Assessment of Isochromosome 12p & 12p Abnormalities in Germ Cell Tumors Using FISH, SNP-Arrays & NGS/ Mate-Pair Sequencing.

The identification of isochromosome 12p [i(12p)] and 12p gains have significant clinical utility in the diagnosis of germ cell tumors (GCT). We have summarized the results of FISH assays to identify i(12p), performed in a Clinical Laboratory Improvement Amendments (CLIA)-validated setting for 536 specimens. In addition, the American Association for Cancer Research (AACR) Project GENIE registry & The Cancer Genome Atlas (TCGA) datasets were evaluated for chromosome 12p gains, and a limited number of cases were concurrently evaluated using FISH, SNP-arrays and NGS (including mate-pair sequencing). Specimens submitted for FISH testing were frequently from potential sites of metastases (male: 70.9%; female: 69.3%) and polysomy of chromosome 12 with or without concurrent i(12p) was a frequent finding, seen in 3% (16 of 536) and 35% (186 of 536) of cases, respectively. Our analysis suggests that 12p gains are likely present in approximately 73% of male GCT, and in 32% of female GCT (AACR GENIE, n=555). When comparing TCGA cases of testicular GCT (n=149) to combined cases of sarcoma, colorectal, prostate, and urothelial carcinoma (n=1754), 12p gains had a sensitivity of 77.2% and specificity of 97.3% for GCT. Some advantages of FISH over SNP-arrays/NGS include relatively lower cost, rapid turnaround time, the ability to analyze biopsy material with a limited number of tumor cells (50 cells), and the ability to distinguish i(12p) from polysomy. The ability to spatially restrict analysis to cells of interest is critical, as specimens submitted for testing often have low tumor purity. Disadvantages include false negative results due to an inability to detect segmental gains due to FISH probe design. With the availability of numerous testing modalities including FISH, SNP-arrays and NGS-based assays, a nuanced understanding of the advantages and disadvantages of each methodology, as has been presented in this study, may inform appropriate testing strategies.