Posts Tagged ‘genomics’

Rethinking our right to privacy

 :: Posted by American Biotechnologist on 04-09-2012

Researchers at the Mount Sinai School of Medicine have recently published a method that may further complicate the way society relates to genetic information and an individual’s right to privacy. Drs. Eric E. Schadt and Ke Hao from Mount Sinai’s Institute for Genomics and Multiscale Biology, have developed a method for identifying an individual’s DNA barcode using only their RNA expression levels. According to Schadt “By observing RNA levels in a given tissue, we can infer a genotypic barcode that uniquely tags an individual in ways that enables matching the individual to an independently derived DNA sample.”

While regulators have established privacy laws related to what can be done with an individual’s genome, very little, (if anything), has been discussed with regards to how personal RNA information can be used. Considering that, until now, it would have been difficult, at best, to identify an individual based on their RNA expression, such laws were considered useless. However, with the development of this new technique all that has changed. Not only will the new technique allow scientists to predict disease risks which were previously done using genomic data information, but it would also enable law enforcement authorities to tie genomic DNA found at a crime scene to individual information stored in a research studies’ RNA database (which are publicly available via a number of databases in the United States and Europe and contain thousands of genomic studies from around the world).

According to the authors, society needs to rethink the way they relate to privacy information. “Rather than developing ways to further protect an individual’s privacy given the ability to collect mountains of information on him or her, we would be better served by a society that accepts the fact that new types of high-dimensional data reflect deeply on who we are,” Dr. Schadt said. “We need to accept the reality that it is difficult—if not impossible—to shield personal information from others. It is akin to trying to protect privacy regarding appearances, for example, in a public place.”

This reminds me of a recent spoof produced by The Onion highlighting the significant paradigm shift social media has created for our right to privacy. What are your thoughts on the matter?

For more information see New ‘genetic bar code’ technique establishes ability to derive DNA information from RNA

Reference: Schadt, E., Woo, S., & Hao, K. (2012). Bayesian method to predict individual SNP genotypes from gene expression data Nature Genetics DOI: 10.1038/ng.2248

New strategies for decoding genomes

 :: Posted by American Biotechnologist on 03-29-2012

Following up on yesterday’s post “New Layer of Genetic Information Discovered,” here is a talk by Professor Jonathan Weissman on applications of the ribosome profiling approach. The talk covers:

  1. Development of ribosome profiling protocols for a wide variety of eukaryotic and prokaryotic organisms.
  2. Uses of ribosome profiling to globally monitor when chaperones, targeting factors or processing enzymes engage nascent chains.
  3. Deciphering the driving force and biological consequences underlying the choice of synonymous codons.

Spliceman to the rescue

 :: Posted by American Biotechnologist on 03-12-2012

In a brief paper in the journal Bioinformatics, Brown University researchers describe a new, freely available Web-based program called Spliceman for predicting whether genetic mutations are likely to disrupt the splicing of messenger RNA, potentially leading to disease.

“Spliceman takes a set of DNA sequences with point mutations and computes how likely these single nucleotide variants alter splicing phenotypes,” write co-authors Kian Huat Lim, a graduate student, and William Fairbrother, assistant professor of biology, in an “application note” published in advance online Feb. 10. It will appear in print in April.

Spliceman can be found at fairbrother.biomed.brown.edu/spliceman.

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Analyzing complex plant genomes with the newest next-generation DNA sequencing techniques

 :: Posted by American Biotechnologist on 02-27-2012

Richard Cronn and colleagues (from the USDA Forest Service, Oregon State University, Brigham Young University, and Linfield College) have published an overview of newly developed, up-and-coming DNA sequencing techniques as one of a series of articles in a Special Issue on Methods and Applications of Next-Generation Sequencing in Botany in the American Journal of Botany. In their article, Cronn and co-authors summarize “targeted enrichment” strategies that can be used to obtain specific DNA sequences from complex plant genomes. Articles in the Special Issue provide a detailed snapshot of how “next-generation” sequencing is transforming plant biology.

“Plant genomes range from simple to exceptionally complex,” noted Cronn. “Combining next-generation sequencing with targeted enrichment allows plant scientists to reduce the complexity of plant genomes and focus on specific genes or unique regions that are easy to analyze.”

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The special issue also includes a comprehensive review article on NGS technologies. Click here to read the review.

Grass to gas: genome map speeds biofuel development

 :: Posted by American Biotechnologist on 02-14-2012

Researchers at the University of Georgia have taken a major step in the ongoing effort to find sources of cleaner, renewable energy by mapping the genomes of two originator cells of Miscanthus x giganteus, a large perennial grass with promise as a source of ethanol and bioenergy.

Changsoo Kim, a postdoctoral research associate in the UGA Plant Genome Mapping Laboratory, identified a set of approximately 600 bits of Miscanthus DNA that can serve as diagnostic tools. The next step is to determine which pieces of DNA are diagnostic of genes that can make the plant an even better biofuel crop.

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