2011 course on Molecular Diagnostic Automation - Part 2 - Amplification.
This is from early 2011. Prices and Specifications of instruments may have changed.
Part 2 of 3
The document discusses the conceptual design and experimental setup of a Visible Light Communication system called VIDAS for transmitting traffic information to vehicles. VIDAS uses LED traffic lights to transmit data to onboard vehicle receivers via visible light modulation. Key components discussed include the multiple LED emitter source, PIN photodiode detector, front-end amplifier, direct sequence spread spectrum modulation, and considerations for noise and signal variation over distance. Experimental results showed VIDAS enabled reception of traffic information from 100m away and adaptation to changing signal strength as vehicles approached intersections.
This document discusses various molecular techniques used for diagnosis of infectious diseases. It notes that molecular methods are most important for pathogens that are difficult to detect by conventional methods, like Mycobacterium tuberculosis and Chlamydia trachomatis. Several amplification techniques are described, including PCR, NASBA, TBA, SDA, and LAMP. These allow detection of pathogens in clinical samples and identification of antibiotic resistance. The document also discusses probe-based methods like hybrid capture, signal amplification techniques like branched DNA, and other methods like plasmid profiling, nucleotide sequencing, and RFLP for microbial classification and epidemiological analysis.
The document discusses the VIDAS and MINI VIDAS automated immunoassay systems for pathogen detection. It provides an overview of their features, including their use for food quality control and personal care testing. It describes their reliability, flexibility, and ability to process samples efficiently with minimal hands-on time. The document also lists various reagent tests available to detect pathogens like E. coli, Salmonella, Listeria, and Campylobacter.
The document describes the ELISA (enzyme-linked immunosorbent assay) technique for detecting and quantifying proteins, antibodies, and hormones. In an ELISA, an antigen is immobilized to a plate and detected using an antibody linked to an enzyme. Detection involves incubating the plate with a substrate to produce a measurable product, allowing quantification of the antigen. There are different types of ELISA including direct, indirect, sandwich, and competitive formats that vary the immobilization and detection steps. Proper sample preparation and reagent dilution are important for accurate ELISA results.
The document summarizes laboratory tests for diagnosing HIV infection. It describes the structure of the HIV virus and how it infects CD4+ T-cells. The main purposes of HIV testing are to prevent transmission through blood or from mother to child. HIV diagnosis involves screening assays like ELISA and rapid tests, followed by confirmatory tests like Western blot. Viral load and CD4 count are used to monitor disease progression. New techniques allow detection of HIV in alternative specimens like saliva, urine and oral fluids. Diagnosis in infants is challenging due to passive antibody transfer.
The document discusses the conceptual design and experimental setup of a Visible Light Communication system called VIDAS for transmitting traffic information to vehicles. VIDAS uses LED traffic lights to transmit data to onboard vehicle receivers via visible light modulation. Key components discussed include the multiple LED emitter source, PIN photodiode detector, front-end amplifier, direct sequence spread spectrum modulation, and considerations for noise and signal variation over distance. Experimental results showed VIDAS enabled reception of traffic information from 100m away and adaptation to changing signal strength as vehicles approached intersections.
This document discusses various molecular techniques used for diagnosis of infectious diseases. It notes that molecular methods are most important for pathogens that are difficult to detect by conventional methods, like Mycobacterium tuberculosis and Chlamydia trachomatis. Several amplification techniques are described, including PCR, NASBA, TBA, SDA, and LAMP. These allow detection of pathogens in clinical samples and identification of antibiotic resistance. The document also discusses probe-based methods like hybrid capture, signal amplification techniques like branched DNA, and other methods like plasmid profiling, nucleotide sequencing, and RFLP for microbial classification and epidemiological analysis.
The document discusses the VIDAS and MINI VIDAS automated immunoassay systems for pathogen detection. It provides an overview of their features, including their use for food quality control and personal care testing. It describes their reliability, flexibility, and ability to process samples efficiently with minimal hands-on time. The document also lists various reagent tests available to detect pathogens like E. coli, Salmonella, Listeria, and Campylobacter.
The document describes the ELISA (enzyme-linked immunosorbent assay) technique for detecting and quantifying proteins, antibodies, and hormones. In an ELISA, an antigen is immobilized to a plate and detected using an antibody linked to an enzyme. Detection involves incubating the plate with a substrate to produce a measurable product, allowing quantification of the antigen. There are different types of ELISA including direct, indirect, sandwich, and competitive formats that vary the immobilization and detection steps. Proper sample preparation and reagent dilution are important for accurate ELISA results.
