Microarray Analysis

Department of Biostatistics, University of Alabama at Birmingham, Hoover, AL, USA.
Methods in Molecular Biology (Impact Factor: 1.29). 02/2007; 404:409-30. DOI: 10.1007/978-1-59745-530-5_20
Source: PubMed


Microarrays and related technologies have allowed investigators to ask biological questions in far greater detail than has previously been possible. Microarrays had a troubled beginning, but most of these problems resulted from the growing pains of this technology, which, like many new things, was initially more promise than delivery. Nevertheless, over the past few years, investigators have learned how to achieve optimal performance of technology, and now exciting discoveries are made using microarray-based research. Many of the advances have come from the realization that microarrays are not a magic tool but rather are like any other measurement device. Unless microarray experimentation is coupled with good experimental practices, it will not yield valid results or, worse yet, may lead to misleading results. In this chapter, we highlight some of the important steps that should be taken to successfully conduct a microarray study. These steps include a clearly stated biological question, experimental design, careful experimental conduct, complete statistical analysis, validation/verification of results, and dissemination of the data.

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Available from: Kui Zhang, Sep 02, 2014
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    • "Instead of the analyses of single genes described above, technologies such as cDNA microarrays can analyze thousand of transcripts in one chip [22]. However, it is expensive, has low sample throughput, and standardized procedures for optimization of the signal/noise ratio are lacking [23]. "
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    BMC Cardiovascular Disorders 07/2012; 12:51. DOI:10.1186/1471-2261-12-51 · 1.88 Impact Factor
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    • "In spite of the exciting prospects implied by that 2005 review, relatively little work has been published in the intervening three years to validate such genome-scale neonatal screening [6,7]. Microarray technology has improved significantly in that period, in terms of diminished cost and sample requirement, and has yielded increased data density and quality [8]. However, such genome-scale microarray analysis continues to require an input DNA mass (about 250 ng) that is about 100 times larger than required for simple PCR testing; requires DNA that is double stranded; and requires DNA with a length-span that is about 5 times longer than required for most PCR reactions. "
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    ABSTRACT: Neonatal blood, obtained from a heel stick and stored dry on paper cards, has been the standard for birth defects screening for 50 years. Such dried blood samples are used, primarily, for analysis of small-molecule analytes. More recently, the DNA complement of such dried blood cards has been used for targeted genetic testing, such as for single nucleotide polymorphism in cystic fibrosis. Expansion of such testing to include polygenic traits, and perhaps whole genome scanning, has been discussed as a formal possibility. However, until now the amount of DNA that might be obtained from such dried blood cards has been limiting, due to inefficient DNA recovery technology. A new technology is employed for efficient DNA release from a standard neonatal blood card. Using standard Guthrie cards, stored an average of ten years post-collection, about 1/40th of the air-dried neonatal blood specimen (two 3 mm punches) was processed to obtain DNA that was sufficient in mass and quality for direct use in microarray-based whole genome scanning. Using that same DNA release technology, it is also shown that approximately 1/250th of the original purified DNA (about 1 ng) could be subjected to whole genome amplification, thus yielding an additional microgram of amplified DNA product. That amplified DNA product was then used in microarray analysis and yielded statistical concordance of 99% or greater to the primary, unamplified DNA sample. Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.
    BMC Genetics 02/2009; 10(1):38. DOI:10.1186/1471-2156-10-38 · 2.40 Impact Factor
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