A Prospective Study Using Genomic Screening to Select Patients for Targeted Molecular Treatment

Two ultrasound-guided biopsies obtained to be stored in RNAlater® for DNA and RNA purification. A 3rd biopsy for histology is paraffin embedded. SNP-array (Affymetrix Cytoscan HD) from DNA (tumor) is performed to identify copy number changes. Whole exome sequencing (WES) from DNA (tumor and blood) will be performed using sequence capture, SureSelect v5 (Agilent) and Illumina HiSeq2500 to call tumor specific mutations. Expression levels of therapeutic targets are revealed by expression Array from tumor RNA. In addition to the expression array, RNA-seq (Nugens Ovation RNA-seq system v2) is performed to investigate whether chromosomal translocations were the reason for tumor specific expression of an oncogene. Results will be reviewed by a tumor board. Patients with specific genetic profiles that can be targeted with marketed drugs or drugs under development are offered such treatment. PFS from the treatment is compared to PFS of the most recent standard treatment (PFS ratio).