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

Colston, Jr, Bill W.; Fitch, J. Patrick; Gardner, Shea N.; Williams, Peter L.; Wagner, Mark C.

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

Patent · Tue Sep 06 00:00:00 EDT 2016

OSTI ID:1321910

Colston, Jr, Bill W.; Fitch, J. Patrick; Gardner, Shea N.; Williams, Peter L.; Wagner, Mark C.

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.

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Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC52-07NA27344

Assignee:: Lawrence Livermore National Security, LLC (Livermore, CA)

Patent Number(s):: 9,434,997

Application Number:: 12/196,238

OSTI ID:: 1321910

Resource Relation:: Patent File Date: 2008 Aug 21

Country of Publication:: United States

Language:: English

References (31)

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A. Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402 https://doi.org/10.1093/nar/25.17.3389	journal	September 1997
The elimination of primer-dimer accumulation in PCR Brownie, J. Nucleic Acids Research, Vol. 25, Issue 16 https://doi.org/10.1093/nar/25.16.3235	journal	August 1997
Fast and sensitive quantitative detection of HIV DNA in whole blood leucocytes by SYBR green I real-time PCR assay Casabianca, Anna; Gori, Caterina; Orlandi, Chiara Molecular and Cellular Probes, Vol. 21, Issue 5-6, p. 368-378 https://doi.org/10.1016/j.mcp.2007.05.005	journal	October 2007
Multiple sequence alignment with the Clustal series of programs Chenna, R. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg500	journal	July 2003
High-Density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity than Typical Clone Library When Sampling the Environment DeSantis, Todd Z.; Brodie, Eoin L.; Moberg, Jordan P. Microbial Ecology, Vol. 53, Issue 3 https://doi.org/10.1007/s00248-006-9134-9	journal	March 2007
The Ibis T5000 Universal Biosensor: An Automated Platform for Pathogen Identification and Strain Typing Ecker, D.; Drader, J.; Gutierrez, J. Journal of the Association for Laboratory Automation, Vol. 11, Issue 6, p. 341-351 https://doi.org/10.1016/j.jala.2006.09.001	journal	December 2006
Profile hidden Markov models Eddy, S. R. Bioinformatics, Vol. 14, Issue 9 https://doi.org/10.1093/bioinformatics/14.9.755	journal	October 1998
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Viral metagenomics Edwards, Robert A.; Rohwer, Forest Nature Reviews Microbiology, Vol. 3, Issue 6 https://doi.org/10.1038/nrmicro1163	journal	May 2005
SYBR Green real-time reverse transcription-polymerase chain reaction assay for the generic detection of coronaviruses Escutenaire, S.; Mohamed, N.; Isaksson, M. Archives of Virology, Vol. 152, Issue 1 https://doi.org/10.1007/s00705-006-0840-x	journal	August 2006
Primaclade--a flexible tool to find conserved PCR primers across multiple species Gadberry, M. D.; Malcomber, S. T.; Doust, A. N. Bioinformatics, Vol. 21, Issue 7 https://doi.org/10.1093/bioinformatics/bti134	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 Gardner, S. N.; Kuczmarski, T. A.; Vitalis, E. A. Journal of Clinical Microbiology, Vol. 41, Issue 6 https://doi.org/10.1128/JCM.41.6.2417-2427.2003	journal	June 2003
Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens Huang, Y. -C.; Chang, C. -F.; Chan, C. -h. Bioinformatics, Vol. 21, Issue 24 https://doi.org/10.1093/bioinformatics/bti730	journal	October 2005
Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments Jabado, Omar J.; Palacios, Gustavo; Kapoor, Vishal Nucleic Acids Research, Vol. 34, Issue 22 https://doi.org/10.1093/nar/gkl966	journal	November 2006
Amplicon: software for designing PCR primers on aligned DNA sequences Jarman, S. N. Bioinformatics, Vol. 20, Issue 10 https://doi.org/10.1093/bioinformatics/bth121	journal	February 2004
