Clinical Genomics LundNational facility
Translational and Clinical Genomics (TACG) was established in January 2016 as a joint strategic initiative between the Medical Faculty at Lund University (LU) and the Division of Laboratory Medicine at the University Hospital in Region Skåne (RS). The facility encompasses two fully aligned units: Translational Sequencing Unit (TSU) and Clinical Sequencing Unit (CSU, a.k.a Center for Molecular Diagnostics, CMD). TSU and CSU operate in tight synergy, but with separate responsible bodies and budgets. The main scope of TACG is 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.
TACG offers expertize and service in NGS-based technologies for investigators at Lund University/Region Skåne in projects with a strong translational edge or aiming at clinical implementation of new diagnostic assays. TACG also constitutes a physical node at which knowhow, services, education and outreach activities by the national platform Clinical Diagnostics will take place. TACG will also offer national services within specific high-profile areas of the facility.
TSU 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.
CSU has organized its services mainly around different focus areas, including cancer, inherited disorders, and microbiology.
TSU currently uses instruments available at different research Departments at the Medical Faculty and include one HiSeq2500, 3 NextSeq500, and 3 MiSeq. New instruments specifically devoted for the services at TSU will be purchased.
Available instruments at CSU include 1 PGM, 1 IonChef, 1 IonProton and 1 IonS5. The instrument park will be expanded during 2016.
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.
Examples of projects within the different work packages at TSU
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: SCAN-B, first generation RNAseq biomarkers for molecular subtype, cell proliferation/grade and steroid/HER2 receptors are developed and delivered in real-time for multidisciplinary conferences as complement to current prognostic and treatment-predictive histopathological and immunochemical markers.
WP4. Inherited Mendelian Disorders (WP leader: Maria Soller):
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 CSU
Focus Area: Cancer
Gene panels for colon cancer, lung cancer, and melanoma in clinical routine. Gene panels for myeloid malignancies and acute lymphoblastic leukemia in testing.
Focus Area: Inherited Mendelian Disorders
Clinical exome sequencing in testing. Non-invasive prenatal testing (NIPT) under evaluation.
Focus Area: Microbiology