Ultraview sish dnp

Rearrangements of the ALK and ROS1 genes were identified using ALK and ROS1 rearrangement DNA probe sets (Ventana Medical Systems Inc, Tucson, AZ), respectively. Target sequences for probe design for each gene region were analyzed using an in-house bioinformatics software package. The sub-sequences within the each genomic target region were further tested using a Roche NimbleGen Comparative Genomic Hybridization custom array. DNA target sequence hybridization to a human genomic probe, and a Cot1 DNA probe were analyzed and sequences with high hybridization scores following the Comparative Genomic Hybridization analysis were eliminated. Specificity of each probe was confirmed on a metaphase spread. The dual-color brightfield CISH assays were conducted with the BenchMark XT and Ultra automated slide processing systems (Ventana Medical Systems Inc, Tucson, AZ). For detection of the ALK rearrangements, DNP-3′-ALK and DIG-5′-ALK probes were hybridized to targets and detected using ultraView SISH DNP and ultraView Red ISH DIG detection kits, respectively (Ventana Medical Systems Inc, Tucson, AZ). ROS1 rearrangements were measured with the same detection method using DNP-3′-ROS1 and DIG-5′-ROS1. The scoring criteria for both ALK and ROS1 dual-color CISH were the same as those described for FISH.