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Mostafa Ronaghi

Mostafa Ronaghi, Palo Alto, CA US

Patent application numberDescriptionPublished
20090155801METHOD OF SEQUENCING DNA - The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether PPi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an α-thio triphosphate analogue of said nucleotide is used, ant the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.06-18-2009
20100330619DIRECT MULTIPLEX CHARACTERIZATION OF GENOMIC DNA - The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.12-30-2010

Patent applications by Mostafa Ronaghi, Palo Alto, CA US

Mostafa Ronaghi, San Diego, CA US

Patent application numberDescriptionPublished
20090286299ENGINEERED LUCIFERASES - DNA sequencing techniques are important for a variety of research and diagnostic applications. Pyrosequencing is a “sequencing by synthesis” technique that makes use of luciferase. Modified luciferase enzymes and methods of DNA pyrosequencing are provided. Means of preparing and producing mutant luciferases that have enhanced selectivity for ATP or dATP are described.11-19-2009
20100173303MULTIBASE DELIVERY FOR LONG READS IN SEQUENCING BY SYNTHESIS PROTOCOLS - The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data.07-08-2010
20100279882SEQUENCING METHODS - The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.11-04-2010

Mostafa Ronaghi, Menlo Park, CA US

Patent application numberDescriptionPublished
20100224494Isotachophoretic Focusing of Nucleic Acids - A method and system are presented for fast and efficient isolation, purification and quantitation of nucleic acids from complex biological samples using isotachophoresis in microchannels. In an embodiment, a sieving medium may be used to enhance selectivity. In another embodiment, PCR-friendly chemistries are used to purify nucleic acids from complex biological samples and yield nucleic acids ready for further analysis including for PCR. In another embodiment, small RNAs from biological samples are extracted, isolated, preconcentrated and quantitated using on-chip ITP with a high efficiency sieving medium. The invention enables fast concentration and separation (takes 10s to 100s of seconds) of nucleic acids with high selectivity and using lower volumes of reagents (order of 10s of μL to focus less than 1 pg/μL of nucleic acid).09-09-2010

Mostafa Ronaghi, Los Altos Hills, CA US

Patent application numberDescriptionPublished
20090032401Method and Apparatus Using Electric Field for Improved Biological Assays - Disclosed are a method and apparatus that use an electric field for improved biological assays. The electric field is applied across a device having wells, which receive reactants, which carry a charge. The device thus uses a controllable voltage source between the first and second electrodes, which is controllable to provide a positive charge and a negative charge to a given electrode. By controlled use of the electric field charged species in a fluid in a fluid channel are directed into or out of the well by an electric field between the electrodes. The present method involves the transport of fluids, as in a microfluidic device, and the electric field-induced movement of reactive species according to various assay procedures, such as DNA sequencing, synthesis or the like.02-05-2009
20090298064Genomic Sequencing - Genomic sequencing is implemented for high throughput applications that can include short reads. In one example, whole-genome sequencing involves a method in which a subset of fragments of a target genome are selected as a random function, and each fragment is replicated into clones. The clones are ordered into clone contigs based on sets of overlapping clones, and potential read overlaps are determined from clone read data. The method can also involve reading local assemblies of contigs from regions smaller than a clone length and assembling the local assemblies into read sets, combining the assembled read sets into clone-sized regions and assembling the clone-sized regions, and assembling the clone-sized regions into clone contigs. Overlapping sets of clones and their ordering can be determined computationally from read data, with a high depth of clone coverage to provide a large number of boundaries on which the assemblies can be segmented into overlapping regions of pooled reads.12-03-2009
20090309773SEMICONDUCTOR SENSOR CIRCUIT ARRANGEMENT - An error-corrected representation of an input signal, such as a bioluminescence signal, is generated. An analog representation of the input signal is oversampled and quantized to provide a first-stage digital output and a residual error. The residual error is provided as a second-stage digital output using successive approximation. The first-stage and second-stage digital outputs are used to generate an error-corrected representation of the bioluminescence signal.12-17-2009
20100075340Electrical Detection Of Biomarkers Using Bioactivated Microfluidic Channels - The present disclosure encompasses the manufacture and use of rapid and inexpensive electrical biosensors comprising microelectrodes in a micro-channel. The devices of the disclosure can be used to detect and quantify target cells, protein biomarkers, and nucleic acid biomarkers, and the like, by measuring instantaneous changes in ionic impedance. The micro-channel devices of the disclosure are also suitable for the detection of target protein and oligonucleotide, and small molecule target biomarkers using protein-functionalized micro-channels for the rapid electrical detection and quantification of any type of target protein biomarker in a sample. The biochip microfluidic devices may be combined with an integrated circuitry into a portable handheld device for multiplex high throughput analysis using an array of micro-channels for probing clinically relevant samples, such as the human serum, for multiple protein and nucleic acid biomarkers for disease diagnosis, and the detection of potentially pathogenic organisms.03-25-2010

Patent applications by Mostafa Ronaghi, Los Altos Hills, CA US