September 3, 2009
Expanding NextGen Sequencing Applications
Next-Generation Sequencing (NGS) technologies are not only beginning to supplant traditional Sanger sequencing methodology but are also giving DNA microarrays a run for the money as well, reports Genetic Engineering & Biotechnology News (GEN). Advantages of NGS include a streamlined workflow that eliminates transformation and colony picking and massive parallelism, according to the September 1 issue of GEN (www.genengnews.com/articles/chitem.aspx?aid=3016).
"De novo and resequencing projects have boosted interest in NGS," says John Sterling, Editor in Chief of GEN. "Other drivers include amplicon, transcriptome, and metagenomics research."
Jin Billy Li, Ph.D., from the Church Laboratory at Harvard Medical School, uses Illumina's Solexa sequencing system to do targeted sequencing of RNA editing sites. Targeted sequencing is an increasingly popular practice to further reduce the costs associated with sequencing. Rather than sequencing a whole genome or a whole library, targeted pieces are selected based on the nature of the study.
Matthew Ferber, Ph.D., codirector of the clinical molecular genetics laboratory at Mayo Clinic, is working on hereditary colon cancer. His team starts with 22 colon cancer genes on a Roche NimbleGen capture array, then elutes the DNA and submits it for second-generation sequencing on the 454 Life Sciences and Solexa platforms.
Nicholas Bergman, Ph.D., assistant professor in the school of biology at Georgia Institute of Technology, studies bacterial gene expression. He utilizes the Solexa platform and the SOLiD system from Applied Biosystems, a part of Life Technologies, to probe the functions and relationships of the Bacillus anthracis transcriptome.
Broad Institute scientists are working on identifying genetic changes that may cause glioblastoma, such as point mutations, structural rearrangements, and other events in the genome. One of the key strategies of their approach is targeting only the coding portion of the genome, which is just 1Ã°”Æ% of the overall genome. They utilize a method invented at the institute and work in collaboration with Agilent.
A companion article in the September 1 issue entitled "Next-Gen Presents Array of Opportunities" (www.genengnews.com/articles/chitem.aspx?aid=3017) explores the latest technological developments and platform improvements in the field.
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