Clinical Genomics Lund

National facility, part of Diagnostics Development

Clinical Genomics Lund was established in 2016 as a joint strategic initiative between the Medical Faculty at Lund University and the Division of Laboratory Medicine, Medical Services, Region Skåne. The facility encompasses two units, Center for Translational Genomics (CTG) and Center for Molecular Diagnostics (CMD) that are fully aligned and operate in tight synergy, but with separate responsible bodies and budgets. Clinical Genomics Lund aim to provide state-of-the-art next generation sequencing (NGS-) based services to strong and high-profile translational research projects and to implement new NGS-based tests for clinical diagnostics within the health-care system aiming at broader national coverage and consensus.

SERVICES

Clinical Genomics Lund offers expertise and service in NGS-based technologies for investigators at Lund University and Region Skåne in projects with a strong translational edge or aiming at clinical implementation of new diagnostics assays.

Clinical Genomics Lund also constitutes a physical node at which knowhow, services, education and outreach activities by the national platform Diagnostics Development will take place. Clinical Genomics Lund will also offer national services within specific high-profile areas of the facility.

CTG has initially identified 5 work packages (WP) with a strong translational profile and clearly defined deliverables (see recent projects). Calls for new WPs will be announced on a regular basis.

CMD has organized its services around focus areas, including cancer, inherited disorders, and microbiology.

APPLICATIONS

Genome-wide and targeted DNA and RNA sequencing. Method development for variant detection, fusion gene detection, and structural variation detection for translational research projects and for diagnostic purposes.

EQUIPMENT

CTG

Library preparation

  • *NeoPrep System
  • *JunoTargeted DNA Sequencing Library Preparation System

Sequencing systems

  • NextSeq 500
  • *HiSeq 2500
  • *MiSeq

*CTG also uses instrument available at different research Departments at the Medical Faculty

 

CMD

Library preparation

  • IonChef

Sequencing systems

  • PGM
  • Ion S5
  • Ion Proton
  • NextSeq 500
  • MiSeq
  • MiniSeq

RECENT PROJECTS

 

Examples of projects within the different work packages at CTG:

WP1: Inherited cancer genetics (WP leaders: Anders Kvist and Hans Ehrencrona).
“Pan cancer panel”. A comprehensive hybrid selection gene panel including genes predisposing for both common and rare cancers and a bioinformatics pipeline allowing detection of all sequence variants including genome rearrangements will be constructed to meet diagnostic needs.

WP2. Cancer genetics of leukemia, bone- and soft tissue tumors and pediatric cancers (WP leader: Thoas Fioretos):
AML and ALL: Implementation and validation of “gene panels”, WES, RNA-seq and low-pass WGS for the detection of clinically relevant variants, fusion genes and copy number alterations/structural rearrangements.

WP3. Cancer genetics of solid tumors (WP leader: Åke Borg):
Breast cancer: RNA-seq biomarkers for tumor molecular subtype, cell proliferation/grade and steroid/HER2 receptors are developed for prognostic and treatment predictive purposes. Laboratory and data analysis pipelines for real-time sample assessment and RNA-seq biomarker reports are developed.

WP4. Inherited Mendelian Disorders (WP leader: Maria Soller and Markus Heidenblad):
Improved WES in clinical routine for children with mental retardation and dysmorphic features (trio analysis to screen for recessive and de novo mutations).

WP5. Genomics data management and analysis (WP leaders, Anders Kvist and Henrik Lilljebjörn):
An IT infrastructure solution for secure storage, transfer and analysis of NGS data generated within the facility. Project and laboratory information management systems integrated with the laboratory workflows.

 

Examples of projects within the focus areas of CMD:

Focus Area: Cancer
Gene panels for colorectal cancer, lung cancer, gastrointestinal tumors and malingt melanoma in clinical routine. Gene panels for myeloid malignancies, acute lymphoblastic leukemia, and ovarian cancer in clinical validation.

Focus Area: Inherited Mendelian Disorders
Exome sequencing for rare disease diagnostics in clinical validation.
Non-invasive prenatal testing (NIPT) in clinical validation.
Gene panel for cystic fibrosis in clinical routine.

Focus Area: Microbiology
To start