UCSF Clinical Cancer Genomic Laboratory

The UCSF Clinical Cancer Genomics Laboratory (CCGL) was created in 2014 to perform standard-of-care and advanced molecular testing for patients with cancer, and to provide special expertise in solid tumors.  The laboratory's diverse capabilities include targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS).  Importantly, CCGL is staffed with board-certified surgical pathologists and board-certified molecular pathologists who can properly evaluate the quality of samples submitted for testing as well as make correlations between the pathologic diagnosis of a tumor and the molecular findings in the tumor.  A selection of the testing available at CCGL includes:

  • Lynch syndrome screening tests (microsatellite instability, and MLH1 methylation)
  • FISH testing for soft tissue tumors/sarcoma (EWSR1, SS18, MDM2, ALK) and breast, gastroesophageal and endometrial serous cancer (HER2)
  • Extensive testing for brain tumors, including FISH for 1p/19q deletion, EGFR amplification, PTEN deletion, and BRAF rearrangement; IDH1 and IDH2 sequencing; and TERT promoter sequencing
  • Oncogene hotspot sequencing in BRAF, KRAS, NRAS, KIT and EGFR
  • Molar pregnancy genotyping to diagnose hydatidiform molar pregnancy

We also offer the UCSF500 Cancer Panel, a comprehensive genomic profiling assay covering nearly 500 cancer-related genes that can interrogate, lung, GI, neurological, gynecological and other pediatric and adult tumors. The UCSF500 assay can be performed as tumor only or paired tumor-normal testing to improve the accuracy of identification of tumor-specific mutations. Germline pathogenic variants identified on paired tumor-normal testing is reported back to the provider.  The UCSF500 detects a broad range of genomic changes in cancer that can help guide targeted treatments and assist in diagnosis.