Affymetrix

Santa Clara, CA, United States

Affymetrix

Santa Clara, CA, United States
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Patent
Affymetrix | Date: 2017-01-27

Silanation compositions containing a mixture of two or more silanation reagents, where at least one silanation reagent includes a functional group capable of supporting polymer synthesis and at least one silanation reagent includes no functional group capable of supporting polymer synthesis are useful in modulating the active site density and hydrolytic stability of a surface. These compositions are particularly useful in silanating a surface prior to preparation of a polymer array and provide for increased hybridization results.


Patent
Affymetrix | Date: 2017-03-01

Methods are provided for detecting and optionally quantitating multiple analytes, including nucleic acid and/or polypeptide analytes, in assays that can be highly multiplexed. Compositions, systems, and kits relating to the methods are also featured.


The invention provides methods and compositions to enhance the efficiency and sensitivity of molecular inversion probe (MIP) reactions. Probes include elements that allow MIP ends to abut for ligation while avoiding the possibility of polymerase strand displacement errors. Elements facilitate multiplexed detections, including MIP reaction product detections employing next generation sequencing (NGS) techniques.


Patent
Affymetrix | Date: 2016-11-16

Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5 or 3 flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5 and 3 flaps are generated. The flaps are cleaved using 5 or 3 flap endonucleases or 3 to 5 exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.


Patent
Affymetrix | Date: 2016-11-16

Methods for multiplex amplification of a plurality of targets of distinct sequence from a complex mixture are disclosed. In one aspect targets are circularized using a single circularization probe that is complementary to two regions in the target that flank a region to be amplified. The targets may hybridize to the circularization probe so that 5 or 3 flaps are generated and methods for removing flaps and circularizing the resulting product are disclosed. In another aspect targets are hybridized to dU probes so that 5 and 3 flaps are generated. The flaps are cleaved using 5 or 3 flap endonucleases or 3 to 5 exonucleases. The target sequences are then ligated to common primers, the dU probes digested and the ligated targets amplified.


Patent
Affymetrix | Date: 2016-06-16

Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. In preferred aspects the analysis is a determination of sequence at one or more locations in the amplified target. The methods may be used for genotyping, sequencing and analysis of copy number.


Patent
Affymetrix | Date: 2016-09-30

Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.


Disclosed are calibration apparatuses for fluorescent microscopy instruments and methods of making and using them. Specifically, disclosed are calibration apparatuses with a fluorescent layer, such as photoresist, deposited on a substrate, with an optional layer of a reflective material, such as chrome. Illumination of the fluorescent and/or reflective layers, and detection and analysis of the resulting emissions allows evaluation of the instrument with respect to both reflective and fluorescent channels. Selection of appropriate fluorescent materials for the one or more fluorescent layers allows the evaluation of an instrument with respect to different fluorophores, as would be used with an instrument capable of two color detection. Inclusion of a reflective layer further allows the evaluation and calibration of all optical channels of an instrument, including the reflective channel and two or more fluorescent channels, with a single calibration apparatus for imaging criteria such as uniformity, contrast and emission signal strength.


Patent
Affymetrix | Date: 2016-06-16

Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.


Grant
Agency: GTR | Branch: Innovate UK | Program: | Phase: Small Business Research Initiative | Award Amount: 149.01K | Year: 2016

Abstract: Urothelial bladder cancer (UBC) is the 7th most common cancer in Western societies with a rising global incidence. Disease management currently poses numerous challenges because of the variable risk of progression to Muscle Invasive Bladder Cancer (MIBC) and the propensity of Non-Muscle-Invasive Bladder Cancer (NMIBC) to recur, necessitating long-term surveillance at high cost to the NHS. UBCs are thus highly heterogenous in their clinical characteristics and this is mirrored in their genomics, features of which traverse conventional grade and stage groupings. Current detection and monitoring of bladder cancer is by cystoscopy, which is both expensive for the NHS and also burdensome for the patient. Following any subsequent biopsy or resection procedure, tumours are typically characterised by conventional histopathology using formalin-fixed paraffin-embedded (FFPE) tumour tissue to allow grading and staging of the tumour. Despite the genomic heterogeneity of UBCs and uncertainties in management across NMIBC risk categories, the potentially informative data from genomic characterisation is not routinely utilised outside of the research setting. Within our current IUK-funded project Developing a Robust, Reliable Multiplex Clinical Tool for Guiding Tumour Therapy we have reported utilisation of the Affymetrix OncoScan® FFPE Assay Kit for genomic profiling of UBC using cell-free DNA (cfDNA) from urine. Further, we have demonstrated that the informative genomic aberrations evident in FFPE tumour material are echoed in urinary cfDNA, even for very early stage NMIBCs down to 0.5cm in diameter. Identifying such genomic complexity in a non-invasive fashion would likely be highly advantageous for facilitation of the diagnosis, management and surveillance of patients with NMIBC or MIBC, with significant cost-savings for the NHS. This proposal, in response to Part I of the IUK competition Stratified Medicine: connecting the UK infrastructure, is to collaborate with a network of specialists and infrastructure available in the UK to report on specific health and economic benefits of applying the OncoScan assay to non-invasive detection, characterisation and monitoring of UBC as compared to current procedures and workflows. Within this project phase we also plan to generate further evidence of the value of genomic grading of UBC with OncoScan. We will also work with the NIHR and bladder cancer CIs/PIs to generate a detailed plan for Phase II of the competition where we would trial this platform within the NHS to assess the utility and health-economic benefit compared to current practices.

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