Pan‐Viral Screening of Respiratory Tract Infections in Adults With and Without Asthma Reveals Unexpected Human Coronavirus and Human Rhinovirus Diversity Kistler, Amy; Avila, Pedro C.; Rouskin, Silvi The Journal of Infectious Diseases, Vol. 196, Issue 6 https://doi.org/10.1086/520816	journal	September 2007
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 Lamson, Daryl; Renwick, Neil; Kapoor, Vishal The Journal of Infectious Diseases, Vol. 194, Issue 10 https://doi.org/10.1086/508551	journal	November 2006
Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays Lin, B. Genome Research, Vol. 16, Issue 4 https://doi.org/10.1101/gr.4337206	journal	March 2006
Using a Resequencing Microarray as a Multiple Respiratory Pathogen Detection Assay Lin, B.; Blaney, K. M.; Malanoski, A. P. Journal of Clinical Microbiology, Vol. 45, Issue 2 https://doi.org/10.1128/JCM.01870-06	journal	November 2006
Genome sequencing in microfabricated high-density picolitre reactors Margulies, Marcel; Egholm, Michael; Altman, William E. Nature, Vol. 437, Issue 7057, p. 376-380 https://doi.org/10.1038/nature03959	journal	July 2005
DINAMelt web server for nucleic acid melting prediction Markham, N. R.; Zuker, M. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki591	journal	July 2005
Universal virus detection by degenerate-oligonucleotide primed polymerase chain reaction of purified viral nucleic acids Nanda, Santosh; Jayan, Geetha; Voulgaropoulou, Frosso Journal of Virological Methods, Vol. 152, Issue 1-2, p. 18-24 https://doi.org/10.1016/j.jviromet.2008.06.007	journal	September 2008
Quantitative multiplex degenerate PCR for human endogenous retrovirus expression profiling Pichon, Jean-Philippe; Bonnaud, Bertrand; Mallet, François Nature Protocols, Vol. 1, Issue 6 https://doi.org/10.1038/nprot.2006.475	journal	December 2006
MuPlex: multi-objective multiplex PCR assay design Rachlin, J.; Ding, C.; Cantor, C. Nucleic Acids Research, Vol. 33, Issue Web Server https://doi.org/10.1093/nar/gki377	journal	July 2005
Rapid Identification of Emerging Infectious Agents Using PCR and Electrospray Ionization Mass Spectrometry Sampath, Rangarajan; Hall, Thomas A.; Massire, Christian Annals of the New York Academy of Sciences, Vol. 1102, Issue 1 https://doi.org/10.1196/annals.1408.008	journal	April 2007
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design Rose, T. Nucleic Acids Research, Vol. 31, Issue 13 https://doi.org/10.1093/nar/gkg524	journal	July 2003
A simplified procedure for developing multiplex PCRs. Shuber, A. P.; Grondin, V. J.; Klinger, K. W. Genome Research, Vol. 5, Issue 5 https://doi.org/10.1101/gr.5.5.488	journal	December 1995
Development and application of an oligonucleotide microarray for the detection of food-borne bacterial pathogens Wang, Xin-Wei; Zhang, Liang; Jin, Lian-Qun Applied Microbiology and Biotechnology, Vol. 76, Issue 1 https://doi.org/10.1007/s00253-007-0993-x	journal	May 2007
Microarray-based detection and genotyping of viral pathogens Wang, D.; Coscoy, L.; Zylberberg, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 24, p. 15687-15692 https://doi.org/10.1073/pnas.242579699	journal	November 2002
Viral Discovery and Sequence Recovery Using DNA Microarrays Wang, David; Urisman, Anatoly; Liu, Yu-Tsueng PLoS Biology, Vol. 1, Issue 2 https://doi.org/10.1371/journal.pbio.0000002	journal	November 2003
Real-Time PCR Assay for Detection and Quantification of Hepatitis B Virus Genotypes A to G Welzel, T. M.; Miley, W. J.; Parks, T. L. Journal of Clinical Microbiology, Vol. 44, Issue 9 https://doi.org/10.1128/JCM.00024-06	journal	September 2006

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