Next Generation Sequencing

As a doctor, you want the best possible treatment for your patients. The genetic profile may be a useful addition to tumour typing, grading, and staging. With Next Generation Sequencing we look for relevant mutations. If a tumour has a mutation with a significant therapy response, the patient may benefit from treatment. This knowledge also reduces the number of ineffective treatments, preventing unnecessary toxicity and high costs for the patient.

Advantages of Next Generation Sequencing

  • Mutation status of all relevant genes is determined in a single experiment
  • Very small quantity of tissue required
  • Relatively low costs
  • We strive to
NGS Sequencer

Technique

In order to conduct Next Generation Sequencing we have at our disposal

  • Ion Torrent: a pH-mediated next-generation sequencer whereby the base pair sequence is read based on a pH change after incorporating a specific nucleotide.
  • Ion Chef: robot for the standardised preparation of patient materials and preparing the libraries on the sequencing chip. This reduces the number of manual steps and possibilities for (human) error.
  • Sequencing chips: Chips on which millions of sequencing reactions can be conducted in parallel. This makes it possible to measure all relevant genes within a matter of hours.
  • Ion Reporter: Standardised analysis software that has been specifically designed for the Ion Torrent technology.
  • Laboratory: ISO15189-accredited molecular laboratory.
NGS Sequencer 2 20160225_134126-klein

The Key to Targeted Therapy

At Pathology-DNA, you can request various standard gene panels to optimize your diagnosis for targeted therapy and differential diagnosis purposes. Besides testing the standard indicated genes (as listed below), we can also detect mutations in additional genes that may become important in the near future and are still being tested in clinical trials.

Targeted therapy

  • Lung cancer: KRAS, EGFR, BRAF, ERBB2, MEKI, PIK3CA, ALK
  • Colorectal cancer: KRAS, NRAS, BRAF, PIK3CA
  • Melanoma: BRAF, NRAS, KIT
  • Gastrointestinal stromal tumours: KIT, PDGFRA, BRAF
  • Breast cancer: ERBB2, PIK3CAThyroid cancer: BRAF, KRAS, NRAS, HRAS

Differential diagnostics

  • Relation of multiple tumours (question of second primary tumour or metastasis): TP53, CDKN2A + full Cancer Hotspot Panel (50 genes)
  • Papillary thyroid cancinoma: BRAF
  • Low-grade glioma: IDH1, IDH2
  • Uveal melanoma and spitzoid naevus: BRAF, NRAS, HRAS, KIT, GNAQ, GNA11
  • Desmoid tumour: CTNNB1
  • Langerhans cell histiocytosis: BRAF
  • Hairy-cell leukemia: BRAF

New developments

At Pathology-DNA we are currently working on

  • Centralisation of molecular techniques and knowledge to increase knowledge and efficiency
  • Staying up to date to be able to immediately respond to new mutations or targeted means in terms of diagnostics.
  • Expansion of the NGS portfolio for an even more complete molecular diagnosis
  • Detection of translocations and fusion genes
  • Analysis of copy number variations (amplification and deletions)
  • Development of a specific panel for lymphoma diagnostics
  • B-cell and T-cell clonality assay (currently still conducted using fragment analysis)

Reference

My cancerGenome website: www.mycancergenome.org

Chip NGS

Specific requests

Consult with our molecular biologists about other genes that may possibly be determined for specific questions.

Email us at: moleculair@pathologie-dna.nl