Abstracts Archive

2007 Abstracts

November 11-14, 2007
13th International Symposium of the World Association of Veterinary Laboratory Diagnosticians (WAVLD)
Melbourne, Australia

LATE-PCR with PrimeSafeTM - Maximum Diagnostic Information from a Closed-Tube

Conventional PCR and even real-time PCR assays that depend on symmetric amplification of double-stranded DNA do not readily achieve the levels of sensitivity, specificity, or multiplicity needed for rapid, quantitatively accurate diagnosis of small samples containing mixtures of pathogenic or drug resistant organisms.  These limitations have been overcome by use of LATE-PCR and PrimeSafeTM.

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October 15-18
Cambridge Health Institute's Quantitative PCR, Microarray, and Biological Validation Conference
Providence, RI

LATE-PCR Endpoint Assays for Reliable and Clinically-Compatible Detection of Allele Copy Number Variations (Duplications/Deletions)

Overview: We describe a clinically-compatible method for reproducible endpoint detection of allele deletion and duplication events using Linear-After-The-Exponential (LATE) PCR.  This technology is currently being used for the construction of assays for detection of loss of tumor suppressor genes in human cancers (loss of heterozygosity, LOH) and gain of chromosome 21 responsible for Down Syndrome (chromosome 21 trisomy).

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October 13-17, 2007
63rd Annual Meeting
American Society of Reproductive Medicine
Washington, DC

Cdx2 and Oct4 mRNA in pre-implantation stage mouse embryos and their single cells

Odelya Hartung, Cristina Hartshorn, and Lawrence J. Wangh, Brandeis University

Introduction:  The formation of the blastocyst marks the differentiation event in mammalian embryogenesis.  During this event, the embryo forms two distinct cell lineages:  the inner cell mass (ICM) and the trophectoderm (TE).  Many important cell markers have been identified for TE and ICM cell lineages, among them the transcription factors Cdx2 (trophectodermal marker) and Oct4 (ICM marker).  Cdx2 is involved in TE formation and is necessary for TE maintenance in mice.  Oct4 is required to maintain pluripotency in the ICM.  These two factors appear to have a reciprocal inhibition pattern outlined by Hitoshi Niwa, diagramed in slide I-2 [1].  High Oct4 expression down-regulates Cdx2 and maintains pluripotency in the ICM lineage.  Conversely, high Cdx2 expression down-regulates Oct 4 and otehr related pluripotency factors, maintaining the TE lineage.
Cdx2 and Oct 4 protein data, also published by Hitoshi Niwa shows a reciprocal pattern of expression in mouse morulas and blastocysts, see slide I-1 below [1].  the aim of our present study is to verify this result with the highly sensitive and quantitative techniques for mRNA detection developed in our laboratory, and to dissect single cells of morulas to determine if reciprocal expression exists at the single cell level.

[1] Niwa et al. Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation.  Cell. 123: 917-929 December 2005.

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October 6-8, 2007
National Human Genome Research Institute (NHGRI)
Center of Excellence in Genomic Science (CEGS)
Baltimore, MD

Measurements of mRNA Levels in Single cells and Small Groups of Normal and Neoplastic Cells Using Novel Technologies

C. Hartshorn, O. Hartung, Y. Jia, and L.J. Wangh See Poster

September 17-19, 2007
IBC's 14th Annual Discovery-2-Diagnostics Conference
Philadelphia Convention Center, Philadelphia, PA

LATE-PCR End-Point Assays for Detection of LOH Biomarkers in Human Cancers

Overview:  We describe a clinically-compatible platform for reproducible LOH biomarker detection in human cancers.  LOH involving tumor suppressor genes are important biomarkers of future cancer risk in many pre-malignant conditions.

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August 9, 2007 10th Annual Force Health Protection Conference
Louisville, Kentucky

Improved Multiplexed PCR Assays for Detection of Pathogenic Bacteria using LATE-PCR and PrimeSafeTM, a PCR Additive.

John E. Rice, Kenneth E. Pierce, Arthur H. Reis, J. Aquiles Sanchez, John Czajka, and Lawrence J. Wangh

Overview:  Brandeis University and Smiths Detection, Inc. are developing highly informative single-tube multiplex assays for detection of viral and bacterial pathogens.

LATE-PCR, an advanced form of asymmetric PCR developed at Brandeis University generates single-stranded amplicons.  The multiplex assays described here amplify any one of five possible products, each for different BW pathogen.  In these mono-multiplex assays all but one pair of primers remains un-employed.  Addition of PrimeSafeTM suppresses mis-priming.  PrimeSafeTM, also developed at Brandeis University, functions by inactivating Taq polymerase in a temperature dependent manner during all steps of the reaction.  Each of the possible amplicons is detected via Quantitative End-Point Analysis, rather than real-time analysis, using one or more low-temperature sequence-specific fluorescent probes. (/div>


May 21-25, 2007
107th General Meeting of the American Society of Microbiology
Toronto, ON, Canada

LATE-PCR Detection of Foot and Mouth Disease Virus (FMDV)

Kenneth E. Pierce, Juliet P. Dukes, Scott M. Reid, Donald P. King, Rohit Mistry, and Lawrence J. Wangh.  A collaboration between Brandeis University, Waltham, Massachusetts USA; the Institute for Animal Health, Pirbright, UK and Smiths Detection, Watford, UK.

