Fig. 1

Index case BAP1: Established cell line, primary culture and formalin-fixed paraffin-embedded tumor. a Established cell line array comparative genomic hybridization profile for 3p21.1 locus showing the 145 kb Homozygous deletion (log2 ratio = −4) involving BAP1 gene. SEMA3G gene is also biallelically deleted while PBRM1 gene appear to be within the single copy (log2 ratio = −1) loss region. The vertical green line on the right indicates the position of the 180 kb RP11-630O10 clone employed for BAP1 FISH analysis. b Karyogram of the established cell line. The karyotype is described in the text. Red arrow indicates Marker 1 (mar1), green arrow indicates der (22) add (22)(q12.2). c Partial metaphase spread from the established cell line hybridized with BAP1 (Spectrum Green) and MITF (Spectrum Orange) probe mixture (counterstained with DAPI). BAP1 single signal on the der (22). MITF single signal on the mar1. d G banded partial metaphase from index case primary culture: Green arrow indicates der (22), Red arrow indicates mar1 and double Red arrow indicates the ring chromosome. e Partial metaphase spread from the index case primary culture hybridized with BAP1 (Spectrum green) and MITF (Spectrum Orange) probe mixture (counterstained with DAPI). BAP1 single signal on the der (22) indicated with green arrow. MITF single signal on the mar1, indicated with red arrow and two further MITF signals on the ring chromosome indicated with double red arrow. f Tumor tissue section from the index case hybridized with BAP1 (Spectrum Green) and MITF (Spectrum Orange) probe mixture counterstained with DAPI. Tumor cells display a variable number of MITF signals and a single BAP1 signal. A nontumor cell and a tumor cell are highlighted in white and yellow boxes, respectively, and shown at higher magnification on the right. Notice loss of association between BAP1 and MITF signals in the tumor cells coherent with cytogenetic profile. BAP1 FISH signal is diminished in the tumor cell compared with nontumor cells. Figure 1F inset: Box plot representing the distribution of FISH signal size in nontumor (WT) and tumor (dim) cells. p = 0.001419. g Tumor tissue section BAP1 immunohistochemistry indicate complete loss of expression. Positive controls represented by lymphocytes and stromal cells