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Title: Methods, compounds and systems for detecting a microorganism in a sample

Abstract

Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.

Inventors:
; ; ; ;
Issue Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1321910
Patent Number(s):
9,434,997
Application Number:
12/196,238
Assignee:
Lawrence Livermore National Security, LLC (Livermore, CA)
DOE Contract Number:  
AC52-07NA27344
Resource Type:
Patent
Resource Relation:
Patent File Date: 2008 Aug 21
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Colston, Jr, Bill W., Fitch, J. Patrick, Gardner, Shea N., Williams, Peter L., and Wagner, Mark C. Methods, compounds and systems for detecting a microorganism in a sample. United States: N. p., 2016. Web.
Colston, Jr, Bill W., Fitch, J. Patrick, Gardner, Shea N., Williams, Peter L., & Wagner, Mark C. Methods, compounds and systems for detecting a microorganism in a sample. United States.
Colston, Jr, Bill W., Fitch, J. Patrick, Gardner, Shea N., Williams, Peter L., and Wagner, Mark C. Tue . "Methods, compounds and systems for detecting a microorganism in a sample". United States. https://www.osti.gov/servlets/purl/1321910.
@article{osti_1321910,
title = {Methods, compounds and systems for detecting a microorganism in a sample},
author = {Colston, Jr, Bill W. and Fitch, J. Patrick and Gardner, Shea N. and Williams, Peter L. and Wagner, Mark C.},
abstractNote = {Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2016},
month = {9}
}

Patent:

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Works referenced in this record:

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

The elimination of primer-dimer accumulation in PCR
journal, August 1997


Fast and sensitive quantitative detection of HIV DNA in whole blood leucocytes by SYBR green I real-time PCR assay
journal, October 2007

  • Casabianca, Anna; Gori, Caterina; Orlandi, Chiara
  • Molecular and Cellular Probes, Vol. 21, Issue 5-6, p. 368-378
  • DOI: 10.1016/j.mcp.2007.05.005

Multiple sequence alignment with the Clustal series of programs
journal, July 2003


High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment
journal, March 2007


The Ibis T5000 Universal Biosensor: An Automated Platform for Pathogen Identification and Strain Typing
journal, December 2006

  • Ecker, D.; Drader, J.; Gutierrez, J.
  • Journal of the Association for Laboratory Automation, Vol. 11, Issue 6, p. 341-351
  • DOI: 10.1016/j.jala.2006.09.001

Profile hidden Markov models
journal, October 1998


MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Viral metagenomics
journal, May 2005

  • Edwards, Robert A.; Rohwer, Forest
  • Nature Reviews Microbiology, Vol. 3, Issue 6
  • DOI: 10.1038/nrmicro1163

SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses
journal, August 2006


Primaclade--a flexible tool to find conserved PCR primers across multiple species
journal, November 2004


Limitations of TaqMan PCR for Detecting Divergent Viral Pathogens Illustrated by Hepatitis A, B, C, and E Viruses and Human Immunodeficiency Virus
journal, June 2003


Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens
journal, October 2005


Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments
journal, November 2006

  • Jabado, Omar J.; Palacios, Gustavo; Kapoor, Vishal
  • Nucleic Acids Research, Vol. 34, Issue 22
  • DOI: 10.1093/nar/gkl966

Amplicon: software for designing PCR primers on aligned DNA sequences
journal, February 2004


Pan‐Viral Screening of Respiratory Tract Infections in Adults With and Without Asthma Reveals Unexpected Human Coronavirus and Human Rhinovirus Diversity
journal, September 2007

  • Kistler, Amy; Avila, Pedro C.; Rouskin, Silvi
  • The Journal of Infectious Diseases, Vol. 196, Issue 6
  • DOI: 10.1086/520816

MassTag Polymerase‐Chain‐Reaction Detection of Respiratory Pathogens, Including a New Rhinovirus Genotype, That Caused Influenza‐Like Illness in New York State during 2004–2005
journal, November 2006

  • Lamson, Daryl; Renwick, Neil; Kapoor, Vishal
  • The Journal of Infectious Diseases, Vol. 194, Issue 10
  • DOI: 10.1086/508551

Using a Resequencing Microarray as a Multiple Respiratory Pathogen Detection Assay
journal, November 2006

  • Lin, B.; Blaney, K. M.; Malanoski, A. P.
  • Journal of Clinical Microbiology, Vol. 45, Issue 2
  • DOI: 10.1128/JCM.01870-06

The degenerate primer design problem
journal, July 2002


Genome sequencing in microfabricated high-density picolitre reactors
journal, July 2005

  • Margulies, Marcel; Egholm, Michael; Altman, William E.
  • Nature, Vol. 437, Issue 7057, p. 376-380
  • DOI: 10.1038/nature03959

DINAMelt web server for nucleic acid melting prediction
journal, July 2005

  • Markham, N. R.; Zuker, M.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki591

Universal virus detection by degenerate-oligonucleotide primed polymerase chain reaction of purified viral nucleic acids
journal, September 2008

  • Nanda, Santosh; Jayan, Geetha; Voulgaropoulou, Frosso
  • Journal of Virological Methods, Vol. 152, Issue 1-2, p. 18-24
  • DOI: 10.1016/j.jviromet.2008.06.007

Quantitative multiplex degenerate PCR for human endogenous retrovirus expression profiling
journal, December 2006

  • Pichon, Jean-Philippe; Bonnaud, Bertrand; Mallet, François
  • Nature Protocols, Vol. 1, Issue 6
  • DOI: 10.1038/nprot.2006.475

Detection of Respiratory Viruses and Subtype Identification of Influenza A Viruses by GreeneChipResp Oligonucleotide Microarray
journal, June 2007

  • Quan, P. -L.; Palacios, G.; Jabado, O. J.
  • Journal of Clinical Microbiology, Vol. 45, Issue 8
  • DOI: 10.1128/JCM.00737-07

MuPlex: multi-objective multiplex PCR assay design
journal, July 2005

  • Rachlin, J.; Ding, C.; Cantor, C.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki377

Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry
journal, April 2007

  • Sampath, Rangarajan; Hall, Thomas A.; Massire, Christian
  • Annals of the New York Academy of Sciences, Vol. 1102, Issue 1
  • DOI: 10.1196/annals.1408.008

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design
journal, July 2003


A simplified procedure for developing multiplex PCRs.
journal, December 1995

  • Shuber, A. P.; Grondin, V. J.; Klinger, K. W.
  • Genome Research, Vol. 5, Issue 5
  • DOI: 10.1101/gr.5.5.488

Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens
journal, May 2007

  • Wang, Xin-Wei; Zhang, Liang; Jin, Lian-Qun
  • Applied Microbiology and Biotechnology, Vol. 76, Issue 1
  • DOI: 10.1007/s00253-007-0993-x

Microarray-based detection and genotyping of viral pathogens
journal, November 2002

  • Wang, D.; Coscoy, L.; Zylberberg, M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 24, p. 15687-15692
  • DOI: 10.1073/pnas.242579699

Viral Discovery and Sequence Recovery Using DNA Microarrays
journal, November 2003


Real-Time PCR Assay for Detection and Quantification of Hepatitis B Virus Genotypes A to G
journal, September 2006

  • Welzel, T. M.; Miley, W. J.; Parks, T. L.
  • Journal of Clinical Microbiology, Vol. 44, Issue 9
  • DOI: 10.1128/JCM.00024-06