Clinical Genomics Uppsala

National facility

Clinical Sequencing

Clinical Sequencing develops and provides clinical genetic tests for various cancer forms and inherited diseases using state-of-the-art next-generation sequencing technology and bioinformatics. With our team of facility associated geneticists and medical doctors, we can deliver clinical assessments of the detected variants, with the aim to truly provide bench-to-bedside service.

SERVICES

Clinical Sequencing started as a facility autumn 2013, organized jointly by SciLifeLab, Uppsala University Hospital, and Uppsala University. Since then we have successfully implemented tests based on next-generation sequencing in clinical routine and developed a number of methods and services to provide Swedish researchers and clinicians. We take on projects in the following three categories:

  • Routine diagnostics
  • Development projects for implementing NGS based methods in clinical use
  • Translational research project with strong clinical utility

EQUIPMENT

  • One Illumina HiSeq
  • One Illumina NextSeq
  • Two Illumina MiSeq

APPLICATIONS

Genome-wide, exome and targeted DNA and RNA sequencing. Method development for variant detection, fusion gene detection, structural variation detection, for diagnostic purposes or translational research. Focus areas for development are:

  • solid tumors
  • leukemia
  • inherited diseases
  • clinical immunology

RECENT PROJECTS

  • Evaluation of different methods for sequencing targeted gene panels on DNA extracted from FFPE samples
  • Diagnostic tests for colon cancer developed and implemented in routine care (HaloPlex based panel for 32 genes)
  • Diagnostic tests for lung cancer developed and implemented in routine care
  • Evaluation and development of targeted gene panels to detect variants associated with AML and MDS
  • Collaboration with Uppsala Genome Center to develop and run PacBio based test for mutations that confer TKI-resistance in BCR-ABL1 fusion genes in Chronic Myeloid Leukemia
  • Development of gene panels for inherited diseases have resulted in tests that are now in clinical utility
  • Implementation of clinical exome sequencing