Open Access Highly Accessed Research

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability

Charlotte Welinder1, Göran Jönsson1, Christian Ingvar2, Lotta Lundgren1, Håkan Olsson1, Thomas Breslin1, Ákos Végvári3, Thomas Laurell3, Melinda Rezeli3, Bo Jansson14, Bo Baldetorp1 and György Marko-Varga35*

Author Affiliations

1 Department of Oncology and Cancer Epidemiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund 221 85, Sweden

2 Department of Surgery, Clinical Sciences, Lund University, SUS, Lund 221 85, Sweden

3 Clinical Protein Science & Imaging, Biomedical Center, Dept. of Measurement Technology and Industrial Electrical Engineering, Lund University, BMC C13, Lund 221 84, Sweden

4 BioInvent Int. AB, Sölvegatan 41, Lund SE-223 70, Sweden

5 First Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo 160-0023, Japan

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Clinical and Translational Medicine 2013, 2:7  doi:10.1186/2001-1326-2-7

Published: 27 February 2013

Abstract

Background

The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits.

Methods

Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources.

Results

An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients.

Conclusions

We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market.

Keywords:
Malignant melanoma; Protein sequencing; Proteomics; Genes; Antibodies; mRNA; Mass spectrometry; Bioinformatics