Patents

1. Linear-Expo-Linear PCR (LEL-PCR)

Inventors: Lawrence J. Wangh, Jesus A. Sanchez

Patent Number: WO2016014921A1

Abstract: Disclosed herein is a nucleic acid amplification process referred to as Linear-Expo-Linear Polymerase Chain Reaction (LEL-PCR).

2. Methods and Kits for Detecting Nucleic Acid Mutants in Wild-type Populations

Inventors: Yanwei Jia, Jesus A. Sanchez, John E. Rice, Lawrence J. Wangh

Patent Number: US20160040242, EP2646576A1, EP2646576B1, CN103459612A, WO2012075231A1

Abstract: This disclosure relates to amplification and detection of a rare variant or variants of a DNA sequence in an abundant variant of the sequence, such as detection of a low-level somatic mutations and minority alleles in an excess of normal nucleic acid target sequences.

3. Treatment of DNA Damage and Mitochondrial Dysfunction Using Palm Fruit Juice

Inventors: Adam E. Osborne, Lawrence J. Wangh, Kenneth C. Hayes, Ravigadevi Sambanthamurthi

Patent Number: US20160000854, EP2953639A1, CN105377283A, WO2014124140A1

Abstract: Methods, compositions and kits for the prevention and treatment of mitochondrial dysfunction, mitochondrial DNA damage and genomic DNA damage are provided. The methods use the administration of palm fruit juice and/or compositions containing phenolic compounds present in palm fruit juice. The methods, compositions, and kits can be used to reduce DNA damage in subjects being treated with nucleoside reverse transcriptase inhibitors, such as patients having HIV or AIDS.

4. Reagents and Methods for PCR

Inventors: Lawrence J. Wangh, John Rice, Nicholas Rice, Yanwei Jia

Patent Number: US20150322503, US20120088275, US9034605, EP2703501A1, EP2406394A1, EP2406394B1, CA2755207A1, CN102421918A, CN102421918B, WO2010105074A1

Abstract: Modified double-stranded oligonucleotides that have terminal regions on each of their strands, that have a hybrid length of 6-50 nucleotides long, that have a melting temperature Tm of at least 32° C., and that include 2-4 modifying groups, each covalently attached to a different terminal region, preferably to a terminal nucleotide, said modifying groups being polycyclic substituents that do not have bulky portions that are non-planar, said modified oligonucleotide being capable of binding to the 5′ exonuclease domains of DNA polymerases and, when included in a PCR or other primer-dependent DNA amplification reaction at a concentration, generally not more than 2000 nM, that is effective for at least one of the functions of suppressing mispriming, increasing polymerase selectivity against 3′ terminal mismatches. increasing polymerase selectivity against AT-rich 3′ ends, reducing scatter among replicates, suppressing polymerase 5′ exonuclease activity, and inhibiting polymerase activity; as well as amplification reaction mixtures containing such modified double-stranded oligonucleotides, and amplification reactions, amplification assays and kits that include such modified double-stranded oligonucleotides.

5. Combination of dsDNA Binding Dye and Probes for Characterization of ssDNA Sequences

Inventors: John Rice, Yanwei Jia, Lawrence J. Wangh

Patent Number: US20150218625, EP2895627A2, CA2885195A1, CN104995312A, WO2014043660A2, WO2014043660A3

Abstract: This invention includes methods for analyzing single-stranded nucleic acid sequences, either RNA sequences or DNA sequences (ssDNA) utilizing dyes that fluoresce when associated with double strands, so-called DNA binding dyes or dsDNA-dyes. Methods according to this invention utilize a dsDNA-dye in combination with one or more hybridization probes that hybridize to a target nucleic acid sequence and that are labeled with a non-fluorescent quencher moiety, for example, a Black Hole quencher.

