Bio-rad Laboratories, Inc.

Eli Hefner

Dianna Maar

Samantha Cooper

John Frederick Regan

Wei Yang

Niels Klitgord

Dawne N Shelton

Tina C Legler

Daniel Y Chu

Yann Jouvenot

Paul J Patt

Xin Heng

Tom McCollum

Mike Griffin

Don Flory

Frank Shen

Nick Heredia

Jen Berman

Viresh Patel

Tom Mccollum

Method of analysis for alleles of a target. In the method, a plurality of fluid volumes may be formed. Each fluid volume may contain a first primer pair to amplify a first allele of a target, a second primer pair to amplify a second allele of the target, a first reporter including a first photoluminophore and providing a primer of the first primer pair, and a second reporter including a second photoluminophore and providing a primer of the second primer pair. Each of the first and second reporters may include an oligomer having a quencher, and the oligomer may be configured to base-pair with the primer of the first primer pair and the primer of the second primer pair. The first and second alleles may be amplified using the first and second primer pairs. Photoluminescence may be detected. A level of each allele may be determined.

Amplification reporter with base-pairing oligomers

Compositions, kits, and methods are provided for the normalization of a quantitative polymerase chain reaction (PCR) amplification. Also provided are compositions, kits, and methods for multiplexing qPCR amplification of two or more target nucleic acids in the same well.

Quantitative amplification normalization with quenchers

System, including methods, apparatus, and compositions, for performing amplification assays with an amplification reporter including a first oligomer and a second oligomer capable of base-pairing with one another below a melting temperature of the reporter. The reporter may have a detectable photoluminescence that is affected, such as reduced, by base-pairing of the first and second oligomers with one another. A target, such as a nucleic acid target sequence, may be amplified in at least one volume, such as a plurality of partitions, above the melting temperature, and photoluminescence of the reporter may be detected from the at least one volume below the melting temperature. A property of the target, such as a concentration of the target, may be determined based on the photoluminescence detected.

Methods of, and compositions for, analysis using digital amplification assays with unconventional/inverse changes in photoluminescence to indicate the presence of one or more targets. In an exemplary method, isolated volumes may be formed, only a subset of which contain a target. Each volume may include a probe having a label, a sink having a quencher and configured to hybridize with the probe to quench the label, and a separator configured to hybridize with the probe and/or the sink to block hybridization of the sink with the probe. An amplification reaction may be performed in the volumes to generate an amplicon corresponding to the target. The separator may hybridize with the amplicon, and may be extended or degraded by the amplification reaction. Photoluminescence of the label may be detected from the volumes, and the photoluminescence of target-positive volumes may be less than that of target-negative volumes.

Digital amplification assays with unconventional and/or inverse changes in photoluminescence

Methods, compositions, and kits are provided for quantifying a number or frequency of double stranded breaks in the genome of a cell or in the genomes of a population of cells.

Detection of genome editing

Biological cells in a liquid suspension are counted in an automated cell counter that focuses an image of the suspension on a digital imaging sensor that contains at least 4,000,000 pixels each having an area of 2&#xd7;2 &#x3bc;m or less and that images a field of view of at least 3 mm. The sensor enables the counter to compress the optical components into an optical path of less than 20 cm in height when arranged vertically with no changes in direction of the optical path as a whole, and the entire instrument has a footprint of less than 300 cm. Activation of the light source, automated focusing of the sensor image, and digital cell counting are all initiated by the simple insertion of the sample holder into the instrument. The suspension is placed in a sample chamber in the form of a slide that is shaped to ensure proper orientation of the slide in the cell counter.

Compact automated cell counter

An automated system captures multiple digital images of a sample, from different viewing areas of the sample. The images are analyzed and a test result may be reported based on the count of cells in all of the digital images. The system may be especially applicable to the testing of samples having low cell concentrations, as the variability between tests may be reduced as compared with a system that bases its test results on only a single image of the sample. The system may count the cells in a first digital image of the sample, and may capture or analyze one or more additional digital images only when it is recognized that additional measurements are needed to ensure adequate accuracy and repeatability of the test.

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Fairfield, CA, United States of America

Eli Hefner