Nuvelo, Inc.

Callida Genomics, Inc.

Complete Genomics, Inc.

Hyseq, Inc.

Other

Siemens Healthcare Diagnostics Gmbh

George Yeung

Radoje Drmanac

Matthew J Callow

Brian K Hauser

John E Ford

Snezana Drmanac

Y Tom Tang

Chenghua Liu

Nancy K Mize

Bryan J Boyle

Matthew C Arterburn

Julio J Mulero

Hua Zhou

George N Zantos

Ryle W Goodrich

Ping Zhou

Shubhada D Godbole

Cenhua Deng

George Zantos

Random arrays of single molecules are provided for carrying out large scale analyzes, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 μmand have nearest neighbor distances that permit optical resolution of on the order of 10single molecules per cm. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

DNA array

DNA concatemers on a surface

In one embodiment, a biological sample analyzer has a housing having at least one outer wall that defines a cavity therein. A receptacle, which can support a consumable holder containing a biological sample, is disposed within the internal cavity. At least one heater applies heat to the receptacle when the consumable holder is supported by the receptacle. At least one heater sensor detect temperatures of the receptacle over time. A controller detects whether the consumable holder is below an ambient temperature based on a decrease in temperature of the receptacle when the consumable holder is inserted into the receptacle. The controller also increases an amount of thermal energy transferred from the at least one heater to the consumable holder when the controller detects that the consumable holder is below the ambient temperature so as to heat the consumable holder to a target temperature.

Biological sample analyzer with cold consumable detection

The invention relates to an automated method for high-throughput DNA sequencing from high density DNA arrays by (a) initiating a first sequencing reaction on a first high density DNA array; and imaging said first high density DNA array using a detector, and (b) initiating a first sequencing reaction on a second high density DNA array; and imaging said second high density DNA array using the detector, wherein the first sequencing reaction in (a) is initiated before the first sequencing reaction in (b) is initiated such that the sequencing reactions in (a) and (b) are staggered. By using asynchronous sequencing reactions and imaging two separate arrays using one detector, imaging can be carried out on one array while sequencing reactions are carried out on one the other, substrate, the other substrate is imaged, reducing the idle time of the imaging system.

DNA sequencing from high density DNA arrays using asynchronous reactions

A high density DNA array comprising a patterned surface, said surface comprising a pattern of small DNA binding regions separated by a non-DNA binding surface, wherein the DNA binding regions comprise DNA capture chemistry and the non-DNA binding surface does not have the DNA capture chemistry wherein more than 50% of the DNA binding regions in the array have single informative DNA species.

High density DNA array

Random arrays of single molecules are provided for carrying out large scale analyzes, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 &#x3bc;mand have nearest neighbor distances that permit optical resolution of on the order of 10single molecules per cm. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

Single molecule arrays for genetic and chemical analysis

The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are 'self-assembled' in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.

Self-assembled single molecule arrays and uses thereof

Random arrays of single molecules are provided for carrying out large scale analyses, particularly of biomolecules, such as genomic DNA, cDNAs, proteins, and the like. In one aspect, arrays of the invention comprise concatemers of DNA fragments that are randomly disposed on a regular array of discrete spaced apart regions, such that substantially all such regions contain no more than a single concatemer. Preferably, such regions have areas substantially less than 1 &#x3bc;mand have nearest neighbor distances that permit optical resolution of on the order of 10single molecules per cm. Many analytical chemistries can be applied to random arrays of the invention, including sequencing by hybridization chemistries, sequencing by synthesis chemistries, SNP detection chemistries, and the like, to greatly expand the scale and potential applications of such techniques.

Methods for making single molecule arrays

The invention provides novel polynucleotides isolated from cDNA libraries of human fetal liver-spleen and fetal liver as well as polypeptides encoded by these polynucleotides. The polypeptide is a human chemokine receptor that is a member of a family of G protein-coupled receptors characterized by seven transmembrane domains. Other aspects of the invention include vectors containing polynucleotides of the invention and related host cells as well a processes for producing chemokine receptor polypeptides, and antibodies specific for such polypeptides.

Chemokine receptor obtained from a cDNA library of fetal liver-spleen

Chemokine receptor obtained from a CDNA library of fetal liver-spleen

The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human secreted semaphorin-like polypeptide. These polynucleotides comprise nucleic acid sequences isolated from cDNA library from fetal liver-spleen (Hyseq clone identification numbers 5688868 (SEQ ID NO: 1)). Other aspects of the invention include vectors containing processes for producing novel human secreted semaphorin-like polypeptides, and antibodies specific for such polypeptides.

Methods and materials relating to semaphorin-like polynucleotides

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Mountain View, CA, United States of America

George Yeung