6. Multiplex Target Detection Assay

Inventors: Lawrence J. Wangh, Kenneth E. Pierce, John E. Rice

Patent Number: US20150148252, WO2015077242A1

Abstract: Provided herein are reagents and kits for detection of multiple target sequences in a single-tube, single-color assay, and methods of use thereof. In particular, multiplex assays are provided for the detection of Mycobacterium tuberculosis complex target sequences (e.g., katG, rpoB, inhA promotor, pncA, etc.).

7. DNA Methylation Analysis

Inventors: Lawrence J. Wangh, Jesus Aquiles Sanchez

Patent Number: WO2015013521A1

Abstract: Disclosed herein are methods for determining whether one or more CpG dinucleotides are methylated using Linear After the Exponential Polymerase Chain Reaction ("LATE-PCR") or Linear-Expo-Linear Polymerase Chain Reaction ("LEL- PCR").

8. Reagents for Improving PCR Accuracy

Inventors: John Rice, Lawrence J. Wangh, Jr. Arthur H. REIS, Kenneth Pierce, Cristina Hartshorn, J. Aquiles Sanchez, Hooser Stephen Van, Skye Fishbein

Patent Number: US20140206564, EP2948564A1, CA2898613A1, CN105164274A, WO2014116860A1

Abstract: Provided herein are reagents for improving PCR accuracy.

9. Detection of Sequence Variants in the Human Epidermal Growth Factor Receptor (EGFR) Gene

Inventors: Lawrence J. Wangh, Shana Marie Tetrault, J. Aquiles Sanchez

Patent Number: US20140147846, EP2715347A2, EP2715347A4, WO2012162613A2, WO2012162613A3

Abstract: Provided herein are methods for detecting and identifying sequence variants in the human epidermal growth factor receptor (EGFR) gene, and compositions and kits for performing such methods. In particular, nucleic acid amplification and fluorescence detection methods are provided for the detection and identification of EGFR sequence variants.

10. Detecting Nucleic Acid Variations within Populations of Genomes

Inventors: Yanwei Jia, J. Aquiles Sanchez, John E. Rice, Lawrence J. Wangh

Patent Number: US20140024033, US9169514

Abstract This disclosure relates to amplification and detection of a rare variant or variants of a DNA sequence in an abundant variant of the sequence, such as detection of a low-level somatic mutations and minority alleles in an excess of normal nucleic acid target sequences.

11. Compositions, Methods, and Kits for Detecting and Identifying Mycobacteria

Inventors: Lawrence J. Wangh, John Rice

Patent Number: US20140004513, EP2638178A2, EP2638178A4, CN103562405A, WO2012064978A2, WO2012064978A3

Abstract: Provided herein are methods for detecting and identifying strains of mycobacteria, and compositions and kits for performing such methods. In particular, nucleic acid amplification and fluorescence detection methods are provided for the detection and differentiation of mycobacteria based on, for example, pathogenicity, species, and antibiotic resistance or sensitivity. Compositions and methods are provided herein to identify and differentiate mycobacteria in mixtures of different mycobacteria and mycobac teria and non-mycobacteria.

12. Compositions and Methods for the Detection and Analysis of African Swine Fever Virus

Patent Number: US20140004504, EP2649201A1, EP2649201A4, WO2012079016A1

Abstract: Provided herein are compositions and methods for the detection and analysis of African swine fever virus (ASFV). In particular, kits, compositions, and methods employing LATE-PCR reagents and processes for the detection and analysis of ASFV are provided.

13. Detecting Mutations in DNA

Inventors: Adam E. Osborne, Lawrence J. Wangh, John E. Rice

Patent Number: US20130344484, EP2646575A1, WO2012075230A1

Abstract: Provided herein are methods for detecting mutations in nucleic acid, and compositions and kits for performing such methods. In particular, nucleic acid amplification and fluorescence detection methods are provided to detect mutations and assess the mutational load. The methods are based on a set of adjacently binding probes wherein one probe is labelled with a quencher and the other is a self-indicating probe labelled with fluorophore and quencher. The binding of the probes is analysed by melting curve analysis.

