Superimposed coding for iterative detection of DNA microarray spot failures

Huang, Duruo; Milenković, Olgica

doi:10.1109/gensips.2008.4555682

Cited by 2 publications

References 11 publications

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Gene expression reliability estimation through cluster-based analysis

Sterpone

Benso

Carlo

et al. 2009

2009 IEEE International Workshop on Medical Measurements and Applications

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Gene expression is the fundamental control of the structure and functions of the cellular versatility and adaptability of any organisms. The measurement of gene expressions is performed on images generated by optical inspection of microarray devices which allow the simultaneous analysis of thousands of genes. The images produced by these devices are used to calculate the expression levels of mRNA in order to draw diagnostic information related to human disease. The quality measures are mandatory in genes classification and in the decision-making diagnostic. However, microarrays are characterized by imperfections due to sample contaminations, scratches, precipitation or imperfect gridding and spot detection. The automatic and efficient quality measurement of microarray is needed in order to discriminate faulty gene expression levels. In this paper we present a new method for estimate the quality degree and the data's reliability of a microarray analysis. The efficiency of the proposed approach in terms of genes expression classification has been demonstrated through a clustering supervised analysis performed on a set of three different histological samples related to the Lymphoma's cancer disease.

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Gene expression reliability estimation through cluster-based analysis

Sterpone

Benso

Carlo

et al. 2009

2009 IEEE International Workshop on Medical Measurements and Applications

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Compressed Genotyping

Erlich

Gordon

Brand³

et al. 2010

IEEE Trans. Inform. Theory

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Over the past three decades we have steadily increased our knowledge on the genetic basis of many severe disorders. Nevertheless, there are still great challenges in applying this knowledge routinely in the clinic, mainly due to the relatively tedious and expensive process of genotyping. Since the genetic variations that underlie the disorders are relatively rare in the population, they can be thought of as a sparse signal. Using methods and ideas from compressed sensing and group testing, we have developed a cost-effective genotyping protocol to detect carriers for severe genetic disorders. In particular, we have adapted our scheme to a recently developed class of high throughput DNA sequencing technologies. The mathematical framework presented here has some important distinctions from the â€™traditionalâ€™ compressed sensing and group testing frameworks in order to address biological and technical constraints of our setting.

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Superimposed coding for iterative detection of DNA microarray spot failures

Cited by 2 publications

References 11 publications

Gene expression reliability estimation through cluster-based analysis

Gene expression reliability estimation through cluster-based analysis

Compressed Genotyping

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