Special Issue "Clinical Applications of Microarrays"

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A special issue of Microarrays (ISSN 2076-3905).

Deadline for manuscript submissions: closed (30 June 2014)

Special Issue Editor

Guest Editor
Prof. Dr. Reinhold Schäfer (Website)

Laboratories of Molecular Tumor Pathology and of Functional Genomics, Charité - Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany
Fax: +49 30 450 536 909
Interests: cancer transcriptomics; oncogenic signal transduction; systems biology & oncology

Special Issue Information

Dear Colleagues,

This special issue summarizes reports on current development and application of microarray technology in the cancer field.

Prof. Dr. Reinhold Schäfer
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microarrays is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • microarray-based analysis of microRNAomes and mRNAomes
  • development of secondary assays based on microarray studies for cancer diagnostics
  • breast cancer
  • lung cancer
  • prognostic markers
  • work flow from research lab to clinical practice
  • reverse phase protein arrays

Published Papers (4 papers)

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Review

Open AccessReview Molecular Diagnostic Applications in Colorectal Cancer
Microarrays 2014, 3(3), 168-179; doi:10.3390/microarrays3030168
Received: 28 March 2014 / Revised: 4 June 2014 / Accepted: 16 June 2014 / Published: 26 June 2014
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Abstract
Colorectal cancer, a clinically diverse disease, is a leading cause of cancer-related death worldwide. Application of novel molecular diagnostic tests, which are summarized in this article, may lead to an improved survival of colorectal cancer patients.  Distinction of these applications is based [...] Read more.
Colorectal cancer, a clinically diverse disease, is a leading cause of cancer-related death worldwide. Application of novel molecular diagnostic tests, which are summarized in this article, may lead to an improved survival of colorectal cancer patients.  Distinction of these applications is based on the different molecular principles found in colorectal cancer (CRC). Strategies for molecular analysis of single genes (as KRAS or TP53) as well as microarray based techniques are discussed. Moreover, in addition to the fecal occult blood testing (FOBT) and colonoscopy some novel assays offer approaches for early detection of colorectal cancer like the multitarget stool DNA test or the blood-based Septin 9 DNA methylation test. Liquid biopsy analysis may also exhibit great diagnostic potential in CRC for monitoring developing resistance to treatment. These new diagnostic tools and the definition of molecular biomarkers in CRC will improve early detection and targeted therapy of colorectal cancer. Full article
(This article belongs to the Special Issue Clinical Applications of Microarrays)
Open AccessReview Lung Cancer Gene Signatures and Clinical Perspectives
Microarrays 2013, 2(4), 318-339; doi:10.3390/microarrays2040318
Received: 16 October 2013 / Revised: 19 November 2013 / Accepted: 6 December 2013 / Published: 13 December 2013
Cited by 3 | PDF Full-text (212 KB) | HTML Full-text | XML Full-text
Abstract
Microarrays have been used for more than two decades in preclinical research. The tumor transcriptional profiles were analyzed to select cancer-associated genes for in-deep functional characterization, to stratify tumor subgroups according to the histopathology or diverse clinical courses, and to assess biological [...] Read more.
Microarrays have been used for more than two decades in preclinical research. The tumor transcriptional profiles were analyzed to select cancer-associated genes for in-deep functional characterization, to stratify tumor subgroups according to the histopathology or diverse clinical courses, and to assess biological and cellular functions behind these gene sets. In lung cancer—the main type of cancer causing mortality worldwide—biomarker research focuses on different objectives: the early diagnosis of curable tumor diseases, the stratification of patients with prognostic unfavorable operable tumors to assess the need for further therapy regimens, or the selection of patients for the most efficient therapies at early and late stages. In non-small cell lung cancer, gene and miRNA signatures are valuable to differentiate between the two main subtypes’ squamous and non-squamous tumors, a discrimination which has further implications for therapeutic schemes. Further subclassification within adenocarcinoma and squamous cell carcinoma has been done to correlate histopathological phenotype with disease outcome. Those tumor subgroups were assigned by diverse transcriptional patterns including potential biomarkers and therapy targets for future diagnostic and clinical applications. In lung cancer, none of these signatures have entered clinical routine for testing so far. In this review, the status quo of lung cancer gene signatures in preclinical and clinical research will be presented in the context of future clinical perspectives. Full article