14. Compositions and Methods for Nucleic Acid Based Diagnostic Assays

Inventors: J. Aquiles Sanchez, Lawrence J. Wangh

Patent Number: US20130295570, WO2012048207A2, WO2012048207A3

Abstract: The present invention relates to compositions and methods for nucleic acid based diagnostic assays. In particular, the present invention provides probes and non-amplifiable controls for asymmetric PCR and other amplification modalities. In some embodiments, the present invention provides probe design criteria for probes for use in amplification/detection assays. Further embodiments of the present invention provide non-amplifiable controls for use in generating reference probe signal ratios in amplification detection assays.

15. LATE-PCR

Inventors: Lawrence J. Wangh, Kenneth Pierce, Cristina Hartshorn, John Rice, J. Aquiles Sanchez

Patent Number: US20130210656, US20080280292, US20040053254, US8367325, US7198897, EP1942196A2, EP1942196A3, EP1942196B1, EP1468114A1, EP1468114A4, EP1468114B1, CA2511128A1, CA2511128C, DE60226500D1, WO2003054233A1

Abstract: A non-symmetric polymerise chain reaction (PCR) amplification method employing a limiting primer in low concentration whose concentration-adjusted melting point at least equals, and preferably exceeds, that of the excess primer, the latter in turn not being more than 25° C. below the melting temperature of the amplicon. Assays employing such amplification and labeled hybridization probes, including assays that include a detection step following primer extension or a low-temperature probe, or both. Kits for performing such assays and primer or primer-and-probe sets for performing the foregoing amplifications and assays.

16. Compositions and Methods for Nucleic Acid Based Diagnostic Assays for Variable Sequence Targets

Inventors: Kenneth E. Pierce, John E. Rice, Lawrence J. Wangh

Patent Number: US20130203626, EP2614157A2, EP2614157A4, WO2012033875A2, WO2012033875A3

Abstract: The present invention relates to compositions and methods for nucleic acid based diagnostic assays. In particular, the present invention provides primers for asymmetric PCR and other amplification modalities. In some embodiments, the present invention provides multiple primers for amplification of related nucleic acid targets in a single reaction.

17. Primers, Probes and Methods for Nucleic Acid Amplification

Inventors: Lawrence J. Wangh, John Rice, J. Aquilles Sanchez, Kenneth Pierce, Jesse Salk, Arthur Reis, Cristina Hartshorn

Patent Number: US20130095479, US20120040352, US20060177841, US7632642, EP2927238A1, EP2351766A2, EP2351766A3, EP2351766B1, EP1805199A2, EP1805199A4, EP1805199B1, CA2584569A1, CA2584569C, CA2855748A1, CN101076607A, CN101076607B, DE602005025791D1, WO2006044994A2, WO2006044994A3

Abstract: Homogenous detection during or following PCR amplification, preferably LATE-PCR, utilizing fluorescent DNA dye and indirectly excitable labeled primers and probes, improves reproducibility and quantification. Low-temperature homogeneous detection during or following non-symmetric PCR amplification, preferably LATE-PCR, utilizing fluorescent DNA dye and indirectly excitable labeled mismatch-tolerant probes permits analysis of complex targets. Sequencing sample preparation methods following LATE-PCR amplifications reduce complexity and permit “single-tube” processing.

18. Methods, Kits and Reaction Mixtures for Analyzing Single-stranded Nucleic Acid Sequences

Inventors: Lawrence Wangh, John Rice, Arthur Reis, J. Aquiles Sanchez

Patent Number: US20120282611, EP2491144A1, EP2491144A4, EP2491144B1, EP2980224A1, WO2011050173A1

Abstract: Provided herein are fluorescence detection methods for nucleic acid sequences and to kits for performing such methods.

