HapMap browsing and DDDP methods for genetic analysis featured in CSH Protocols

July 02, 2008

COLD SPRING HARBOR, N.Y. (Tuesday, July 1, 2008) - To aid in the study of genetic diseases, scientists with the International Haplotype Map Project have developed a haplotype map of the human genome, a tool that displays common patterns of genetic variation. While data from the project are available for unrestricted public use from the project's website (www.hapmap.org), the new tools needed to browse the map can be difficult to master for the beginner. This month's issue of Cold Spring Harbor Protocols (www.cshprotocols.org/TOCs/toc7_08.dtl) features a set of articles with clear, step-by-step instructions for the analysis of HapMap data.

"Browsing HapMap Data Using the Genome Browser" provides details on how to navigate to and explore HapMap data for a gene or region of interest. Written by Albert Vernon Smith, this protocol shows how to analyze a candidate gene to find out whether there are any common single nucleotide polymorphisms (SNPs) in the immediate vicinity, what those SNPs' alleles are, and the relative frequencies of the alleles in the population. The protocol is freely accessible on the website for Cold Spring Harbor Protocols (http://www.cshprotocols.org/cgi/content/full/2008/8/pdb.prot5023).

The second featured method for July, "In Vitro Screening for Regulated Transcription Factors with Differential Display of DNA-Binding Proteins (DDDP)," provides a method for identifying proteins that are actively binding DNA and playing a role in gene regulation. Developed in the laboratory of Ueli Schibler (http://www.molbio.unige.ch/schibler/index.php), this method provides a new level of sensitivity to complement standard genomic screening and proteomic methods for finding transcription factors. This method is freely accessible on the website for Cold Spring Harbor Protocols (http://www.cshprotocols.org/cgi/content/full/2008/8/pdb.prot5028).
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About Cold Spring Harbor Protocols:

Cold Spring Harbor Protocols (www.cshprotocols.org) is a monthly peer-reviewed journal of methods used in a wide range of biology laboratories. It is structured to be highly interactive, with each protocol cross-linked to related methods, descriptive information panels, and illustrative material to maximize the total information available to investigators. Each protocol is clearly presented and designed for easy use at the bench--complete with reagents, equipment, and recipe lists. Life science researchers can access the entire collection via institutional site licenses, and can add their suggestions and comments to further refine the techniques.

About Cold Spring Harbor Laboratory Press: Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. Since 1933, it has furthered the advance and spread of scientific knowledge in all areas of genetics and molecular biology, including cancer biology, plant science, bioinformatics, and neurobiology. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit www.cshlpress.com.

Cold Spring Harbor Laboratory

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