Large deletion of part of the HMGIC locus accompanying a t(3;12)(q27∼q28;q14∼q15) in a lipoma

The high mobility group protein gene HMGIC has been found to be rearranged in a variety of human benign solid tumors. Often, these rearrangements lead to fusion genes of which that between HMGIC and LPP underlying t(3;12)(q27∼q28;q14∼q15) is by far the most common. Herein, we analysed a lipoma with a t(3;12)(q27∼q28;q14∼q15). RT-PCR revealed the presence of a HMGIC-LPP fusion transcript composed of exons 1–3 of HMGIC and exons 9–11 of LPP, but the absence of the reverse LPP-HMGIC fusion transcript. Fluorescence in situ hybridization experiments using different probes derived from the HMGIC gene and its 3′ vicinity showed the absence of FISH signals on the derivative chromosome 3. Thus, in the present tumor the t(3;12)(q27∼q28;q14∼q15) was accompanied by a large genomic deletion. Roughly, it can be estimated that at least 170 kb of chromosome 12 material were deleted. To the best of our knowledge, this is the first report showing that the “simple” t(3;12)(q27∼q28;q14∼q15) results in a large deletion of DNA.