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Oxford University Hospitals NHS Foundation Trust

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Cancer Next Generation Sequencing Panel

Testing strategy

The laboratory utilises the Ion Ampliseq Cancer Hotspot Panel (v2) with sequencing on the Ion Torrent Personal Genome Machine to detect oncogenic variants in 50 individual genes.

Analysed and reported gene content varies dependent on the clinical indication and is reflective of the National Genomic Test Directory for cancer.

Whole-genes are not captured by this testing kit, with the focus being on 'hotspot' regions of recurrent variation as identified within the COSMIC database.

Detailed information on target regions is available on request, although we estimate that analysis will capture >95 percent of clinically actionable variants in the KRAS, NRAS, BRAF, PDGFRA, PIK3CA, KIT and EGFR genes.

The limit of detection (percent mutant detectable in a background of wild type DNA) of this assay is 5-10 percent for single nucleotide variants, and higher for insertion/deletions.

Limit of detection is based on a vertical read-depth of 500 reads, targeted regions falling below this threshold will be indicated on reports.

NHSE funded test referrals should be in accordance with the National Genomic Test Directory for cancer and meet eligibility criteria:

National Genomic Test Directory (NHS England)

Target reporting times

21 calendar days from receipt of sample in the laboratory for routine referrals.

Sample requirements and referral information

Please see referral form for referral information and sample requirements.

Requesting specialties

  • Histopathology
  • Oncology

Contact details

Molecular Pathology enquiries: oxford.molecularhaem@nhs.net

Gene list

Hotspot regions in the following genes can be targeted by this assay:

  • ABL1
  • AKT1
  • ALK
  • APC
  • ATM
  • BRAF
  • CDH1
  • CDKN2A
  • CSF1R
  • CTNNB1
  • EGFR
  • ERBB2
  • ERBB4
  • EZH2
  • FBXW7
  • FGFR1
  • FGFR2
  • FGFR3
  • FLT3
  • GNA11
  • GNAS
  • GNAQ
  • HNF1A
  • HRAS
  • IDH1
  • IDH2
  • JAK2
  • JAK3
  • KDR
  • KIT
  • KRAS
  • MET
  • MLH1
  • MPL
  • NOTCH1
  • NPM1
  • NRAS
  • PDGFRA
  • PIK3CA
  • PTEN
  • PTPN11
  • RB1
  • RET
  • SMAD4
  • SMARCB1
  • SMO
  • SRC
  • STK11
  • TP53
  • VHL

Last reviewed:02 August 2021