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The Exploitation of Formalin Fixed Tissues for High-Throughput Genetic Analyses: An HIV-1-HLA Cointeraction Case Study

The Exploitation of Formalin Fixed Tissues for High-Throughput Genetic Analyses: An HIV-1-HLA Cointeraction Case Study

Objective

The use of formalin-fixed specimens in genetic studies has been limited due to damage of the nucleic acids through contact with the formalin. However, recent developments in extraction and repair techniques have increased both the yields and quality of the DNA and RNA sequences that can be retrieved from such specimens. Additionally, the invention of advanced Multi-Plex PCR techniques has made it possible to quickly screen a large number of genomic markers. Thus, for the first time, formalin-fixed specimens have become available to large-scale genetic analyses.This proposal will enable the principal applicant to become an expert on the retrieval and analyses of nucleic acid from formalin fixed specimens. Based at the University of Copenhagens Centre for Anci ent DNA and Evolutionary Biology, the applicant will be trained by a team of expert mentors in the use, design and theory behind modern high-throughput genetic screening assays for ancient and contemporary DNA. He will also be trained in advanced statistic al and analytical techniques required to develop and analyze the data from genetic association studies. The applicant will apply these techniques to anonymous, HIV-1 infected, fixed biopsy and autopsy specimens that date to the early period of the epidemic in Northern Europe (and lt 1990). Thereby, he will investigate the dynamics of the evolutionary interaction between HIV-1 and the human genome, principally focusing on association studies between the virus and the Human Leukocyte Antigen (HLA) system. The outcomes of this project will not only confirm current hypotheses, and shed new insights, into the model HIV-1-human system, but will develop the tools through which future investigations that require high-throughput screening techniques of fixed specimen s can be achieved.

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Coordinator

UNIVERSITY OF COPENHAGEN

Address

Norregade 10
Copenhagen

Denmark

Administrative Contact

Eske WILLERSLEV (Prof.)

Project information

Grant agreement ID: 25002

  • Start date

    1 November 2005

  • End date

    31 October 2007

Funded under:

FP6-MOBILITY

Coordinated by:

UNIVERSITY OF COPENHAGEN

Denmark