Background: Foot and Mouth Disease is caused by a positive-strand RNA virus.  FMDV outbreaks are highly contagious and have serious financial consequences.  Detection of FMDV is complicated by teh presence of 7 serotypes and additional sequence variation within serotypes.  Here we describe a novel pan-FMDV assay which ultimately will be used in the field in combination with a handheld PCR Device.

See Poster.

Detection and Discrimination of Orthopox Viruses using LATE-PCR and Mismatch Tolerant Probes

Lawrence J. Wangh, Kenneth E. Pierce, John F. Rice, and J. Aquiles Sanchez

Background:  A smallpox outbreak due to terrorist action would pose a serious health threat, but a false positive or false negative Variola warning would also have severe consequences.  This report describes a novel PCR-based orhopox assay that is sensitive, accurate, and able to distinguish among orthopox viruses. 

See Poster.

Improved Multiplexed PCR Assays for Detection of Pathogenic Bacteria using PrimeSafeTM, a PCR Additive

John E. Rice, Cristina Hartshorn, J. Aquiles Sanchez, Kenneth E. Pierce, Arthur H. Reis, Jr., and Lawrence J. Wangh

Background:  Diagnosis in critical care situations, such as sepsis-causing Gram-negative bacteria, could be greatly improved by use of multiplexed PCR assays that are rapid and able to distinguish among multiple organisms in a single reaction.  However, practical application of such assays is hampered by mis-priming, a problem that is inherent to all types of PCR and is exacerbated in reactions containing several pairs of primers.  We tested PrimeSafeTM, a recently commercialized PCR additive, for its capacity to suppress mis-priming in multiplex assays for the identification of pathogenic bacteria.

See Poster.

A Highly Multiplexed RT-LATE-PCR Assay for Detection of Avian and Seasonal Flu

A. H. Reis, Jr. C. Hartshorn, J.E. Rice, and L.J. Wangh, Brandeis University, Waltham MA.

Background: Highly pathogenic H5N1 avian flu has already directly and indirectly caused the deaths of millions of wild and domestic birds, as well as several hundred people, and threatens to evolve into a very lethal human pandemic influenza virus.  Identification of H5N1 and other subtypes of influenza is critical as a first line of defense and containment.  The challenge is to generate the maximum amount of reliable information in the minimum amount of time using a protable instrument.

See Poster.

p>March 26-30, 2007
3rd International qPCR Symposium and Application Workshop Freising-Weihenstephan, Germany

Duplex RT-LATE-PCR Reveals Transcript Gradients in Sets of Single Cells Recovered from 8-Cell Mouse Embryos

Cristina Hartshorn, Odelya Hartung, and Lawrence J. Wangh

The formation of two distinctive cell lineages in preimplantation mouse embryos is characterized by differential gene expression. The cells of the inner cell mass (ICM) are pluripotent and express transcripts such as Oct4 RNA, which are down-regulated in the surrounding, differentiated trophectoderm (TE). Conversely, other genes are active in the TE and silenced in the ICM. These include Xist (expressed only in females) and Cdx2 (in both sexes). Prior to blastocyst formation, all these RNAs are ubiquitously found in blastomeres of embryos at the 8-cell stage. It is plausible, however, that transcript levels differ among blastomeres of the same embryo, and that these quantitative differences may presage the fate of their daughter cells. Testing this hypothesis presents numerous technical challenges because it requires simultaneous quantification of different RNAs in sets of single cells isolated from the same embryo. We have overcome these difficulties by combining PurAmp, a single-tube method for RNA preparation and quantification, with LATE-PCR, an advanced form of asymmetric PCR.

We initially constructed a duplex RT-LATE-PCR assay for real-time measurement of Oct4 and Xist templates and confirmed its specificity and quantitative accuracy using both biological samples and analysis of the LATE-PCR fluorescent signals. The linear slope of these signals is a sensitive tool to establish that amplification has been achieved with comparable efficiency for all templates analyzed. The Oct4/Xist duplex was an ideal test system, because comparison of data from males and females allowed us to determine that, due to the properties of LATE-PCR, Oct4 amplification was unaffected by sex-related differences in Xist expression (females: Oct4 +, Xist ++; males: Oct4 +, Xist -).

