Looking for breakthrough ideas for innovation challenges? Try Patsnap Eureka!

System and method for high resolution of nucleic acids to detect sequence variations

A variation and sequence technology, applied in the field of detection of sequence variation related to drug resistance and/or sensitivity, can solve the problems of ignoring sequence variation and limitations

Inactive Publication Date: 2010-12-01
SIGNAL DIAGNOSTICS
View PDF19 Cites 4 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0007] Although methods have been established to identify nucleic acid sequence variations in microorganisms, existing methods are limited by the requirement to know in advance the specific mutations or other variations used as diagnostic indicators
As a result, de novo and / or unidentified sequence variants that are associated with drug resistance or other traits of interest are often overlooked by known screening programs

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • System and method for high resolution of nucleic acids to detect sequence variations
  • System and method for high resolution of nucleic acids to detect sequence variations
  • System and method for high resolution of nucleic acids to detect sequence variations

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0189] Example 1 -Amplification and analysis of drug-sensitive regions of Mycobacterium tuberculosis

[0190] A. Whole-genome amplification of Mycobacterium tuberculosis genomic DNA

[0191] If the amount of sample DNA is insufficient to obtain amplified products from drug-sensitive regions, genome-wide enrichment can be used to amplify sample DNA before amplifying specific regions or amplicons. Genome-wide enrichment in MycoBuffer samples was performed in parallel with the same starting copy number of template DNA suspended in water only. To monitor overall M. tuberculosis genome-wide enrichment, three different target regions of the M. tuberculosis genome were selected to evaluate enrichment for each. A real-time PCR assay was used to screen for enrichment of each of these different target regions, compared to a non-enriched control sample. The point on the x-axis where the sample line starts to rise is an indication of the amount of starting genetic material in the samp...

Embodiment 2

[0314] Example 2 : Determination of drug resistance or sensitivity in human MTb samples

[0315] The purpose of these experiments was to demonstrate that clinical samples previously tested and determined to contain MTb could be rapidly assayed for drug resistance or sensitivity. Blinded clinical samples from MTb patients prepared according to the Petroff method were probed and resuspended in MGIT buffer (Becton Dickinson). The samples were assayed for rifampicin and streptomycin resistance using primer pairs, amplicons and melting temperatures as shown in Tables 2 and 3.

[0316] MTb test program:

[0317] Samples were run against the H37RV standard using the cfp32 Taqman assay to quantify the samples.

[0318] Master mix: 1x Kappa, Sybr-free buffer (Kappa Biosystems SYBRG1 master mix without SYBR), 1 μl cfp32 oligonucleotide (oligo), 1.75 mM MgCl, made up to 9 μl with water

[0319] Add 18 μl master mix per sample to 384-well plate

[0320] Add 2 μl of sample

[0321] ...

Embodiment 3

[0372] Example 3 : Determination of resistance to antifungal agents

[0373] Fungal and yeast infections cause a large number of diseases in humans. Some simple examples of clinically important fungi include:

[0374] Malassezia furfur and Exophialawneckii (surface skin)

[0375] Piedraia hortae and Trichosporonbeigelii (hair)

[0376] Microsporum species (skin and hair)

[0377] Epidermophyton species (skin and nails)

[0378] Trichophyton species (skin, hair, and nails)

[0379] Sporothrix schenckii, Cladosporium species, Phialophora species, and Fonsecaea species (subcutaneous / lymphoid tissue-chromoblastomycosis)

[0380] Histoplasma capsulatum, Coccidioidesimmitis, Fusarium species, Penicillium species (systemic respiration)

[0381] Blastomyces dermatitidis (subcutaneous / respiratory)

[0382] Cryptococcus neoformans (respiratory / CNS)

[0383] Aspergillus species, Mucor species, Candida species and Rhizopus species (opportunity to be involved in various body parts)...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

No PUM Login to View More

Abstract

Provided herein are methods for assaying a biological sample for microorganisms having drug resistant and / or drug sensitive phenotypes, wherein the methods are capable of detecting resistant and sensitive phenotypes associated with known and / or unknown mutations. In some aspects, methods are provided for detecting drug resistant Myobacterium tuberculosis (MTb), including multi-drug resistant MTb, wherein drug resistance is associated with one or more novel mutations. Also provided are systems, kits, and compositions related to such methods.

Description

[0001] Cross References to Related Applications [0002] This application claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application 60 / 908,604, filed March 28, 2007, which is incorporated herein by reference in its entirety. technical field [0003] The present invention generally relates to systems and methods for preparing and analyzing biological samples to detect nucleic acid sequence variations associated with phenotypes of interest. In certain embodiments, methods and systems are provided for amplifying nucleic acids from microorganisms in biological samples and detecting sequence variations associated with drug resistance and / or sensitivity. Background technique [0004] Few in the history of science have had such a dramatic impact on human life as the advances made in the control of pathogenic microorganisms. It was not until the late 19th century and early 20th century that the work of Pasteur and Koch established microorganisms as the cause of infect...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
IPC IPC(8): C12Q1/68G01N1/38G01N33/48
CPCC12Q1/703C12Q1/6827C12Q1/6886C12Q2600/106C12Q1/6846C12Q1/689C12Q1/6858C12Q2527/101C12Q2527/107C12Q1/6844C12Q1/6825C12Q1/6876C12Q2600/136C12Q2600/156C12Q1/6816C12Q1/6848
Inventor B·E·凯普林
Owner SIGNAL DIAGNOSTICS
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Patsnap Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Patsnap Eureka Blog
Learn More
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic, Popular Technical Reports.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap|About US| Contact US: help@patsnap.com