The document summarizes laboratory tests for diagnosing HIV infection. It describes the structure of the HIV virus and how it infects CD4+ T-cells. The main purposes of HIV testing are to prevent transmission through blood or from mother to child. HIV diagnosis involves screening assays like ELISA and rapid tests, followed by confirmatory tests like Western blot. Viral load and CD4 count are used to monitor disease progression. New techniques allow detection of HIV in alternative specimens like saliva, urine and oral fluids. Diagnosis in infants is challenging due to passive antibody transfer.
Molecular Techniques For Disease DiagnosisPriyanka Gupta
Molecular techniques are used to analyze biological markers in genomes and proteomes. They provide several advantages over traditional diagnostic methods such as faster diagnosis, increased sensitivity and specificity, and ability to detect pathogens more rapidly. Common molecular techniques include PCR, real-time PCR, nucleic acid sequencing, microarrays, and nucleic acid amplification methods like NASBA. These techniques are useful for diagnosing infectious diseases and genetic conditions.
Blood culturing is the most important test for detecting pathogens in the bloodstream. It involves collecting blood in specialized bottles that contain growth media for aerobic and anaerobic organisms. It is critical that the collection procedure is done aseptically. Newer automated systems can continuously monitor blood cultures and detect microbial growth within 24-48 hours, providing faster results than conventional methods. Rapid identification of pathogens in positive blood cultures is important for guiding appropriate treatment.
The EMIT technique is an immunoassay method used to screen blood and urine samples for therapeutic drugs and abused substances. It works by using antibodies linked to enzymes that react with the target substance in a sample. This reaction is then measured spectrophotometrically. EMIT assays are homogeneous, requiring no separation steps, and provide reliable quantitative results. While less sensitive than other immunoassays like ELISA, EMIT is widely used in clinical settings due to its low cost, simplicity, and long shelf life of reagents.
The document discusses the storage and collection of biological specimens for viral testing. It lists the types of specimens that can be collected from different sites of infection, such as respiratory tract infections, eye infections, gastrointestinal infections, skin rashes, and bloodborne infections. Specimens include nasal swabs, throat swabs, sputum, stool samples, vesicle fluid, tissue biopsies, cerebrospinal fluid, and blood. Direct examination methods to detect viruses or parts of viruses in clinical specimens are also covered, such as electron microscopy, antigen detection assays, and molecular detection of viral nucleic acids.
The document discusses HIV/AIDS, including:
- HIV was identified as the cause of AIDS in 1983.
- HIV is transmitted through unprotected sex, contaminated blood, and from mother to child.
- India's HIV epidemic began in the 1980s, with over 2 million new infections globally in 2013.
- HIV diagnosis involves antibody and antigen tests, while treatment and monitoring involves CD4 counts and viral load tests.
This presentation on how dried blood spot testing may overcome some of the barriers to HIV testing was given by Philip Cunningham, NSW State Reference Laboratory for HIV, at the AFAO Members Forum - May 2015.
This document discusses various molecular techniques used for diagnosis of infectious diseases. It notes that molecular methods are most useful for pathogens that are difficult to detect by conventional methods, like Mycobacterium tuberculosis and Chlamydia trachomatis. It describes techniques like PCR, NASBA, TBA, SDA, LAMP that amplify nucleic acids from pathogens. Other methods discussed include plasmid profiling, nucleotide sequencing, restriction fragment length polymorphism (RFLP), and nucleic acid hybridization. The document provides details on how several of these techniques work and their applications in microbial identification, detection of antibiotic resistance, and epidemiological studies.
Hepatitis B Surface Antigen (HBsAg), also known as Australia antigen is present on the surface of the Hepatitis B virus (HBV). This test detects the presence of Hepatitis B Surface Antigen (HBsAg) in the blood.
Reference: https://www.1mg.com/labs/test/hepatitis-b-s-1837
1. The document discusses the use of nucleic acid testing (NAT) to screen blood donations for HIV, HCV, and HBV. NAT helps reduce the window period by directly detecting viral nucleic acids, providing an additional layer of safety beyond serological testing alone.
2. Data from testing over 40,000 blood donations in India showed a NAT yield rate of 1 in 598 donations, detecting 68 donations that were infectious by NAT but non-reactive by serology.
3. Studies comparing different NAT assays found that the Ultrio Plus assay had greater sensitivity than older assays, detecting more true positive donations during the window period.
The hepatitis B virion (Dane particle):
outer lipid envelope with the surface antigen (HBsAg).
an electron-dense core (nucleocapsid): ds circular DNA and polymerase surrounded by the core antigen (HBcAg).
The HBsAg is produced in excess by the infected hepatocytes and is secreted in the form of spherical
and filamentous particles.
Variability of clinical chemistry laboratory resultsAdetokunboAjala
Understanding the concepts associated with variability of laboratory results would help laboratorians improve the quality of laboratory service as well as aid the drive towards harmonization of laboratory quality practices.
