Integrative analysis of cancer‐related data using CAP

Dönnes, Pierre; Höglund, Annette; Sturm, Marc; Comtesse, Nicole; Backes, Christina; Meese, Eckart; Kohlbacher, Oliver; Lenhof, Hans‐Peter

doi:10.1096/fj.04-1797fje

Cited by 9 publications

(6 citation statements)

References 30 publications

(22 reference statements)

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“…1,13 Our previous studies with cancer-associated protein database failed to provide evidence that mutations significantly contribute to immunogenicity of tumor antigens. 14 Sequence analysis of several antigens including MGEA6, GLEA2 and EIF4G found in meningioma, glioma and lung cancer, respectively, did not reveal mutations in any of the antigens. 12,15,16 Although these three studies were based on tumor-derived libraries, the present study is based on fetal brain libraries.…”

Section: Discussionmentioning

confidence: 89%

Combining gene expression signatures and autoantibody profiles in human meningioma

Keller

Ludwig

et al. 2008

Gene Ther

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Gene expression profiling has emerged as powerful technique for studying the mechanisms of tumor genesis and development. Seroreactivity profiling of tumor antigens is a more recent technique that further contributes to the understanding of tumors and that offers itself for noninvasive tumor diagnosis. We performed expression profiling of 55 000 transcripts and expressed-sequence-tags for 24 meningiomas and related these data to autoantibody profiles of more than 50 antigens immunogenic in the autologous patients. The expression values of antigens in WHO grade I meningioma were significantly higher if the patients' sera reacted with these antigens as confirmed by a two-tailed Wilcoxon-Mann-Whitney test. Specifically, KIAA1344 that was previously identified as frequent antigen marker in meningioma, showed increased expression if antigens against KIAA1344 were detected in autologous patients. Our study is the first to combine genomewide expression signatures and comprehensive seroreactivity patterns toward a more complete view on tumor immunology, especially concerning the overall role of the level of gene expression on the immunogenicity of meningioma antigens.

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Section: Discussionmentioning

confidence: 89%

Combining gene expression signatures and autoantibody profiles in human meningioma

Keller

Ludwig

et al. 2008

Gene Ther

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“…Challenges remain in identifying novel molecular, histological and clinical risk factors for stratification of treatment intensity. This could allow a safe reduction in therapy for patients known to have an excellent chance of cure with the current therapy, while identifying, at diagnosis, the minority of children at risk of relapse, who will require more aggressive treatments [6].…”

Section: Post-genomic Clinical Trials On Cancermentioning

confidence: 99%

Developing a European grid infrastructure for cancer research: vision, architecture, and services

Tsiknakis¹

2015

ecancer

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Life sciences are currently at the centre of an information revolution. The nature and amount of information now available opens up areas of research that were once in the realm of science fiction. During this information revolution, the data-gathering capabilities have greatly surpassed the data-analysis techniques. Data integration across heterogeneous data sources and data aggregation across different aspects of the biomedical spectrum, therefore, is at the centre of current biomedical and pharmaceutical R&D. This paper reports on original results from the ACGT integrated project, focusing on the design and development of a European Biomedical Grid infrastructure in support of multi-centric, post-genomic clinical trials (CTs) on cancer. Post-genomic CTs use multi-level clinical and genomic data and advanced computational analysis and visualization tools to test hypotheses in trying to identify the molecular reasons for a disease and the stratification of patients in terms of treatment.The paper provides a presentation of the needs of users involved in post-genomic CTs and presents indicative scenarios, which drive the requirements of the engineering phase of the project. Subsequently, the initial architecture specified by the project is presented, and its services are classified and discussed. A range of such key services, including the Master Ontology on sCancer, which lie at the heart of the integration architecture of the project, is presented. Special efforts have been taken to describe the methodological and technological framework of the project, enabling the creation of a legally compliant and trustworthy infrastructure. Finally, a short discussion of the forthcoming work is included, and the potential involvement of the cancer research community in further development or utilization of the infrastructure is described.

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“…Immunogenic tumour-associated antigens have been reported for a variety of malignant tumours, including brain tumours and prostate, lung and colon cancer [53 54]. In a first step, immunogenic Wilms tumour-associated antigens will be identified by immuno-screening of a cDNA expression library.…”

Section: Wilms-scenario: Tumour-specific Antigensmentioning

confidence: 99%