Targeted genome-wide enrichment of functional regions

• Published in: PloS one Vol. 5; no. 6; p. e11138
• Main Authors: Senapathy, Periannan, Bhasi, Ashwini, Mattox, Jeffrey, Dhandapany, Perundurai S, Sadayappan, Sakthivel
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 16.06.2010; Public Library of Science (PLoS)
• Subjects: Analysis; Base Sequence; Bioinformatics; Biotechnology; Candida albicans; Capillary electrophoresis; Carrier Proteins - genetics; Complementarity; Computational Biology/Genomics; Computer applications; Deoxyribonucleic acid; DNA; DNA Primers; Enhancers; Enrichment; Exons; Feasibility Studies; Fingerprinting; Gene Regulatory Networks; Gene sequencing; Genes; Genetic aspects; Genetics; Genetics and Genomics/Bioinformatics; Genetics and Genomics/Functional Genomics; Genetics and Genomics/Gene Discovery; Genome, Human; Genomes; Genomics; Heart diseases; HIV; Human immunodeficiency virus; Humans; Medical screening; Methods; Multiplexing; Mutation; Myosin; Nucleotide sequence; Permutations; Primers; Promoter Regions, Genetic; Promoters; Protein binding; Proteomics; Randomization; Trends; New York; United States > US; Wisconsin
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0011138

Only a small fraction of large genomes such as that of the human contains the functional regions such as the exons, promoters, and polyA sites. A platform technique for selective enrichment of functional genomic regions will enable several next-generation sequencing applications that include the discovery of causal mutations for disease and drug response. Here, we describe a powerful platform technique, termed "functional genomic fingerprinting" (FGF), for the multiplexed genomewide isolation and analysis of targeted regions such as the exome, promoterome, or exon splice enhancers. The technique employs a fixed part of a uniquely designed Fixed-Randomized primer, while the randomized part contains all the possible sequence permutations. The Fixed-Randomized primers bind with full sequence complementarity at multiple sites where the fixed sequence (such as the splice signals) occurs within the genome, and multiplex amplify many regions bounded by the fixed sequences (e.g., exons). Notably, validation of this technique using cardiac myosin binding protein-C (MYBPC3) gene as an example strongly supports the application and efficacy of this method. Further, assisted by genomewide computational analyses of such sequences, the FGF technique may provide a unique platform for high-throughput sample production and analysis of targeted genomic regions by the next-generation sequencing techniques, with powerful applications in discovering disease and drug response genes.