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  • monte.core monte.core Jun 3, 2010 5:22 PM Flag

    Hey Ledakh let's see your science

    To Ledakh:

    You're an insider. You're a scientist. Per your own words.

    Please in a scientific/objective/empirical manner refute the abstract below. Show me a non-amplification based sequencer that has superior specs to the Heliscope. Show me stats/data/real-world results. NAME THE LAB, because attribution is the only collateral a scientist has. Break out that big-brain science that you claim you possess.

    You can't. Prove me wrong, "insider".

    Dr. John Thompson, Ph.D.
    Director, Genomic Research, Helicos Biosciences
    A True Unbiased View of Genome Biology: Helicos Single Molecule Sequencing

    Dr. John Thompson has been Senior Director of Genomic Research at Helicos BioSciences since 2007. In that capacity, he has focused on developing and improving novel applications for ultra-high-throughput sequencing using the unique single-molecule capabilities of the HeliScopeTMGenetic Analysis System. He has worked with numerous collaborators in extending the range of samples that can be sequenced and improving data quality and quantitation. This has enabled applications that allow sequencing of sub-nanogram amounts of DNA in an amplification-free and ligation-free manner. The simple sample preparation has opened up whole new types of sequencing projects that would not be possible in an amplification-dependent system. Prior to Helicos BioSciences, Dr. Thompson worked at Pfizer in various discovery and development roles, addressing the molecular biology and genetics of cardiovascular disease as a means to develop and refine novel therapeutics. This included research on the genetics of CETP, statin response, metabolic syndrome, and related areas. Prior to joining Pfizer, he was a Research Assistant Professor of Molecular Biology at BrownUniversity researching lambda recombination, DNA bending, and protein-DNA interactions. This followed a PhD from the Department of Chemistry, University of California, Berkeley in which he studied RNA and DNA structure and a BS in chemistry from YaleUniversity.

    Presentation Abstract: Helicos Single Molecule Sequencing provides a unique view of genome biology through direct sequencing of cellular nucleic acids in an unbiased manner providing unparalleled quantitative and functional information. Using a simple sample preparation involving no ligation or PCR amplification, DNA is sheared, tailed with poly A and hybridized to the flow cell surface containing oligo-dT for sequencing by synthesis. RNA measurements include both single stranded cDNA based measurements as well as a new approach that allows direct hybridization of RNA to the flow cell to directly sequence and quantitate RNA molecules, providing tremendously improved quantitative and complete transcriptome information. A diverse array of applications have now be successfully demonstrated on the HeliScopeTM Sequencer including human genome sequencing for accurate variant detection, ChIP Seq studies involving picogram quantities of DNA obtained from as few as 10,000 cells, copy number variation studies from both fresh tumor tissue and formalin-fixed paraffin embedded tissue and archival tissue samples, the study of ancient and degraded DNAs, small RNA studies leading to the identification of new classes of RNAs and the direct capture and sequencing of RNA from as few as 200 cells. We continue to optimize our sample preparation protocols to allow preparation and sequencing from picogram quantities of nucleic acid – all important for maximizing researchers ability to perform important biological experiments with limiting biological sample amounts. Quantitative accuracy unachievable with amplification-based sequencing systems will be shown. Results from the HelicosTM Genetic Analysis System and their use to study important biological questions will be discussed.