Cambridge, MA, United States
Cambridge, MA, United States

Helicos BioSciences Corporation, NASDAQ: HLCS was a publicly traded life science company headquartered in Cambridge, Massachusetts focused on genetic analysis technologies for the research, drug discovery and diagnostic markets. The firm's Helicos Genetic Analysis Platform was the first DNA-sequencing instrument to operate by imaging individual DNA molecules. In May 2010, the company announced a 50% layoff and a re-focusing on molecular diagnostics. After long financial troubles, in April 2010, Helicos was delisted from NASDAQ.Helicos was co-founded in 2003 by life science entrepreneur Stanley Lapidus, Stephen Quake, and Noubar Afeyan with investments from Atlas Venture, Flagship Ventures, Highland Capital Partners, MPM Capital, and Versant Ventures. Helicos's technology images the extension of individual DNA molecules using a defined primer and individual fluorescently labeled nucleotides, which contain a "Virtual Terminator" preventing incorporation of multiple nucleotides per cycle. The "Virtual Terminator" technology was developed by Dr. Suhaib Siddiqi, while at Helicos Biosciences.In the August 2009 issue of Nature Biotechnology, Dr. Stephen Quake, a professor of bioengineering at Stanford University and a co-founder of Helicos BioSciences, sequenced his own genome, using Single Molecule Sequencing for under $50,000 in reagents.On November 15, 2012, Helicos BioSciences filed for Chapter 11 bankruptcy. Wikipedia.

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Ozsolak F.,Helicos BioSciences
Expert Opinion on Drug Discovery | Year: 2012

Introduction: There is an immediate need for functional and molecular studies to decipher differences between disease and 'normal' settings to identify large quantities of validated targets with the highest therapeutic utilities. Furthermore, drug mechanism of action and biomarkers to predict drug efficacy and safety need to be identified for effective design of clinical trials, decreasing attrition rates, regulatory agency approval process and drug repositioning. By expanding the power of genetics and pharmacogenetics studies, next-generation nucleic acid sequencing technologies have started to play an important role in all stages of drug discovery. Areas covered: This article reviews the first- and second-generation sequencing technologies (SGSTs) and challenges they pose to biomedicine. The article then focuses on the emerging third-generation sequencing technologies (TGSTs), their technological foundations and potential contributions to drug discovery. Expert opinion: Despite the scientific and commercial success of SGSTs, the goal of rapid, comprehensive and unbiased sequencing of nucleic acids has not been achieved. TGSTs promise to increase sequencing throughput and read lengths, decrease costs, run times and error rates, eliminate biases inherent in SGSTs and offer capabilities beyond nucleic acid sequencing. Such changes will have positive impact on all sequencing applications to drug discovery. © 2012 Informa UK, Ltd.


Thompson J.F.,Helicos BioSciences | Milos P.M.,Helicos BioSciences
Genome Biology | Year: 2011

Single-molecule sequencing enables DNA or RNA to be sequenced directly from biological samples, making it well-suited for diagnostic and clinical applications. Here we review the properties and applications of this rapidly evolving and promising technology. © 2011 BioMed Central Ltd.


Hart C.,Helicos BioSciences
Methods in enzymology | Year: 2010

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. Copyright 2010 Elsevier Inc. All rights reserved.


Ozsolak F.,Helicos BioSciences | Milos P.M.,Helicos BioSciences
Nature Reviews Genetics | Year: 2011

In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials. © 2011 Macmillan Publishers Limited. All rights reserved.


Patent
Helicos BioSciences | Date: 2011-10-27

The invention provides for nucleotide analogs and methods of using the same, e.g., for sequencing nucleic acids.


The present invention relates to a novel method for analyzing nucleic acid sequences based on real-time detection of DNA polymerase-catalyzed incorporation of each of the four nucleotide bases, supplied individually and serially in a microfluidic system, to a reaction cell containing a template system comprising a DNA fragment of unknown sequence and an oligonucleotide primer. Incorporation of a nucleotide base into the template system can be detected by any of a variety of methods including but not limited to fluorescence and chemiluminescence detection. Alternatively, microcalorimetic detection of the heat generated by the incorporation of a nucleotide into the extending template system using thermopile, thermistor and refractive index measurements can be used to detect extension reactions.


Patent
Helicos BioSciences | Date: 2011-01-18

The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.


Patent
Helicos BioSciences | Date: 2011-01-18

The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.


Patent
Helicos BioSciences | Date: 2011-01-18

The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.


Patent
Helicos BioSciences | Date: 2011-05-23

The present invention relates to apparatus, systems, and methods for analyzing biological samples. The apparatus, systems, and methods can involve using a vacuum source to pull microfluidic volumes through analytical equipment, such as flow cells and the like. Additionally, the invention involves using optical equipment in conjunction with the analytical equipment to analyze samples and control the operation thereof.

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