Specimen Type: Peripheral blood, Saliva (collected in Oragene kit), Buccal cells, DNA (minimum 2 micrograms)
Methodology: Next generation sequencing
Turnaround time: 14 – 28 days
Designed for patients with a family history suggestive of a common hereditary cancer. The common hereditary cancer panel tests for variants in 47 genes associated with hereditary breast, ovarian, uterine, colorectal, melanoma, and prostate cancers.
DNA is extracted for library preparation. Genomic regions of interest are targeted using a custom capture reagents (Sophia Genetics) for target enrichment and sequenced using an Illumina sequencing system with 150bp paired-end reads. The resulting DNA sequences are mapped to and analyzed in comparison with the published human genome (UCSC hg19 reference sequence). Variants, including SNVs and CNVs, are called and annotated using a custom bioinformatics pipeline developed in collaboration with Sophia Genetics.
All pathogenic, likely pathogenic, and variants of uncertain significance meeting the reportable criteria are reported. SNVs and indel variants are specified using the numbering and nomenclature recommended by the Human Genome Variation Society (HGVS, http://www.hgvs.org/). Benign variants are not reported. Variant classification and confirmation are consistent with ACMG standards and guidelines (Richards, PMID:25741868; Rehm, PMID:23887774).
GENES ANALYZED: This list represents a complete list of genes analyzed for this individual. This assay covers the coding and splice regions (+/- 10bp) of the included genes, including the relevant gene transcript(s). Results are negative unless otherwise indicated in the report. Benign and Likely Benign variants are not included in this report but are available upon request. An asterisk (*) indicates that this gene has a limitation. Please see the Limitations section for details.
Genes: APC, ATM, AXIN2, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, CTNNA1, EPCAM, GREM1, HOXB13, MEN1, MITF*, MLH1, MLH3, MRE11, MSH2, MSH3, MSH6, MUTYH, NF1, NTHL1, PALB2, PMS2, PMS2CL, POLD1, POLE, POT1, PTEN, RAD50, RAD51C, RAD51D, RNF43, RPS20, SMAD4, STK11, TP53, TSC1, TSC2, VHL and XRCC2
Absence of a plausible explanation for the reported clinical phenotype by this sequencing test does not exclude a genetic basis for disease. Some types of genetic variation, including germline mosaicism, or the presence of large chromosomal aberrations such as structural rearrangements, gene fusions, or variants in regions or genes not included in this test, may not be detectable with the technologies used by this test. Regions outside of the coding regions, so called non-coding sequences, are not captured and analyzed, but may harbor disease-causing variants. In the event of a negative result, the presence of an inherited cancer syndrome due to a different genetic cause cannot be ruled out. Variant classification and/or interpretation may change over time, when additional information becomes available. It is also possible that incomplete scientific and/or medical knowledge of genes and variants, pseudogene interference, technical issues including sample mislabeling, blood transfusions, bone marrow transplantation, or erroneous misrepresentation of family relationships, may result in a false negative or false positive test result. For heterozygous variants in the same gene, the assay typically cannot determine whether they are on the same (in cis) or different (in trans) chromosomes. In order to determine variant phase, parental testing may be required.
This test was developed and its performance characteristics determined by the UCSF Clinical Cancer Genomics Laboratory. It has not been cleared or approved by the U.S. Food and Drug administration. This test is for clinical purposes and should not be considered as investigational or for research purposes.
- Blood collected in EDTA (lavender top), 4 cc - APeX test code PBCGL
- Buccal swabs, minimum 3 swabs (available upon request, email [email protected])
- Saliva in Oragene collection kit, minimum 1 cc
- DNA, minimum 2 micrograms
UCSF Clinicians — Inpatient and Ambulatory Providers are able to place orders electronically in APeX
- LAB6239 - COMMON HEREDITARY CANCER PANEL
- Blood draws can be ordered through APeX - Peripheral blood draw for CCGL (PBCGL)
Non-UCSF Clinicians
- Please use the paper requisition form to provide test request details
- Please use the paper consent form to document informed consent
Other Forms
- CCGL Buccal Collection Instructions
- Oragene Saliva Collection Instructions
- Shipment of Blood from Outside of UCSF Instructions
For any questions related to the ordering process, please contact [email protected] or 415-502-3252.
For all specimens, an interpretation of this test by a laboratory physician will automatically be performed and billed for separately.
CCGL Test Order Submission
Download Forms
CCGL Requisition Form
CCGL Buccal Collection Instructions
Oragene Saliva Collection Instructions
CCGL Blood Instructions Shipment for UCSF 500
UCSF 500 Requisition Form
UCSF 500 Cancer Gene Panel Consent Form
CCGL Blood Instructions Shipment for UCSF Common Hereditary Cancer Panel
UCSF Common/Expanded Hereditary Cancer Panel Requisition Form
UCSF Common Hereditary Cancer Panel Consent Form