Affymetrix, Inc.

Centrillion Technology Holdings Corporation

Cellmax, Ltd

Rui Mei

Hajime Matsuzaki

Wei Zhou

Teresa A Webster

Xing Su

Giulia C Kennedy

Huangpin Ben Hsieh

Jen-Chia Wu

Hung-Jen Shao

Jr-Ming Lai

XiaoMing Wang

Sean Walsh

Glenn H McGall

Filip Crnogorac

Shantanu V Kaushikkar

Linda McAllister

Earl A Hubbell

Simon Cawley

Guochun Liao

Moti Jain

Xiaojun Di

Julian Lucas

David J Lockhart

Keith W Jones

Richard Chiles

Yanxiang Cao

Gregory Marcus

Mei-Mei Shen

Guoying Liu

Geoffrey Yang

The present disclosure provides methods, device, and system for a hybridization assay to detect nucleic acid targets. The assay may use a probe array format with addressable microwells. Each microwell may retain a plurality of copies of one probe which may be complementary to a portion of a specific nucleic acid target. The plurality of copies of probes may be produced from a pooled library of probe sequences by amplification techniques, including, rolling circle amplification and emulsion-PCR. Detection of hybridization may rely on methods using ion-sensitive field effect transistor (ISFET) and optical detectors to detect signals indicating the presence of the nucleic acid targets.

Oligonucleotide probe array with electronic detection system

Techniques for identifying and enumerating candidate target cells within a biological fluid specimen are described. A digital image of the biological fluid specimen is received, and one or more candidate regions of pixels in the digital image are identified by identifying connected regions of pixels of a minimum intensity having a size between a minimum size and a maximum size and an aspect ratio that meets a threshold. For each candidate region of at least one of the one or more candidate region, whether the portion of the image corresponding to the candidate region includes more than a threshold number of intensity levels is determined. If the portion of the image corresponding to the candidate region includes more than the threshold number of intensity levels the portion of the image is continued to be treated as a candidate for classification.

Identifying candidate cells using image analysis with intensity levels

A method for identifying candidate target cells within a biological fluid specimen includes a digital image of the biological fluid specimen with the digital image having a plurality of color channels, identifying first connected regions of pixels of a minimum first intensity in a first channel, identifying second connected regions of pixels of a minimum second intensity in a second channel, and determining first connected regions and second connected regions that spatially overlap. For a pair of a first connected region and a second connected region that spatially overlap, whether the second connected region overlaps the first connected region by a threshold amount is determined, and if the second connected region overlaps the first connected region by the threshold amount then the portion of the image corresponding to the overlap is continued to be treated as a candidate for classification.

Identifying candidate cells using image analysis with overlap thresholds

A method for identifying and enumerating candidate target cells within a biological fluid specimen is described. The method includes obtaining a biological fluid specimen, preparing the biological fluid specimen by staining cell features in the biological fluid specimen, capturing a digital image having a plurality of color channels of the biological fluid specimen, and applying image analysis to the digital image. A computer program product for identifying candidate target cells within a biological fluid specimen is also described. The computer program comprises instructions to cause a processor to carry out the image analysis.

Identifying candidate cells using image analysis

The present invention provides methods and systems for sequencing long nucleic acid fragments. In one aspect of the invention, methods, systems and reagent kits are provided for sequencing nucleic acid target sequences. Some embodiments of the methods, systems and reagent kits are particularly suitable for sequencing a large number of fragments, particularly long fragments.

Methods and systems for sequencing long nucleic acids

The present invention provides methods and systems for sequencing long nucleic acid fragment. The present invention also provides a method of sequencing a target polynucleotide with fewer probes. Further, the present invention provides a method of sequencing a target polynucleotide with longer reads. Locus-specific, ligation-assisted sequencing/genotyping method and ligation-captured sequencing method are also provided in the present invention. The methods of the present invention allow low-cost, high-throughput and accurate sequencing of nucleic acids.

The present invention provides methods for targeted sequencing of polynucleotide. In one aspect, the present invention provides a method of sequencing a target polynucleotide with fewer probes. In another aspect, the present invention provides a method of sequencing a target polynucleotide with longer reads. Locus-specific, ligation-assisted sequencing/genotyping method and ligation-captured sequencing method are also provided in the present invention. The methods of the present invention allow low-cost, high-throughput and accurate sequencing of nucleic acids.

Methods of targeted sequencing

The present invention relates generally to methods of sequencing of polynucleotides and compounds, compositions and kits useful for sequencing of polynucleotides. The chemical compounds include nucleotide and nucleoside analogs which possess a blocking group covalently attached to the 3' hydroxyl of the sugar moiety. The blocking group may optionally be additionally covalently attached to a linker and/or detectable label. The nucleotide analogs may be ribonucleotide or deoxyribonucleotide analogs. Methods include incorporation of the reversible terminator molecules into growing polynucleotide strands by polymerase enzymes, such as in single base sequencing methodologies utilizing sequential reversible termination techniques.

Reversible terminator molecules and methods of their use

The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.

Complexity management of genomic DNA

The present invention provides methods and systems for sequencing long nucleic acid fragments.

A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

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Santa Clara, CA, United States of America

Rui Mei