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Development of novel multiplexed SPEX-based methodologies to accurately genotype forensic, archaeological, and other marginal environmental sources of DNA (Multiplexed-SPEX)
Start date: 01 Jan 2009, End date: 31 Dec 2010 PROJECT  FINISHED 

Traces of surviving degraded DNA in marginal clinical, forensic, archaeological, and environmental samples are generally amplified by PCR, which can often produce highly-skewed product distributions dominated by non-authentic sequences (due to DNA damage and PCR-generated artefacts). The applicant has developed the SPEX amplification methodology, an alternative to PCR which has generated sequence data of unprecedented accuracy from specimens up to 60,000 years old. SPEX creates first-generation copies from target template strands at defined loci and can generate a quantifiable redundancy of coverage (providing in-built controls for the detection of contamination and allelic drop-out). SPEX has provided key insights and solved long-standing puzzles in the molecular processes of DNA degradation. The applicant would be fully-trained in every aspect of state-of-the-art multiplexed genotyping methodologies, at a host institution currently providing high-throughput data for population genetics, disease association and forensics studies in worldwide collaborations. The proposed project to develop multiplexed-SPEX systems could reduce genotyping errors down towards the background level of polymerase misincorporation, allowing the rapid and reliable quantifiable genotyping of even highly marginal samples. This could revolutionise the authentication of sequence data in areas as diverse as basic cancer research, forensics, biomolecular archaeology, and conservation biology. In addition, highly-promising prototypes for the whole genome amplification of marginal DNA could allow key samples to be 'immortalised' for prolonged in-depth genetic analyses. The proposed project would create new hybrid technologies, useful in many fields throughout the EU and beyond. The enthusiastic backing of international collaborators provides scope for EU-wide technology transfer, and would leave the applicant with the core skills to take these novel methodologies into further research positions.
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