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  Microarray Technologies for Analysis of Genetic Variations
Summary
Lundeberg
Savolainen
Ahmadian

Principal Investigator (PI): Dr Afshin Ahmadian

Personnel: Julia Sandberg (PhD student), Erik Borgström (PhD student), Yajing Song (PhD student), Mahya Dezfouli (PhD student)

Description:The research of the group focuses on development of molecular methods facilitating highly parallel amplification and analysis of genetic variations and expressed signature genes. Trinucleotide threading (TnT) and protease-mediated allele-specific extension (PrASE) are two techniques that the group has developed to assess DNA variations and profile expressed gene. The PrASE method is particularly suitable for magnetic bead capturing and naked-eye detection of in situ array sequenced and genotyped DNA molecules. This method that increases the spatial size of each DNA molecule by a thousand fold, opens up new possibilities to develop point-of-care devices for DNA analysis that can be produced and used at low cost. The TnT technique is currently adapted for genome-wide exon capturing followed by massive DNA sequencing of the selected exons. Other applications of TnT involve allelotyping by massive DNA sequencing technologies and expression profiling of genes involved in different cancers including basal cell carcinoma and ovarian cancer.

Key publications

Neiman, M., et al., Decoding a Substantial Set of Samples in Parallel by Massive Sequencing. PLoS One, 2011. 6(3).

Pettersson, E., et al., Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA. Nucleic Acids Res, 2006. 34(6): p. e49.

Zajac, P., et al., Expression profiling of signature gene sets with trinucleotide threading. Genomics, 2008. 91(2): p. 209-17.

Pettersson, E., et al., Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads. Hum Mutat, 2008. 29(2): p. 323-9.

Pettersson, E., et al., Visual DNA as a diagnostic tool. Electrophoresis, 2009. 30(21): p. 3691-5.

Hultin, E., et al., Competitive enzymatic reaction to control allele-specific extensions. Nucleic Acids Res, 2005. 33(5): p. e48.

Gharizadeh, B., et al., Viral and microbial genotyping by a combination of multiplex competitive hybridization and specific extension followed by hybridization to generic tag arrays. Nucleic Acids Res, 2003. 31(22): p. e146.

Ahmadian, A., et al., Genotyping by apyrase-mediated allele-specific extension. Nucleic Acids Res, 2001. 29(24): p. E121.

Ahmadian, A., et al., Single-nucleotide polymorphism analysis by pyrosequencing. Anal Biochem, 2000. 280(1): p. 103-10.

Ahmadian, A., et al., Analysis of the p53 tumor suppressor gene by pyrosequencing. Biotechniques, 2000. 28(1): p. 140-4, 146-7.

Last updated: 2011-03-17