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This Week in Genome Research: May 27, 2009

Korean scientists led by Seong-Jin Kim have sequenced the first individual Korean genome. They used Illumina paired-end sequencing on a Korean male, finding 420,083 novel SNPs that are not in the dbSNP database. Also, they found important differences between this genome and the Chinese genome, suggesting that "overall genetic differences among individuals from closely related ethnic groups may be significant."

Michael Hiller from Stanford has led work using systems biology techniques to study mlncRNAs in the fruit fly. These mRNA-like noncoding RNAs are like mRNAs in that they can be spliced, capped, and polyadenylated and have important functions inside the cell. They used genome-wide comparative genomics to look for short conserved introns in order to find conserved transcripts with high specificity. After applying the approach to insect genomes, they predicted 369 novel introns, 129 of which belonged to novel mlncRNAs. Using RT-PCR, they verified seven of 12 tested introns in novel mlncRNAs and 11 of 17 introns in novel coding genes, suggesting that "novel mlncRNAs are good candidates for functional transcripts."

Korean scientists have used engineered zinc finger nucleases to do targeted genome editing in human cells. Their process involves an "efficient and easy-to-practice modular-assembly method using publicly available zinc fingers to make ZFNs that can modify the DNA sequences of predetermined genomic sites in human cells." Testing them on dozens of different sites in the human CCR5 gene, they found many could trigger mutations, thereby making it possible to use them for gene therapy applications in HIV.

John Postlethwait at the University of Oregon led work that developed an automated process to find conserved syntenic regions in a genome using as an outgroup a genome that diverged from the one being studied before a whole genome duplication event. Their Synteny Database "allows a user to examine fully or partially assembled genomes" and is "optimized for the investigation of individual gene families in multiple lineages and can detect chromosomal inversions and translocations as well as ohnologs (paralogs derived by whole-genome duplication) gone missing," they write in the abstract.