-fixed paraffin-embedded tumours using Blood and Tissue Qiagen kit. All samples were tested in triplicate for chromosomal abnormalities using the P027.B1 MLPA assay with probes on chromosomes 1p, 3, 6 and 8. This kit examines thirteen loci on chromosome 3, which are as follows: FANCD2 x2 loci, VHL, MLH1, CTNNB1, SEMA3B, FHIT x2 loci, ROBO1, CPO, RHO, MME, and OPA1. Five normal choroid tissues were used as controls for normalization and equalization of the data. The MLPA results were analysed by an Excel-based spreadsheet designed by the National Genetics Reference Laboratory (NGRL), Manchester, UK and displayed as dosage quotients.
Gains of between one and nine of the tested 13 loci on chromosome 3 were detected in 31 of 371 (8%) UMs. In the majority of these 31 specimens -i.e. 25 UM (80%) - only 1-2 loci were amplified. The remaining 6 tumours (20%) showed gains of 3 loci in 3 tumors, and 6-9 loci in another 3 UM. Amplification of VHL on 3p25.3 and MLH1 on 3p21.1 were the most common affected loci, and were present in 18 (58%) and 8 (26%) of 31 UM, respectively. The least common amplified locus was FHIT (3p14.2), which was seen in only one UM. Interestingly, some UM a mixture of losses and gains across chromosome 3: e.g. losses of loci on 3q and gains of loci on 3p.
Gains of chromosome 3 are rare but were detected in 8% of UM using MLPA. In the majority of cases, the gains involved only one to two loci with 3p25.3 (VHL) and 3p21.1 (MLH1) being the most common. Gains of and greater than 3 loci on chromosome 3 were only seen in 6 (1.6%) of UM. The clinical significance of these partial amplifications in chromosome 3 is unclear at present and is currently being reviewed.
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