This is a presentation giving an overview of the GeneXpert DX system for detection of MTB. The assay described in this presentation is the MTB/RIF test.
The document discusses the diagnosis and classification of lipid disorders. Lipid disorders can be caused by genetic abnormalities, environmental factors, or as a consequence of other diseases. They are generally diagnosed based on a patient's clinical presentation and laboratory tests measuring lipids and lipoproteins. Abnormal lipid levels are associated with conditions like coronary artery disease. Lipid disorders include both overproduction and deficiencies of lipoproteins and are classified into primary categories of hyperlipoproteinemia and hypolipoproteinemia. Common genetic lipid disorders discussed include familial hypercholesterolemia and hypertriglyceridemia.
Enzyme immunoassays (EIAs), also known as enzyme-linked immunosorbent assays (ELISAs), combine antibody binding with enzymatic detection to quantify molecules of interest.
The document discusses several hepatitis viruses including types A, D, E, and G. It provides details on the classification, morphology, transmission, epidemiology, clinical manifestation, laboratory diagnosis, treatment and prevention of each virus. Hepatitis A virus causes infectious hepatitis and is transmitted via the fecal-oral route. Hepatitis D virus is defective and requires hepatitis B virus for replication. It causes more severe disease than hepatitis B alone. Hepatitis E virus causes enterically transmitted hepatitis epidemics in certain regions. Hepatitis G virus does not appear to cause hepatitis but may co-infect with other viruses like HIV.
In this slide contains introduction, genomic materials of virus and testing method of covid 19 by using RT-PCR.
Presented by: R.Rekha (Department of pharmacology),
RIPER, anantapur.
This document discusses quality control and quality assurance in microbiological laboratory investigations. It emphasizes the importance of standard operating procedures, internal quality assessment, and external quality assessment. Quality control occurs at multiple stages of analysis, including pre-analytical (specimen collection and transport), analytical (reagents, equipment, procedures), and post-analytical (reporting and interpretation of results). A quality control officer oversees quality control in the department through regular monitoring, assessment, communication, and analysis of quality control data.
Reverse transcription polymerase chain reaction (RT-PCR) is a technique used to detect RNA expression and qualitatively detect gene expression by creating cDNA from RNA. RT-PCR involves reverse transcribing RNA into cDNA using reverse transcriptase, then amplifying the cDNA using PCR. It can be performed as a one-step or two-step process. RT-PCR is commonly used in research, genetic disease diagnosis, cancer detection, and studying viruses with RNA genomes.
This document discusses different types of polymerase chain reaction (PCR) techniques. It begins by providing background on PCR and its development. It then describes several types of PCR including multiplex PCR, which allows for simultaneous detection of multiple pathogens; nested PCR, which increases specificity; reverse transcription PCR (RT-PCR) and quantitative real-time PCR (qRT-PCR), which are used to detect RNA; quantitative PCR, which measures specific target DNA/RNA amounts; and other variants like hot-start PCR, touchdown PCR, and methylation-specific PCR. Each type is briefly explained along with its uses and applications in medical research.
2011 course on Molecular Diagnostic Automation - Part 1 - DNA ExtractionPatrick Merel
2011 course on Molecular Diagnostic Automation - Part 1 - Nucleic Acid Extraction.
This is from early 2011. Prices and Specifications of instruments may have changed.
Part 1 of 3
Molecular Techniques For Disease DiagnosisPriyanka Gupta
Molecular techniques are used to analyze biological markers in genomes and proteomes. They provide several advantages over traditional diagnostic methods such as faster diagnosis, increased sensitivity and specificity, and ability to detect pathogens more rapidly. Common molecular techniques include PCR, real-time PCR, nucleic acid sequencing, microarrays, and nucleic acid amplification methods like NASBA. These techniques are useful for diagnosing infectious diseases and genetic conditions.
Blood culturing is the most important test for detecting pathogens in the bloodstream. It involves collecting blood in specialized bottles that contain growth media for aerobic and anaerobic organisms. It is critical that the collection procedure is done aseptically. Newer automated systems can continuously monitor blood cultures and detect microbial growth within 24-48 hours, providing faster results than conventional methods. Rapid identification of pathogens in positive blood cultures is important for guiding appropriate treatment.
The EMIT technique is an immunoassay method used to screen blood and urine samples for therapeutic drugs and abused substances. It works by using antibodies linked to enzymes that react with the target substance in a sample. This reaction is then measured spectrophotometrically. EMIT assays are homogeneous, requiring no separation steps, and provide reliable quantitative results. While less sensitive than other immunoassays like ELISA, EMIT is widely used in clinical settings due to its low cost, simplicity, and long shelf life of reagents.
