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Feb 15, 2009 (Vol. 29, No. 4)

Honing In on Targeted Resequencing

Researchers Revisit the Human Genome to Identify Disease-Associated Variants

  • Biochips for Automation

    A microarray-based approach to targeted resequencing is offered by febit. Its HybSelect™ provides a method for capturing genetic regions of interest in high throughput. “One of the main bottlenecks in next-generation sequencing is that the capacity is not large enough for large eukaryotic (e.g., human) genomes,” Daniel Summerer, Ph.D., head of application development, enzyme-on-chip technologies, explains. “There needs to be a method to allow enrichment of desired sequences to enable studies targeted to specific biological questions. The use of microarray-based enrichment methods helps to solve that problem.”

    According to Dr. Summerer, HybSelect employs target-specific DNA extraction using Geniom® biochips. The biochips are directly synthesized with up to 120,000 capture probes specific to the genomic region of interest. Next, the sample (about 1 µg of genomic DNA) is fragmented and adaptors are ligated to the fragments to prepare a DNA library. The library is hybridized to the biochip overnight with active motion enabled by the microfluidics of the Geniom RT analyzer instrument. Finally, the target genomic DNA is recovered and then ready for next-generation sequencing.

    Dr. Summerer says that this technology offers several benefits over traditional DNA microarray approaches. “The biochips have flexible probe content, in that chips can be customized within a day to select any target sequence of interest. They also have a unique microfluidic architecture that minimizes the required sample amount and allows the process to be fully automated.”

    The company recently employed the technology for a large-scale study to enable the discovery of cancer gene SNPs. “This allows us to identify novel SNPs and other genomic variations that are relevant to various cancer types. Overall, the technology is useful for many types of research such as analysis of various diseases, pathogens, or microbial diversity and may contribute to future diagnostic tools.” The technology is currently available for early access.

    Traditional capillary electrophoresis provides a high level of accuracy but is primarily useful for analyzing a limited set of amplicons in a large number of patient samples. The method is both expensive and labor intensive for analyzing a large number of genes. Life Technologies’ SOLiD™ System is designed to tackle large-scale re-sequencing.

    “The SOLiD™ System is a highly accurate, massively parallel genomic analysis platform based on sequential ligation and clonally amplified DNA fragments linked to beads,” Michael Rhodes, Ph.D., senior manager of product applications for SOLiD says. “The core technology utilizes two independent flow cells that provide researchers with the flexibility to run two completely independent experiments in a single run. In addition, the system is based on two-base encoding that offers greater than 99.94% base-calling accuracy.  Combined, these features allow the SOLiD System to support a wide range of applications.”

  • Enhancements to System

    The company recently launched the SOLiD 3 System, which offers several enhancements including higher bead density, walk-away automation, data-analysis tools, and multiplex capability. 

    Applications for the new system include genomic, transcriptomic, and epigenomic analysis. “For example, the platform can be used for genome-wide or targeted resequencing projects as well as de novo assembly of previously uncharacterized genomes where sequencing is done in the  absence of a reference,” Dr. Rhodes explains. “For resequencing projects, researchers use either genomic DNA for whole genome projects or selected DNA regions using a variety of techniques to select specific regions of DNA including PCR (hundreds of bases), long-range PCR (thousands of bases), to arrays (millions of bases).

    “The goal of these projects is to identify causative mutations within a given sample population, such as structural variants including SNPs, copy-number variations (CNV), genomic rearrangements, and insertions and deletions both small (1 base) and large (several kilobases).”

    The massive amounts of data generated, however, demands new means for analysis. “The biggest challenge is undoubtedly the bioinformatics,” according to Dr. Rhodes. “The challenge is caused by the amount of data that can be generated from a single run—20 gigabases and more. Already, several consortia have found the most efficient way to transfer data has been physical transfer of hard drives between sites. The scale of data means that many existing tools either cannot process the data volume or produce graphical representations that are overwhelmed by data points.

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