Bio-Rad Laboratories, Inc.

The J. David Gladstone Institutes

Samantha Cooper

Jeremy Agresti

Ronald Lebofsky

Wei Yang

John Frederick Regan

Dianna Maar

Eli Hefner

Niels Klitgord

Tina C Legler

Dawne N Shelton

Jennifer Berman

George Karlin-Neumann

Bruce Conklin

Josh Shinoff

Yuichiro Miyaoka

Austin So

Yann Jouvenot

Luz Montesclaros

Ryan T Koehler

Nick Heredia

Viresh Patel

Jen Berman

George Karlin-neumann

Eli A Hefner

Josh Schinoff

Ryan Koehler

DETECTION OF GENOME EDITING

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

Methods, compositions, and kits are provided for quantification of genome editing.

Detection of genome editing

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 detecting or quantifying short RNA or DNA molecules using split cycle amplification are provided.

Small nucleic acid quantification using split cycle amplification

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.

Methods and compositions for detecting an allelic form of a target. In an exemplary method, partitions may be created that collectively contain at least one first allelic form and a second allelic form of a target. Each partition may contain (i) a same probe capable of binding specifically to each of the first and second allelic forms of the target and (ii) a competitor configured to bind selectively to the second allelic form relative to the first allelic form and to block binding of the probe to the second allelic form. The first allelic form of the target may be amplified in the partitions. A signal may be detected from a label of the probe while the label is contained by the partitions. A number of partitions that are positive (or negative) for the at least one first allelic form may be determined based on the signal.

Amplification assay with a probe competitor

Provided herein are methods, compositions, and kits for detecting alleles using a single probe or a single primer set. Also, provided herein are methods, compositions, and kits for detecting allelic variants using a single probe or a single primer set. Also, provided herein are methods, compositions, and kits for determining a polymerization error rate.

Digital assays for mutation detection

Growing community of inventors

Berkeley, CA, United States of America

Samantha Cooper