We evaluated tumor-biopsy samples from four consecutive patients with metastatic renal-cell carcinoma who were enrolled in the Personalized RNA Interference to Enhance the Delivery of Individualized Cytotoxic and Targeted Therapeutics clinical trial of everolimus (E-PREDICT; EudraCT number, 2009-013381-54) before and after cytoreductive nephrectomy. Biopsy samples were obtained before the initiation of 6 weeks of treatment with everolimus. After a 1-week washout period in which patients did not receive everolimus, a nephrectomy was performed. Everolimus treatment was continued after recovery from surgery until tumor progression. Figure 1 shows biopsy and treatment timelines.
We performed whole-exome multiregion spatial sequencing on DNA that was extracted from freshfrozen samples obtained from Patients 1 and 2, as described previously,19 (link) with paired-end reads of 72 bp and 75 bp, respectively, on Illumina Genome Analyzer IIx and HiSeq platforms. We performed single-nucleotide polymorphism (SNP) array analysis on Illumina Omni2.5 and messenger RNA (mRNA) expression profiling on Affymetrix Gene 1.0 arrays.
All four patients provided written informed consent. Details regarding materials and methods are provided in theSupplementary Appendix , available with the full text of this article at NEJM.org. The study protocol is also available at NEJM.org.
We performed whole-exome multiregion spatial sequencing on DNA that was extracted from freshfrozen samples obtained from Patients 1 and 2, as described previously,19 (link) with paired-end reads of 72 bp and 75 bp, respectively, on Illumina Genome Analyzer IIx and HiSeq platforms. We performed single-nucleotide polymorphism (SNP) array analysis on Illumina Omni2.5 and messenger RNA (mRNA) expression profiling on Affymetrix Gene 1.0 arrays.
All four patients provided written informed consent. Details regarding materials and methods are provided in the