Helicos Single-Molecule Sequencing provides a unique view of genome biology through direct sequencing of cellular and extracellular nucleic acids in an unbiased manner, providing both quantitation and sequence information. Using a simple sample preparation, involving no ligation or amplification, genomic DNA is sheared, tailed with poly-A and hybridized to the flow-cell surface containing oligo-dT for initiating sequencing-by-synthesis. RNA measurements involving direct RNA hybridization to the flow cell allows for the direct sequencing and quantitation of RNA molecules. From these methods, a diverse array of applications has now been successfully demonstrated with the Helicos Genetic Analysis System, including human genome sequencing for accurate variant detection, ChIP Seq studies involving picogram quantities of DNA obtained from small cell numbers, copy number variation studies from both fresh tumor tissue and formalin-fixed paraffin-embedded tissue and archival tissue samples, small RNA studies leading to the identification of new classes of RNAs, and the direct capture and sequencing of nucleic acids from cell quantities as few as 400 cells with our end goal of single cell measurements. Helicos methods provide an important opportunity to researchers, including genomic scientists, translational researchers, and diagnostic experts, to benefit from biological measurements at the single-molecule level. This chapter will describe the various methods available to researchers.
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