UCSF 500 Cancer Gene Panel Test (UCSF500 / UC500)

Performing Lab: 
UCSF Clinical Cancer Genomics Lab
CPT Code: 
81455

Specimen Type
This test sequences the full coding region of over 500 cancer genes, and requires two specimens: tumor specimen (>=25% neoplastic cells), normal (non‐lesional) specimen.
Acceptable specimens include:

  1. Formalin-fixed tumor tissue with at least 25% malignant cells (5-10 unstained slides at 10-micron thickness on uncharged slides, or FFPE tissue block. One adjacent H&E stained slide should be included. Cytology smears may also be used for testing if there is sufficient tumor present.).
  2. A source of lesional DNA from blood or bone marrow (4cc collected in EDTA).
  3. A source of normal DNA from non-lesional tissue (blood collected in EDTA, 4 cc - APeX test code PBCGL; buccal swab - APeX test code BUCCGL; skin biopsy from non-lesional tissue). Blood or buccal swab sample is preferred.

Methodology: Next-generation sequencing
Turnaround Time: 14-21 days

TEST INDICATIONS: 

The UCSF 500 Cancer Gene Test uses capture-based next-generation sequencing to target and analyze the coding regions (exons) of 529 cancer genes, as well as select introns of 47 genes.  This test can be ordered on solid tumors, hematopoietic malignancies, or lesional tissue specimens.

ANNOUNCEMENT: The new version of the UCSF500 panel is now available to order. The new panel includes additional genes in BOLD below.

UCSF500 V3 Gene List

Additionally, certain regions of some UCSF500 genes are not reported due to consistently low coverage; a list of these regions is available here.

HOW THE TEST WORKS: 

Genomic DNA is extracted from both tumor and normal tissue for library preparation.  Target enrichment is performed by hybrid capture using custom oligonucleotides (Roche Nimblegen).  Sequencing of captured libraries is performed on an Illumina NovaSeq 6000 on the SP or S1 flow cell (2 X 101 bp read length).  Sequence reads are de-duplicated to allow for accurate allele frequency determination and copy number calling.  The analysis uses open source or licensed software for alignment to the human reference sequence UCSC build hg19 (NCBI build 37) and variant calling.  Common germline polymorphisms were eliminated from analysis using the complete list of germline mutations from dbSNP.  Additional filtering to eliminate technology specific sequencing artifacts was performed before analyzing the data.

LIMITATIONS OF THE TEST: 

This assay is designed to detect single nucleotide variants, small to medium insertion/deletions (indels), and copy number changes.  Large insertions/deletions and structural variants (gene rearrangements) may also be detected by the assay.  The test was validated by the UCSF Clinical Cancer Genomics Laboratory to confirm performance characteristics, in compliance with current guidelines for clinical implementation

SPECIMEN REQUIREMENTS FOR A SUCCESSFUL TEST: 

In general, the tumor should be a minimum of 0.4 cm in size. Blocks selected for UCSF500 must contain tumor tissue. Areas of tumor must contain at least 25% neoplastic cells. The lab can remove adjacent non-tumor tissue, so the entire slide does not need 25% tumor cells, just the area with tumor. Contact the laboratory at 415.502.3252 or [email protected] if the specimen suitability is uncertain. Label slides with pathology case number and block identification.

Specimen rejection criteria include: All required slides not included. Insufficient tumor tissue present on slide as determined by pathologist. Outside slides not labeled or not accompanied by printed copy of test order.

HOW TO ORDER THE TEST: 

UCSF Clinicians — Inpatient and Ambulatory Providers are now able to place orders electronically in APeX.  Order panels UC500 Solid Tumor Testing and UC500 Leukemia Testing have been created with detailed instructions on ordering guidelines. APeX Search terms include UC500; UCSF500; UCSF 500. APeX will allow you to order TUMOR only, as well as paired TUMOR:NORMAL tests.

For any questions related to the ordering process, please contact [email protected] or 415-502-3252. 

Blood draws can be ordered through APeX
Peripheral blood draw for CCGL (PBCGL)
UCSF 500 paper requisition form
Please use the paper consent form to document informed consent
CCGL Buccal Collection Instructions
Instructions Shipment of Blood from outside UCSF
For all specimens, an interpretation of this test by a laboratory physician will automatically be performed and billed for separately.