DFCI OncoPanelv2 (DFCI-ONCOPANEL-1)

Overview

DFCI-ONCOPANEL-1 (OncoPanelv2) is a targeted Illumina hybrid-capture sequencing panel covering 504 cancer-associated genes, developed at Dana-Farber Cancer Institute. It detects somatic single-nucleotide variants (SNVs), indels, and copy-number alterations (CNAs) in tumor samples. Sequencing is performed 100 bp paired-end on the HiSeq 2500 platform. The panel is validated for use with FFPE and fresh-frozen tumor material.

Used by

  • cscc_dfarber_2015 — targeted sequencing of 29 lymph-node metastases from HPV-negative cutaneous squamous cell carcinoma patients; mean tumor coverage 82× (range 25–166×); variant calling via mutect with OxoG filtering, annotation via oncotator, significance by mutsig, and CNAs by gistic 2.0 PMID:25589618

Notes

  • Covers 504 cancer-associated genes; suitable for tumor-only or paired tumor/normal sequencing.
  • Reads aligned to b37 reference genome with Picard/Firehose.
  • Typical tumor coverage ~82×; normal ~69× in the cSCC cohort.
  • Variant annotation via Oncotator against dbSNP 134 and 1000 Genomes.
  • CNA calling with Nexus 7.5 and GISTIC 2.0 (arm-level peel correction; minimum segment size 6).
  • HPV status can be independently assessed via hybrid-capture sequencing of HPV E6/E7 sequences.

Sources

  • PMID:25589618 — Li et al. 2015, targeted sequencing of metastatic cSCC

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