The place of scanning all chromosomal abnormalities with microrray- based comparative genomic hybridisation in pediatric cancers posing difficulties in differential diagnosis

Objective: Despite conventional histopathological and immunohistochemical methods, difficulties may be experienced in the differential diagnosis of pediatric cancers, especially in small, round-cell and sometimes in spindle-cell tumours. In these cases, determination of chromosomal abnormalities may be helpful. Examination of a single translocation or deletion with the FISH method in a sample with a single probe may not always yield a definitive response as the chromosomal abnormality in question may not be a single type. Variations may be found and therefore, it may be necessary to examine more than one domain for diagnosis. The aim of this study was to evaluate the place of the whole genome array comparative genomic hybridization method in pediatric cancers where difficulty is experienced in differential diagnosis. Method: In Comparative Genomic Hybridization (CGH), 135,000 probes were scanned as 3 probes per gene in all genomes. It was possible to analyze paraffin block tissues obtained from the archive of the Pathology Laboratory of Dr Behcet Uz Children's Hospital. DNA extraction was made from the paraffin blocks of 24 cases where difficulty had been experienced in making the differential diagnosis and in each case, comparisons with control samples were made for all anomalies in all chromosomes with microarray technology. The chromosomal anomalies determined were compared with the clinicopathological findings. Results: Together with the typically observed chromosomal anomalies, additional derangements with debatable importance were determined. In our ES/ PNET patient cohort, most frequently the number of copies were altered in genes srGAP2, RGPD5, NPHP1, GTF2IRD2, PDXDC1. In our undifferentiated neuroblastoma patient, most frequently the number copies were determined in genes Defensin beta 106A, Defensin beta 103B, RGPD5 gene and MAGE family member A12, SPANX family member D sarcoma antigen. In indifferentiated malignant tumors especially in the group of small round cell malignant tumors, most frequently the number copies were detected in immunoglobulin superfamily member 2, calcium / calmodulin- dependent protein kinase II beta, POM121 transmembrane nucleoporin, Ankyrin repeat domain 30B, Solute carrier family 6 member, Peptidylprolyl isomerase B, cyclophilin A, RLD domain-containing E3 ubiquitin protein ligase 2, Tryptophan 2.3-dioxygenase. Conclusion: The whole genome CGH method may be useful in pediatric cancers where difficulties are experienced in making differential diagnosis. Since, technical difficulties are experienced in the examination of paraffin-embedded tissue samples. storing fresh tissue samples from each tumor will be helpful for genetic and molecular examinations. A limitation of the method is that although chromosomal anomalies can be determined, contrary to in situ hybridization translocation of the chromosomal abnormality can not be determined. Key Words: Comparative Genomic Hybridization (CGH), Rare Pediatric Cancers, Differential Diagnosis