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Eur Urol. 2018 Jan;73(1):71-78. doi: 10.1016/j.eururo.2017.05.033. Epub 2017 Jun 4.

Characterization of Clinical Cases of Advanced Papillary Renal Cell Carcinoma via Comprehensive Genomic Profiling.

Author information

1
Department of Medical Oncology & Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA. Electronic address: spal@coh.org.
2
Foundation Medicine, Cambridge, MA, USA.
3
Department of Pathology, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, RI, USA.
4
Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA.
5
Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
6
Division of Hematology and Oncology, University Hospitals Case Medical Center & Case Western Reserve University, Cleveland, OH, USA.
7
Department of Pathology, Beth Israel Deaconess Medical Center, Chelsea, MA, USA.
8
Foundation Medicine, Cambridge, MA, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA.
9
Division of Medical Oncology, Department of Internal Medicine, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, USA.
10
Division of Urology, Yale Cancer Institute, New Haven, CT, USA.
11
Division of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA. Electronic address: toni_choueiri@dfci.harvard.edu.

Abstract

BACKGROUND:

Papillary renal cell carcinoma (PRCC) is a rare subset of RCC. The Cancer Genome Atlas (TCGA) data largely reflect localized disease, and there are limited data for advanced PRCC.

OBJECTIVE:

To characterize the frequency of genomic alterations (GAs) in patients with advanced PRCC for whom comprehensive genomic profiling (CGP) was performed in the context of routine clinical care.

DESIGN, SETTING, AND PARTICIPANTS:

Formalin-fixed, paraffin-embedded tissue was obtained for 169 consecutive patients with confirmed PRCC. DNA was extracted and comprehensive genomic profiling was performed in a certified central laboratory.

MEASUREMENTS:

Hybrid-capture, adaptor ligation-based libraries of up to 315 genes were sequenced to a median coverage of 648×. All classes of GAs were identified, including substitutions, insertions/deletions, copy number alterations, and rearrangements.

RESULTS AND LIMITATIONS:

From 169 patients, either primary tumor tissue (102 patients, 60%) or metastatic tissue (67 patients, 40%) was collected. In patients with type 1 PRCC, commonly altered genes were MET (33%; 8 activating mutations, 5 amplifications at >6 copies), TERT (30%), CDKN2A/B (13%), and EGFR (8%). In patients with type 2 PRCC, commonly altered genes were CDKN2A/B (18%), TERT (18%), NF2 (13%), and FH (13%); MET GAs (5 mutations, 3 amplifications) were observed in 7% of type 2 cases. Notable differences from TCGA data include higher frequencies of MET, NF2, and CDKN2A/B GAs, association of alterations in SWI/SNF complex genes with type 2 PRCC, and observation of frequent CDKN2A/B alterations in both type 1 and type 2 disease.

CONCLUSIONS:

Both the current study and the TCGA experience represent similarly sized cohorts of patients with PRCC. Key differences in GA frequency probably underscore the marked difference in stage distribution between these data sets. These results may inform planned precision medicine trials for metastatic PRCC.

PATIENT SUMMARY:

Papillary renal cell carcinoma (PRCC) is a rare subtype of kidney cancer, and understanding of the biology of advanced PRCC is limited. This report highlights some of the unique biologic features of PRCC that may inform on future use of targeted therapies for the treatment of metastatic disease.

KEYWORDS:

Genomic profiling; Mutational burden; Papillary renal cell carcinoma

PMID:
28592388
DOI:
10.1016/j.eururo.2017.05.033
[Indexed for MEDLINE]

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