Our results show that both Oct4 and Xist RNA levels vary in individual blastomeres comprising the same embryo, with some cells having particularly elevated levels of either transcript. This is significant because all cells in the 8-cell embryo are believed to be developmentally equivalent. Our data also indicate that Xist and Oct4 expression levels are not correlated at this stage, although transcription of both genes is up-regulated at this time in development. We have now developed an additional assay for simultaneous measurements of Oct4 and Cdx2 RNA, in light of recent findings that these two genes are reciprocally regulated. This work describes the first example of RT-LATE-PCR and its utility for single-tube, multiplex quantitative analysis of transcripts in single cells. Levels of different RNAs can be accurately measured independently of their relative abundance; this is not possible with symmetric PCR. The techniques illustrated here are widely applicable, for instance to gene expression analysis in stem cells and cancer cells and to preimplantation genetic diagnostics. We are also employing these strategies for multiplex quantitative end-point detection of RNA viruses.

March 19-20, 2007
Cambridge Healthtech Institute's Quantitative PCR: Replicating and Validating Success
San Diego, California

Multiplexing, Multiprobing, Multisequencing using LATE-PCR

Lawrence J. Wangh

As reported previously LATE-PCR is an efficient form of asymmetric PCR which uses pairs of primers of unequal concentration designed such that the functional melting temperature of the Limiting Primer is equal to or greater than the functional melting temperature of the Excess Primer (TmL-TmX≥0). 

We are now extending this logic to construction of multiplex reactions for simultaneous amplification of sets of cDNA or genomic DNA target sequences. These multiplexed reactions generate copious levels of several single-stranded targets that can be detected in real-time or at end-point using combinations of sequence-specific probes, or mis-match tolerant probes that hybridize to variant sequences in a temperature-dependent manner. End-point ratios of such probe-target signals can then be computed as “Fluorescent Signatures”, one for each sequence variant.  In addition, multiple single-stranded amplicons in a multi-plex reactions can also be sequenced one-by-one, each with a different primer, using either Dilute-'N'-Go Pyrosequencing or Dilute-‘N’-Go Dideoxy-sequencing. For instance, heteroplasmic mixtures containing mixtures of SNP’s can be identified and quantified. All of these methods are sensitive down to the level of single starting molecules. In sum, these novel methods greatly enhance the information generated from a single closed-tube reactions and promise to revolutionize PCR based in vitro diagnostics. We are currently employing these technologies for construction of diagnostic assays in the fields of infectious diseases, cancer, forensics, and gene expression.

February 27-March 2, 2007
Cambridge Healthtech Institute's Molecular Medicine Tri-Conference
San Francisco, California

LATE-PCR and Related Technologies for Reliable Asymmetric Amplification and Characterization of Single-stranded DNA
Lawrence J. Wangh

  1. The logic of LATE-PCR
  2. PCR-elixirs for suppression of mispriming at all stages of amplification
  3. Separation of primer annealing and probe detection
  4. Quantitative end-point detection over a broad low-temperature range (60 to 25 °C)
  5. Construction of fluorescent fingerprints
  6. Reliable single-molecule detection using LATE-PCR and elixirs
  7. Dilute-‘N’-Go sequencing following LATE-PCR
  8. One-step RT-LATE-PCR

February 23-25, 2007
International Meeting on Emerging Diseases and Surveillance
Vienna, Austria
The Rapid Detection of Influenza A and B Sub-Types, Including Avian: Using a Single-Tube LATE-PCR Assay in a Portable, Point-of-Care System

Arthur H. Reis, Jr., Cristina Hartshorn, John E. Rice, Kenneth E. Pierce, and Lawrence J. Wangh
Background: Brandeis University in collaboration with Smiths Detection is developing a highly informative in vitrodiagnostic point-of-care system that will detect and discriminate between influenza subtypes, including highly pathogenic H5N1.
Methods: Our approach utilizes novel technologies for sample preparation and amplification, as well as a new portable device. Reverse transcription of RNA templates and amplification of the cDNA are both achieved using Linear-After-The-Exponential, LATE-PCR, in a closed-tube. LATE-PCR is an advanced form of asymmetric PCR which generates single-stranded products of each amplicon. The final multiplex assay is designed to simultaneously generate up to three single-stranded amplicons for each of the possible viral subtypes and a positive control. The assay is quantitative over seven orders of magnitude and is sensitive down to fewer than 10 target molecules. Novel fluorescent probes permit Quantitative End-Point Analysis, rather than real-time analysis. In addition, this assay is highly reproducible because it uses special chemistries to suppress mis-priming.
Results: The LATE-PCR influenza assay has the capacity to distinguish 15 different possible outcomes in a single closed-tube. In addition, because LATE-PCR generates single-stranded amplicons, each of the amplified products can be sent to the laboratory for immediate sequencing by a simple Dilute-‘N’-Go procedure in order to characterize new variations of specific sub-types. Specific aspects of assay results will be presented.
Conclusion: The LATE-PCR influenza assay meets the requirements of being both specific and sensitive, while rapidly detecting both current and new varieties of influenza A and B sub-types. Similar LATE-PCR assays are under development for other viral and bacterial pathogens.