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Microarrays 01 00042

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27 views2 pages

Microarrays 01 00042

Uploaded by

Jacobo Gutierrez
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Microarrays 2012, 1, 42-43; doi:10.

3390/microarrays1010042
OPEN ACCESS

microarrays
ISSN 2076-3905
www.mdpi.com/journal/microarrays
Editorial

Microarrays—Current and Future Applications in Biomedical


Research
Ulrich Certa

Editor-in-Chief of Microarrays, Molecular Toxicology, Non-Clinical Safety (pRED),


F. Hoffmann-La Roche AG, Postfach, 4070-Basel, Switzerland; E-Mail: ulrich.certa@roche.com;
Tel.: +41-61-688-5340

Received: 16 November 2011 / Accepted: 22 November 2011 / Published: 22 November 2011

Microarrays covers research where microarrays are applied to address complex biological
questions. This new open access journal publishes articles where novel applications or state-of-the art
technology developments in the field are reported. In addition, novel methods or data analysis
algorithms are under the scope of Microarrays. This journal will serve as a platform for fast and
efficient sharing of data within this large user community. As one of the first microarray users in
Europe back in 1996, I am proud to serve as Editor-in-Chief and I believe we have assembled a highly
proficient Editorial Board, responsible for a fair and fast peer-review of articles.
The first generations of commercial microarrays introduced in the mid-nineties suffered mainly
from sensitivity and reproducibility due to poor production technologies. In the early days of the
technology, the first microarrays had probe sets complementary to about 120 genes and about 30
transcripts were measured in routine experiments. However, it became clear that further reduction of
the feature size would ultimately allow integration of entire genomes, which is the case today. In
addition, array production and sample preparation methods underwent significant improvements
resulting in robust and indispensable tools for routine applications in biomedical research [1].
In parallel microarray technologies for the genome wide analysis of single-nucleotide
polymorphisms (SNPs) [2], copy number variation (CNV) [3] or DNA methylation [4] were
successfully developed and marketed. Today a search for “DNA microarray” yields more than 50’000
PubMed entries which showcases the success of this technology and its wide range of applications. It
is quite amazing that it took only 15 years of development time until multi-parallel interrogation of
entire genomes became available for the research community. Currently, there are serious efforts
ongoing to apply microarrays for protein based applications, such as epitope mapping [5]. However,
this application is more challenging due to different properties of the ligand such as affinity or epitope
folding.
Microarrays 2012, 1 43

Recently exceptionally efficient deep sequencing technologies became available at highly


competitive prices. Measuring clone frequencies in bead libraries has the potential to replace or
complement chip based fluorescence based transcript imaging in the future. One advantage of this
approach is the possibility to detect any genomic transcript of an organism, provided the genome is
available. Today many aspects of next-generation sequencing (NGS) remain to be solved. Although
data generation can be fast, depending on the technology, the data analysis and processing have
currently no user friendly solution, especially when multiple samples and conditions are part of the
experiment. In addition, sample preparation is complex and certainly a source for artifacts which is
reminiscent to the early days of microarray technology. Finally, the poor concordance of chip based
transcript profiling experiments and NGS is inadequately understood in the research community [6]. In
summary, I consider the use of microarrays is still the method of choice for routine experiments or
studies that are carried out under GLP (good laboratory practice) regulations. The availability of user
friendly commercial data analysis packages allows fast, robust and user-friendly data analysis and
integration. Furthermore public expression databases such as GEO [7] allow comparative data
analysis.
We welcome you to Microarrays and encourage submissions of interesting papers. We also
welcome suggestions regarding the scope and content of the journal.

References and Notes

1. Roepman, P. The future of diagnostic gene-expression microarrays: bridging the gap between
bench and bedside. Bioanalysis 2010, 2, 249-262.
2. Beaudet, A.L.; Belmont, J.W. Array-based DNA diagnostics: let the revolution begin.
Annu. Rev. Med. 2008, 59, 113-129.
3. Lam, C.W.; Lau, K.C.; Tong, S.F. Microarrays for personalized genomic medicine.
Adv. Clin. Chem. 2010, 52, 1-18.
4. Gregory, B.D.; Belostotsky, D.A. Whole-genome microarrays: Applications and technical issues.
Methods Mol. Biol. 2009, 553, 39-56.
5. Stoll, D.; Templin, M.F.; Bachmann, J.; Joos, T.O. Protein microarrays: Applications and future
challenges. Curr. Opin. Drug Discov. Devel. 2005, 8, 239-252.
6. Marioni, J.C.; Mason, C.E.; Mane, S.M.; Stephens, M.; Gilad, Y. RNA-seq: an assessment of
technical reproducibility and comparison with gene expression arrays. Genome Res. 2008, 18,
1509-1517.
7. Gene Expression Omnibus. http://www.ncbi.nlm.nih.gov/geo/ (accessed on 20 November 2011).

© 2011 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article
distributed under the terms and conditions of the Creative Commons Attribution license
(http://creativecommons.org/licenses/by/3.0/).

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