FROM AMPLIFICATION TO GENE IN THYROID-CANCER - A HIGH-RESOLUTION MAPPED BACTERIAL-ARTIFICIAL-CHROMOSOME RESOURCE FOR CANCER CHROMOSOME-ABERRATIONS GUIDES GENE DISCOVERY AFTER COMPARATIVE GENOME HYBRIDIZATION

Chromosome rearrangements associated with neoplasms provide a rich res ource for definition of the pathways of tumorigenesis. The power of co mparative genome hybridization (CGH) to identify novel genes depends o n the existence of suitable markers, which are lacking throughout most of the genome. We now report a general approach that translates CGH d ata into higher-resolution genomic-clone data that are then used to de fine the genes located in aneuploid regions. We used CGH to study 33 t hyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed a mplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p 34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial ar tificial chromosomes (BACs) was constructed, and 87 of these were hybr idized to a tumor-cell line. Four BACs carried genomic DNA that was am plified in these cells. The maximum amplified region was narrowed to 3 -6 Mb by multicolor FISH with the flanking BACs, and the minimum ampli con size was defined by a contig of 420 kb. Sequence analysis of the a mplified BAC 1D9 revealed a fragment of the gene, encoding protein kin ase C epsilon (PKC epsilon), that was then shown to be amplified and r earranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs;and large-scale sequencing has led directly to the d efinition of PKC epsilon as a previously unmapped candidate gene invol ved in thyroid tumorigenesis.