The aim of ClinSeq is to develop infrastructure for genomic profiling in cancer to support best-in-class research, clinical studies and implementation of new genomics based diagnostics in clinical care.
ClinSeq’s infrastructure development consists of two parts:
1. Pipeline for genomic profiling at initial cancer diagnosis.
The pipeline will help treating physicians in the classification of the cancer, guide the treatment of cancer, provide information on possible toxicities of treatments and facilitate inclusion of patients into clinical trials.
2. World’s best-characterized dataset of biobanked material and clinical information.
The dataset will include genomic profiles, diagnostic data, long term follow-up and biomaterial, including DNA/RNA, from tens of thousands of consented cancer patients. The dataset can be used to evaluate treatment responses, evaluate new treatments and develop markers for prognostication of cancer patients.
Patient samples are profiled using:
- A custom made capture kit targeting all known disease drivers in cancer, all genes with available therapeutic agents (actionable genes), all known pharmacogenetic loci in cancer, and genes involved in hereditary cancer syndromes. Deep exome sequencing is performed for all of these 550 genes.
- Low-pass whole genomic sequencing to identify chromosomal copy number alterations.
- RNA sequencing to capture gene expression in the tumor, validate point-mutations and to identify gene-fusions.
The whole process, from tissue collection to delivery of the final report is completed within 10 days.
Figure 1: Key steps in the ClinSeq pipeline