UCSF500 Cancer Gene Panel (Bait_UCSF500)

Overview

The UCSF500 cancer gene panel is a targeted DNA sequencing bait set developed at the University of California San Francisco (UCSF). It captures approximately 500 cancer-relevant genes for detection of somatic single nucleotide variants, small insertions/deletions, and copy number alterations from tumor DNA. The panel is used in both clinical and research settings for cancer genomic profiling, including in normal-tissue and somatic-evolution studies.

Used by

• Used alongside whole-exome-seq and smart-seq2 to characterize somatic mutation burden and gene expression in single clonally expanded melanocytes from human skin biopsies PMID:39975212.

Notes

• Panel covers ~500 cancer-related genes; designed for FFPE and fresh-frozen tissue DNA.
• Validated for use in targeted sequencing complementary to whole-exome sequencing (NimbleGen SeqCap EZ Exome+UTR or KAPA HyperExome V1) to confirm somatic variants at known cancer loci.
• Used in a normal-melanocyte atlas study (n=297 single cells from 31 donors) to supplement whole-exome sequencing for variant-calling validation PMID:39975212.

Sources

• PMID:39975212 — Tandukar et al. used the UCSF500 panel alongside whole-exome sequencing for joint DNA/RNA profiling of 297 clonally expanded single melanocytes from 58 skin biopsies of 31 donors; panel sequencing allowed confirmation of somatic variants (UV-signature SBS7 in HighMut and clock-like SBS1/SBS5 in LowMut subpopulations) PMID:39975212.

This page was processed by entity-page-writer on 2026-05-01.