(This article belongs to the Special Issue Clinical Applications of Microarrays)
Open AccessReview Improving Pathological Assessment of Breast Cancer by Employing Array-Based Transcriptome Analysis
Microarrays 2013, 2(3), 228-242; doi:10.3390/microarrays2030228
Received: 29 July 2013 / Revised: 17 August 2013 / Accepted: 22 August 2013 / Published: 29 August 2013
Cited by 3 | PDF Full-text (211 KB) | HTML Full-text | XML Full-text
Abstract
Breast cancer research has paved the way of personalized oncology with the introduction of hormonal therapy and the measurement of estrogen receptor as the first widely accepted clinical biomarker. The expression of another receptor—HER2/ERBB2/neu—was initially a sign of worse prognosis, but targeted [...] Read more.
Breast cancer research has paved the way of personalized oncology with the introduction of hormonal therapy and the measurement of estrogen receptor as the first widely accepted clinical biomarker. The expression of another receptor—HER2/ERBB2/neu—was initially a sign of worse prognosis, but targeted therapy has granted improved outcome for these patients so that today HER2 positive patients have better prognosis than HER2 negative patients. Later, the introduction of multigene assays provided the pathologists with an unbiased assessment of the tumors’ molecular fingerprint. The recent FDA approval of complete microarray pipelines has opened new possibilities for the objective classification of breast cancer samples. Here we review the applications of microarrays for determining ER and HER2 status, molecular subtypes as well as predicting prognosis and grade for breast cancer patients. An open question remains the role of single genes within such signatures. Openly available microarray datasets enable the execution of an independent cross-validation of new marker and signature candidates. In summary, we review the current state regarding clinical applications of microarrays in breast cancer molecular pathology. Full article
(This article belongs to the Special Issue Clinical Applications of Microarrays)
Open AccessReview From High-Throughput Microarray-Based Screening to Clinical Application: The Development of a Second Generation Multigene Test for Breast Cancer Prognosis
Microarrays 2013, 2(3), 243-264; doi:10.3390/microarrays2030243
Received: 17 July 2013 / Revised: 12 August 2013 / Accepted: 22 August 2013 / Published: 29 August 2013
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Abstract
Several multigene tests have been developed for breast cancer patients to predict the individual risk of recurrence. Most of the first generation tests rely on proliferation-associated genes and are commonly carried out in central reference laboratories. Here, we describe the development of [...] Read more.
Several multigene tests have been developed for breast cancer patients to predict the individual risk of recurrence. Most of the first generation tests rely on proliferation-associated genes and are commonly carried out in central reference laboratories. Here, we describe the development of a second generation multigene assay, the EndoPredict test, a prognostic multigene expression test for estrogen receptor (ER) positive, human epidermal growth factor receptor (HER2) negative (ER+/HER2−) breast cancer patients. The EndoPredict gene signature was initially established in a large high-throughput microarray-based screening study. The key steps for biomarker identification are discussed in detail, in comparison to the establishment of other multigene signatures. After biomarker selection, genes and algorithms were transferred to a diagnostic platform (reverse transcription quantitative PCR (RT-qPCR)) to allow for assaying formalin-fixed, paraffin-embedded (FFPE) samples. A comprehensive analytical validation was performed and a prospective proficiency testing study with seven pathological laboratories finally proved that EndoPredict can be reliably used in the decentralized setting. Three independent large clinical validation studies (n = 2,257) demonstrated that EndoPredict offers independent prognostic information beyond current clinicopathological parameters and clinical guidelines. The review article summarizes several important steps that should be considered for the development process of a second generation multigene test and offers a means for transferring a microarray signature from the research laboratory to clinical practice. Full article
(This article belongs to the Special Issue Clinical Applications of Microarrays)

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