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May 01, 2011 (Vol. 31, No. 9)

New Cancer Research Tools Change Paradigm

Increased Speed, Automation, and Visualization Should Bring Field to Another Level

  • Genetic Analysis

    Expression Analysis will be adding Pacific Biosciences’ Pac­Bio S third-generation long-read DNA sequencing platform to its genetic analysis capabilities. Expression Analysis initially plans to use the PacBio RS for viral sequencing, with a focus on hepatitis C virus, followed by HLA typing applications.

    PacBio is using Agilent Technologies’ SureSelectXT target-enrichment technology to perform targeted sequencing of the kinome and to analyze full-length transcripts of cancer-related genes. Agilent’s SureSelect system also supports next-gen sequencing technology from Illumina Applied Biosystems and Roche, and a kit compatible with the Ion Torrent Personal Genome Machine is in development.

    The system includes the Human Kinome Kit, which covers 3.2 megabases and 612 genes including more than 500 known kinases, as well as exome target-enrichment kits for human, mouse, and other model organisms. Agilent recently announced an expansion of its SureSelect custom kits (which previously had a range of <200 Kb to >6.8 Mb) and are now capable of up to 34 Mb. At AACR, Agilent also highlighted the combined gradient functionality and uniformity attributes of its new SureCycler 8800 thermal cycler.

    Affymetrix introduced its OncoScan™ FFPE Express 2.0 service, which provides copy number, allelic ratio, and somatic mutation data from FFPE tissue samples. The company held a workshop in which it presented its Molecular Inversion Probe (MIP) technology for selective amplification of a locus of interest in an FFPE sample. The workshop also focused on the company’s QuantiGene® ViewRNA in situ expression assays for whole-transcriptome analysis to support pathway analysis.

    Life Technologies introduced its TaqMan® Mutation Detection Assays, based on Competitive Allele-Specific TaqMan polymerase chain reaction (castPCR), a technology that combines amplification of gene regions containing targeted mutations and suppression factors capable of silencing other DNA molecules present in the sample. The newly launched Mutation Detection Assays are part of an early-release program focusing on mutation detection in three human genes—KRAS, BRAF, and EGFR—associated with colorectal, lung, pancreatic, and breast cancer.

    New from RainDance Technologies is the HLASeq™ Research Screening Panel for next-gen sequencing of the human leukocyte antigen (HLA) and major histocompatibility complex (MHC) genes. The assay allows researchers to search the entire 3.8-megabase HLA super locus at single-base resolution to identify polymorphisms.

    Stratedigm showcased the S1000Ex 14-color upgrade kit for its S1000 flow cytometers, which are designed to support up to four lasers with spatial separation and include a range of user-interchangeable optical filters, enabling fluorescence detection of up to 14 fluorophores.

  • Epigenetics

    Epigentek introduced the EpiQuik™ hydroxymethylated DNA Immunoprecipitation (hMeDIP) Kit for the selective enrichment of 5-hydroxymethylcytosine (5-hmC)-modified DNA fragments in a 96-well plate format. The company also featured its MethylFlash™ Hydroxymethylated DNA Quantification Kit for colorimetric quantification of 5-hmC at genome-wide scale without cross-reactivity to methycytosine or unmethylated cytosine.

    The AACR meeting marked the launch of New England Biolabs’ EpiMark™ Methylated DNA Enrichment Kit and EpiMark Bisulfite Conversion Kit. The Methylation DNA Enrichment Kit facilitates enrichment of CpG methylated DNA in less than two hours, using human methyl binding domain (MBD2) bound to the Fc tail of the human antibody IgG1 as the capture agent. When further coupled to protein A-coated magnetic beads, this antibody-like protein enables methylated DNA purification with enhanced sensitivity and accuracy.

    The kit is the result of a research collaboration between New England Biolabs and Sequenom; the companies recently announced a licensing and co-marketing agreement to produce research tools for epigenetics.

    To study the role DNA methylation plays in regulating gene expression and contributing to the development of diseases such as cancer, Illumina offers the Infinium Methylation Assays, which are capable of quantitative analysis of methylation sites at single nucleotide resolution in 12 samples run in parallel.

    Illumina’s HumanMethylation27 BeadChip interrogates 27,578 cytosine methylation (CpG) loci; the HumanMethylation450 BeadChip provides coverage of more than 450,000 methylation sites and is designed for high-throughput screening in genome-wide association studies. Illumina presented two posters that focused on the capabilities of the Infinium methylation assays and their use with restored DNA derived from FFPE samples.

    Diagenode spotlighted its automated epigenetics platform, including the SX-8G IP-Star® and SX-8G Compact systems and kits for performing automated chromatin immunoprecipitation and DNA methylation assays.

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