19. Staphylococcus Detection Assays

Inventors: Arthur H. Reis Jr., Lawrence J. Wangh, Kenneth Pierce

Patent Number: US20120208191, EP2464752A2, EP2464752A4, WO2011019836A2, WO2011019836A3

Abstract: Provided herein are methods, kits, and compositions related to nucleic acid detection that allow the detection and discrimination of various Staphylococcus species and types. In particular, provided herein are assays that allow the detection of MSSA, MSSE, MRSA, MRSE, VRSA, VRSE, and MRSA community strain by detecting the presence of absence of one or more target sequences selected from a list of target genes and sequences that include, but are not limited to: mecA, femA-SA, femA-SE, lukF-PV, lukS-PV, VanA, SCCmec type I, type II, type III, type IV, type V, and type VII. In certain embodiments, asymmetric PCR amplification methods are employed. In other embodiments, probe-target generated signals are detected at least two temperatures to generate a temperature/temperature signal ratio.

20. Single Probe, Multiple Temperature, Nucleic Acid Detection Methods, Kits, and Compositions

Patent Number: US20120202203, EP2464737A1, EP2464737A4WO2011019837A1

Abstract: Provided herein are methods, kits, and compositions related to nucleic acid detection assays that allow discrimination of multiple target sequences with a single probe. In particular, provided herein are methods kits, and compositions that include single-probe target sequence discrimination where different target amplicons may have identical probe hybridization sequences by employing multiple temperature end-point signal probe detection. Also provided herein are methods, kits, and compositions for distinguishing between two or more target amplicons using multiple-temperature end-point probe detection. In certain embodiments, asymmetric PCR amplification methods are employed (e.g., LATE-PCR amplification).

21. Methods for Making Embryonic Cells, Embryos, and Animals Sensitized to Stress

Inventors: Lawrence J. Wangh, Cristina Hartshorn, Yanwei Jia

Patent Number: US20120198576, WO2011002955A2, WO2011002955A3

Abstract: Embodiments of the invention are based upon the discovery that exposure of cleavage-stage embryos to a stress inducer, e.g. heat shock or chemical, renders the exposed embryos more sensitive to a secondary treatment with a stress inducer, e.g. heat shock or chemical inducer. Accordingly, the present invention is directed to methods for making embryos, embryonic cells arising from them, and animals and plants that are sensitized to stress, e.g. physiologic or chemical stressors. Methods of screening for inducers and inhibitors of stress using, as test model systems, embryonic cells, embryos, animals, and plants that are sensitized to stress are also disclosed.

22. RT-LATE-PCR

Inventors: Cristina Hartshorn, Kenneth E. Pierce, Arthur Henry Reis, Jr., John E. Rice, J. Aquiles Sanchez, Lawrence J. Wangh

Patent Number: US20110311971

Abstract: An assay comprising more than one primer pair and more than one detection probe, a low copy number synthetic amplicon corresponding to each of the primer pairs. The assay can detect and distinguish between various sub-types and strains of an influenza virus using any suitable nucleic acid amplification technique. Related kits and methods are also described.

23. Reagents and Methods for Improving Reproducibility and Reducing Mispriming in PCR Amplification

Inventors: Lawrence J. Wangh, John Rice, J. Aquiles Sanchez, Kenneth Pierce, Jesse Salk, Arthur Reis, Cristina Hartshorn

Patent Number: US20090226973, US20060177842, US7517977, EP1802774A1, EP1802774A4, EP1802774B1, CA2584576A1, CA2584576C, CN101076608A, CN101076608B, WO2006044995A1,

Abstract: An additive for preventing mispriming in polymerase chain reaction (PCR) amplifications and assays comprising a hairpin oligonucleotide having a stem duplex greater than six nucleotides in length and a stabilized stem terminus. The additive improves PCR amplifications, including LATE-PCR amplifications when added to initial amplification reaction mixtures. It can be included in oligonucleotide sets and in kits for PCR amplification and assays.

