Day 3


Friday, June 20



9:00   Comments by Session Chairperson

9:15   Nucleic Acid-based Diagnostics: From Single Molecule Detection to Diagnostic Genomics
Richard Zhao, Ph.D., Associate Professor and Division Head, Pathology, Microbiology-Immunology, Institute of Human Virology, University of Maryland School of Medicine
Molecular diagnostics, especially nucleic acid-based testing, continues to grow and have a major impact on medical practice. Current molecular diagnostics are mostly concentrated on infectious diseases, genetics, and hematology/oncology with increasing expansion to other disciplines such as cardiovascular diseases, psychiatric disorders, pharmacogenomics and theragnostics.  Nucleic acid-based assays are traditionally classified by the method of gene amplification, which includes probe-, signal- and target-based amplifications. Use of fluorophore-linked nanoparticles, especially the metal enhanced fluorescence in the detection of molecular analytes has tremendous potential that could detect a single DNA or RNA molecule, thus allowing detection of a single copy gene without amplification. Disease profiling such as SNPs analysis at the genomic level provides another yet entire new level of understanding and detection of diseases, which empowers nucleic acid-testing of individual susceptibility to diseases. Combined application of gene arrays with the enhanced fluorescence detection of single molecules will allow simultaneous detection of massive SNPs that are tailored to individualized molecular testing for personalized medicine.

9:45   Unknown Pathogen Discovery Using Next Generation Sequencing
Yuriy Fofanov, Ph.D., Associate Professor, Biology & Biochemistry, University of Houston
High-throughput next generation sequencing technologies such as Genome Analyzer (Illumina Inc.) SOLiD (Applied Biosystems), and HeliScope (Helicos BioSciences) produce several billions bases of sequence per week.  In concert with advanced computational tools developed by UH Bioinformatics lab and Eureka Genomics, these sequencing technologies offer a new opportunity to identify non-host genetic material present in a sample.  Thus, novel pathogens, including non culturable members of host associated microbial communities and significantly modified pathogens may be discovered.

10:15   Nucleic Acid-Based Diagnostics for Opportunistic Pathogens
Rhonda Honeycutt, Ph.D., CEO & Founder, Clarity BioSciences, Inc.
Genomic information universally found in fungi provides the basis for rapid nucleic acid-based diagnostics. This presentation will discuss a patented diagnostic technology platform that exploits genomic regions characteristic of various taxonomic groups. Using clinical isolates, we have amassed an extensive database of fungal-specific polymorphisms. The first clinical products focus on identification at the level of species for Candida, the most commonly encountered fungal pathogen in the immuno-compromised, such as ICU and transplant patients. The technology, currently developed to yield discrete, robust PCR amplicons, is amenable to other amplification and non-amplification platforms.

10:45   Networking Coffee Break

11:15   Technology Focus
PNA Probe Design and the Rapid, Colorimetric Detection of Mycobacterium Tuberculosis
Heather Koshinsky, Ph.D., CEO, TB Diagnostics, Investigen
Investigen™ is developing a peptide nucleic acid (PNA)-based nucleic acid (NA) test for TB that is simple, rapid and inexpensive. This detection technology is called smartDNA™ and is an elegant and innovative approach to detect NA targets.  The diagnosis of tuberculosis (TB) is the major weak link in global TB control.  All steps in the smartDNA TB detection assay are run at room temperature and smartDNA readout is colorimetric.  To reduce human error a portable smartDNA reader has been developed.  The method does not detect NA from human cells or common respiratory tract flora.  This protocol has been used to sensitively and specifically detect Mycobacterium tuberculosis NA from samples of isolated NA, samples of culture grown cells and samples of cells spiked into processed sputum samples.  All eight published genomes of the Mycobacterium tuberculosis Complex (MTB) were compared to the human genome, 5 million human SNPs and over 1800 other complete genomes representing over 100 microorganisms of the human respiratory tract.  This in silico comparison generated 29 ultraspecific signature sequences.  These are being used in further ultraspecific smartDNA based MTB detection assays.

11:30 Solutions Showcase (Sponsorship Available)

12:00 Luncheon Technology Workshop (Sponsorship Available) or Lunch on your own


1:55 Comments by Session Chairperson

2:00  Comparison of the Capabilities of UPLC, HPLC and CGE for the Analysis of Nucleic Acids and Other Large Molecules
Judy Carmody, Ph.D., President, Avatar Pharmaceutical Services, Inc.
The reliability, reproducibility and robustness challenges associated with the determination of nucleic acids and other large molecules with standard analytical techniques have been well documented and discussed.  These, and other, characteristics of the UPLC, HPLC and CGE techniques for determination of nucleic acids and other large molecules will be compared and presented along with discussion of various detection modes.

2:30 qPCR Use in Biopharmaceuticals and Current Issues
Chaminda Salgado, Principal Scientist, Biopharmaceutical Analytical Sciences, GlaxoSmithKline
Brief overview for uses of q-PCR in Biopharmaceuticals, (covering mAbs, DNA vaccines, & SCVs etc) summarizing assay types used, starting with candidate selection, aid to cell line selection, aid to cell line stability issues, use as a potency assay for both DNA vaccines and mAbs (by use of Biomarkers), Process viral clearance validation, Process genomic DNA clearance, Cell bank testing, Biodistribution, biomarker analysis in clinical trials, and finally it’s potential in companion diagnostics. The end of talk will highlight current, general issues with the qPCR technology and the requirement to standardize on analysis methodology and algorithms, future considerations for platform vendors, and future potential for the technique, yet to be exploited.

3:00 Networking Refreshment Break, Poster and Exhibit Viewing

3:30 Microbial Identification with Genotypic Methods – Continuous Improvement to Make Them Faster, Cheaper, Accurate and GMP Approved
Emiliano Toso, Ph.D., Lab Head, Biological Quality Control, Merck Serono
Two genotypic methods have been developed to improve microbial identification in biological manufacturing environments and processes. These methods allow accurate identification of bacteria (genus, species and strain), mycoplasma, yeast and moulds. To improve their features and to encourage manufacturing sites to switch to them, we have introduced an innovative transport support, we have carried out a study comparing with traditional methods, we have introduced automation and get an improved throughput. Moreover a robust validation has been performed to get GMP compliance. This presentation will provide an overview of the steps followed to achieve these targets and to overcome the problems encountered.

4:00 Validation of a Real Time Quantitative PCR (qPCR) Method for the Detection of Residual Host DNA in Drug Products Produced Following Good Manufacturing Practices (GMP)
Ivan Delgado, Ph.D., Principal Scientist, Molecular and Cell Biology, Lancaster Laboratories
A critical step in the manufacturing of biopharmaceuticals is the purification of the drug product. The purification process needs to fulfill a number of requirements, including the removal of contaminating residual host DNA. In order to accomplish this, the purification process needs to be very effective and robust, and the test for the detection of residual host DNA should be both extremely sensitive and reliable. The U.S. FDA requires that final vialed drug products contain less than 100 pg of residual DNA per therapeutic dose. Furthermore, guidance from the ICH (International Conference on Harmonisation) suggests that each analytical procedure be tested for specificity, linearity, range, accuracy, precision, detection limit, quantitation limit, robustness, and system suitability. Real time qPCR is a fast, flexible, reproducible, and cost-effective technology ideally suited to fulfill regulatory requirements. We will present our experience validating real time qPCR assays for the detection of residual host DNA in drug products.

4:30 Close of Conference

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