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Establishing a Southern Swedish Malignant Melanoma OMICS and Biobank Clinical Capability

Welinder, Charlotte LU ; Jönsson, Göran B LU ; Ingvar, Christian LU ; Lundgren, Lotta LU ; Olsson, Håkan LU orcid ; Breslin, Thomas LU ; Végvári, Ákos LU ; Laurell, Thomas LU ; Rezeli, Melinda LU orcid and Jansson, Bo LU , et al. (2013) In Clinical and Translational Medicine 2(1).
Abstract
Background: The Southern Swedish Malignant Melanoma (SSMM) research team is a truly cross functional group with members from oncology, clinical, surgery, bioinformatics, proteomics, and genomics initiatives. The SSMM’s objectives and goals are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. 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. The science output in these resulting... (More)
Background: The Southern Swedish Malignant Melanoma (SSMM) research team is a truly cross functional group with members from oncology, clinical, surgery, bioinformatics, proteomics, and genomics initiatives. The SSMM’s objectives and goals are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. 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. The science output in these resulting study outcomes further strengthens the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market. These patient biobank archives will be fully automated with novel ultralow temperature biobank storage units and used as a clinical resource.

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. We are developing 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.

Results: An IT-infrastructure using a laboratory information management system (LIMS) has been established, that will be 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 will form the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are being associated with the biobank materials, including pathology reports on disease diagnosis on the MM patients.

Conclusions: We provide data on the developments of protein profiling and targeted protein target 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. (Less)
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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Malignant Melanoma, Protein sequencing, Proteomics, Genes, Antibodies, mRNA, Mass spectrometry, Bioinformatics
in
Clinical and Translational Medicine
volume
2
issue
1
article number
7
publisher
Wiley
external identifiers
  • pmid:23445834
ISSN
2001-1326
DOI
10.1186/2001-1326-2-7
language
English
LU publication?
yes
id
b451a8cd-5566-4dca-a50f-3b91952e999b (old id 3172683)
date added to LUP
2016-04-01 14:13:38
date last changed
2019-03-13 15:41:13
@article{b451a8cd-5566-4dca-a50f-3b91952e999b,
  abstract     = {{Background: The Southern Swedish Malignant Melanoma (SSMM) research team is a truly cross functional group with members from oncology, clinical, surgery, bioinformatics, proteomics, and genomics initiatives. The SSMM’s objectives and goals are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. 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. The science output in these resulting study outcomes further strengthens the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market. These patient biobank archives will be fully automated with novel ultralow temperature biobank storage units and used as a clinical resource.<br/><br>
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. We are developing 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. <br/><br>
Results: An IT-infrastructure using a laboratory information management system (LIMS) has been established, that will be 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 will form the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are being associated with the biobank materials, including pathology reports on disease diagnosis on the MM patients. <br/><br>
Conclusions: We provide data on the developments of protein profiling and targeted protein target 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.}},
  author       = {{Welinder, Charlotte and Jönsson, Göran B and Ingvar, Christian and Lundgren, Lotta and Olsson, Håkan and Breslin, Thomas and Végvári, Ákos and Laurell, Thomas and Rezeli, Melinda and Jansson, Bo and Baldetorp, Bo and Marko-Varga, György}},
  issn         = {{2001-1326}},
  keywords     = {{Malignant Melanoma; Protein sequencing; Proteomics; Genes; Antibodies; mRNA; Mass spectrometry; Bioinformatics}},
  language     = {{eng}},
  number       = {{1}},
  publisher    = {{Wiley}},
  series       = {{Clinical and Translational Medicine}},
  title        = {{Establishing a Southern Swedish Malignant Melanoma OMICS and Biobank Clinical Capability}},
  url          = {{https://lup.lub.lu.se/search/files/3854981/3795222.pdf}},
  doi          = {{10.1186/2001-1326-2-7}},
  volume       = {{2}},
  year         = {{2013}},
}