24. Nucleic Acid Processing Methods, Kits and Devices

Inventors: Lawrence J. Wangh, Cristina Hartshorn

Patent Number: US20090111170, US20060275773, US9279121, US7465562, EP1631685A2, EP1631685A4, EP1631685B1, CA2526409A1, DE602004030785D1, WO2004104181A2, WO2004104181A3

Abstract: Biological samples containing nucleic acids, RNA and DNA, are freed from bound proteins by incubation with a chaotropic agent such as a guanidium salt, and the mixture is readied for further processing by dilution of such agent to a concentration below 0.05 M without physical isolation of RNA and DNA from one another or from other components of the reaction mixture. Methods include such preparation and further processing, such as amplification and detection, which may be performed in a single container. Chaotropic agent may be supplied as a dried reagent adhered to a container. Kits may include such reagents, alone or with amplification reagents.

25. Detection and Analysis of Influenza Virus

Inventors: Cristina Hartshorn, Kenneth E. Pierce, Arthur Henry Reis, Jr., John E. Rice, J. Aquiles Sanchez, Lawrence J. Wangh

Patent Number: US20090081648, US7972786

Abstract: An assay comprising more than one primer pair and more than one detection probe, a low copy number synthetic amplicon corresponding to each of the primer pairs. The assay can detect and distinguish between various sub-types and strains of an influenza virus using any suitable nucleic acid amplification technique. Related kits and methods are also described.

26. Specialized Oligonucleotides and Their Use In Nucleic Acid Amplification and Detection

Inventor: Lawrence J. Wangh

Patent Number: CA2658071A1, CA2658071C, CN101506384A, CN101506384B, EP2046989A2, EP2046989A4, EP2046989B1, EP2546364A1, US7915014, US20080193934, WO2008011004A2, WO2008011004A3

Abstract: Described herein are labeled probes and unlabeled oligonucleotides that are useful for use in nucleic acid amplification reactions. These probes and oligonucleotides are modified to alter their sensitivity to primer-independent 5′ exonuclease activity of a thermostable DNA polymerase relative to its corresponding unmodified counterpart. Non-symmetric polymerase chain reaction (PCR) amplification and detection methods employing these labeled probes and unlabeled oligonucleotides are also described. Kits for nucleic acid amplification reactions including labeled probes and unlabeled oligonucleotides are also described.

27. Prenatal Screening

Inventor: Lawrence J. Wangh

Patent Number: US20060021076, US20050055734, US20040177397, US20020178462, EP0686202A1, EP0686202A4, CA2155309A1, WO1994018344A1

Abstract: The present invention concerns products and methods particularly useful for activating and analyzing non-dividing cell nuclei. The featured products include activating egg extracts, cytostatic factor (CSF) extracts, kits containing these extracts, and a microchamber microscope slide useful in analyzing nucleus activation.

28. Detection of Nucleic Acids

Inventors: Lawrence Wangh, Kenneth Pierce, Cristina Hartshorn, John Rice, J. Sanchez

Patent Number: US20030022231, EP1210358A2, EP1210358A4, WO2001013086A2, WO2001013086A3

Abstract: Disclosed are compositions, methods, and kits useful for the detection of the presence and/or quantity of one or more chromosomes from single cells, groups of cells, or subcellular compartments. Provided is a lysis buffer for the preparation of substantially accessible nucleic acid molecules from a single cell. Also provided are moderately-repeated highly-conserved nucleic acid sequences, and oligonucleotide primer and probe molecules which hybridize specifically thereto. Methods for the detection of the presence or quantity of one or more chromosomes from a single cell are included, as are methods for the assessment of the reliability of the results of the methods of the invention. Kits for the convenient practice of the invention are also included.

29. Product and Method for Swelling A Cell Nucleus Without DNA Replication

Inventor: Lawrence J. Wangh

Patent Number: US20020132344, US6878546, US6753457, US6245567, US5773217, US5651992, US5480772, EP1554931A1, EP1554931B1, DE69435234D1, EP0686202B1, DE69434722D1, DE69434722T2

Abstract: The present invention concerns products and methods particularly useful for activating and analyzing non-dividing cell nuclei. The featured products include activating egg extracts, cytostatic factor (CSF) extracts, kits containing these extracts, and a microchamber microscope slide useful in analyzing nucleus activation.