Helicos Biosciences Corporation

Exact Laboratories, Inc.

Praelux Incorporated

Seq, Ltd.

Kevin M Ulmer

Anthony P Shuber

Stanley N Lapidus

Paul Mitsis

Jae-Gyu Kwagh

John J Macklin

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.

Apparatus and methods for analyzing samples

The present invention relates to methods for sequencing a polymeric biomolecule and methods for structurally characterizing the same comprising using aptamers. In a preferred embodiment of this invention, these methods relate to using the single polymeric biomolecule. The invention also relates to a method for selecting aptamers useful for sequencing nucleic acids and aptamers generated by the method. The invention also provides aptamers that recognize and bind to AMP, dAMP, GMP, dGMP, CMP and dCMP.

Method for sequencing and characterizing polymeric biomolecules using aptamers and a method for producing aptamers

The present invention provides a method and apparatus for automated DNA sequencing. The method of the invention includes the steps of: a) using a processive exonuclease to cleave from a single DNA strand the next available single nucleotide on the strand; b) transporting the single nucleotide away from the DNA strand; c) incorporating the single nucleotide in a fluorescence-enhancing matrix; d) irradiating the single nucleotide to cause it to fluoresce; e) detecting the fluorescence; f) identifying the single nucleotide by its fluorescence; and g) repeating steps a) to f) indefinitely (e.g., until the DNA strand is fully cleaved or until a desired length of the DNA is sequenced). The apparatus of the invention includes a cleaving station for the extraction of DNA from cells and the separation of single nucleotides from the DNA; a transport system to separate the single nucleotide from the DNA and incorporate the single nucleotide in a fluorescence-enhancing matrix; and a detection station for the irradiation, detection and identification of the single nucleotides. The nucleotides are advantageously detected by irradiating the nucleotides with a laser to stimulate their natural fluorescence, detecting the fluorescence spectrum and matching the detected spectrum with that previously recorded for the four nucleotides in order to identify the specific nucleotide.

Apparatus for DNA sequencing

An optical trap is used to translate a particle through a thin film coating on an optically-flat surface. Preferably, the thin film coating is heterogeneous and the optical trap is used to move the particle through a succession of different regions of the thin film coating where different chemical, biochemical and/or biological processes take place. Examples of chemical, biochemical and/or biological processes that might be implemented in accordance with the invention include the following: oligonucleotide synthesis and sequencing, peptide synthesis and sequencing, carbohydrate synthesis and sequencing, combinatorial library synthesis and screening, conventional (i.e., Sanger or Maxam-Gilbert) DNA sequengcing, or single-molecule DNA sequencing. In one embodiment of the invention, reaction products are left behind as the particle is moved through the thin film coating. Advantageously, these products can be identified by suitable means.

Chemical biochemical and biological processing in thin films

The present invention provides methods for screening for the presence of a subpopulation of cancerous or precancerous cells in a heterogeneous cellular sample, such as a stool sample. The methods take advantage of the recognition that cellular debris from cancerous and precancerous cells is deposited onto only a longitudinal stripe of stool as the stool is forming in the colon. Accordingly, methods of the invention comprise obtaining a representative sample, such as a cross-sectional sample of stool in order to ensure that any cellular debris that is shed by colonic cells is obtained in the sample.

Methods for detecting colon cancer from stool samples

Methods and apparatus for DNA sequencing

Methods are provided for detecting the presence of mutant sequences in a subpopulation of gene sequences in a biological sample. These methods are particularly useful for identifying individuals with gene mutations indicative of early colorectal cancer.

Growing community of inventors

Cohasset, MA, United States of America

Kevin M Ulmer