The document discusses the storage and collection of biological specimens for viral testing. It lists the types of specimens that can be collected from different sites of infection, such as respiratory tract infections, eye infections, gastrointestinal infections, skin rashes, and bloodborne infections. Specimens include nasal swabs, throat swabs, sputum, stool samples, vesicle fluid, tissue biopsies, cerebrospinal fluid, and blood. Direct examination methods to detect viruses or parts of viruses in clinical specimens are also covered, such as electron microscopy, antigen detection assays, and molecular detection of viral nucleic acids.
The document discusses HIV/AIDS, including:
- HIV was identified as the cause of AIDS in 1983.
- HIV is transmitted through unprotected sex, contaminated blood, and from mother to child.
- India's HIV epidemic began in the 1980s, with over 2 million new infections globally in 2013.
- HIV diagnosis involves antibody and antigen tests, while treatment and monitoring involves CD4 counts and viral load tests.
This presentation on how dried blood spot testing may overcome some of the barriers to HIV testing was given by Philip Cunningham, NSW State Reference Laboratory for HIV, at the AFAO Members Forum - May 2015.
This document discusses various molecular techniques used for diagnosis of infectious diseases. It notes that molecular methods are most useful for pathogens that are difficult to detect by conventional methods, like Mycobacterium tuberculosis and Chlamydia trachomatis. It describes techniques like PCR, NASBA, TBA, SDA, LAMP that amplify nucleic acids from pathogens. Other methods discussed include plasmid profiling, nucleotide sequencing, restriction fragment length polymorphism (RFLP), and nucleic acid hybridization. The document provides details on how several of these techniques work and their applications in microbial identification, detection of antibiotic resistance, and epidemiological studies.
Hepatitis B Surface Antigen (HBsAg), also known as Australia antigen is present on the surface of the Hepatitis B virus (HBV). This test detects the presence of Hepatitis B Surface Antigen (HBsAg) in the blood.
Reference: https://www.1mg.com/labs/test/hepatitis-b-s-1837
1. The document discusses the use of nucleic acid testing (NAT) to screen blood donations for HIV, HCV, and HBV. NAT helps reduce the window period by directly detecting viral nucleic acids, providing an additional layer of safety beyond serological testing alone.
2. Data from testing over 40,000 blood donations in India showed a NAT yield rate of 1 in 598 donations, detecting 68 donations that were infectious by NAT but non-reactive by serology.
3. Studies comparing different NAT assays found that the Ultrio Plus assay had greater sensitivity than older assays, detecting more true positive donations during the window period.
The hepatitis B virion (Dane particle):
outer lipid envelope with the surface antigen (HBsAg).
an electron-dense core (nucleocapsid): ds circular DNA and polymerase surrounded by the core antigen (HBcAg).
The HBsAg is produced in excess by the infected hepatocytes and is secreted in the form of spherical
and filamentous particles.
Variability of clinical chemistry laboratory resultsAdetokunboAjala
Understanding the concepts associated with variability of laboratory results would help laboratorians improve the quality of laboratory service as well as aid the drive towards harmonization of laboratory quality practices.
This is a presentation giving an overview of the GeneXpert DX system for detection of MTB. The assay described in this presentation is the MTB/RIF test.
The document discusses the diagnosis and classification of lipid disorders. Lipid disorders can be caused by genetic abnormalities, environmental factors, or as a consequence of other diseases. They are generally diagnosed based on a patient's clinical presentation and laboratory tests measuring lipids and lipoproteins. Abnormal lipid levels are associated with conditions like coronary artery disease. Lipid disorders include both overproduction and deficiencies of lipoproteins and are classified into primary categories of hyperlipoproteinemia and hypolipoproteinemia. Common genetic lipid disorders discussed include familial hypercholesterolemia and hypertriglyceridemia.
Enzyme immunoassays (EIAs), also known as enzyme-linked immunosorbent assays (ELISAs), combine antibody binding with enzymatic detection to quantify molecules of interest.
The document discusses several hepatitis viruses including types A, D, E, and G. It provides details on the classification, morphology, transmission, epidemiology, clinical manifestation, laboratory diagnosis, treatment and prevention of each virus. Hepatitis A virus causes infectious hepatitis and is transmitted via the fecal-oral route. Hepatitis D virus is defective and requires hepatitis B virus for replication. It causes more severe disease than hepatitis B alone. Hepatitis E virus causes enterically transmitted hepatitis epidemics in certain regions. Hepatitis G virus does not appear to cause hepatitis but may co-infect with other viruses like HIV.
In this slide contains introduction, genomic materials of virus and testing method of covid 19 by using RT-PCR.
Presented by: R.Rekha (Department of pharmacology),
RIPER, anantapur.
This document discusses quality control and quality assurance in microbiological laboratory investigations. It emphasizes the importance of standard operating procedures, internal quality assessment, and external quality assessment. Quality control occurs at multiple stages of analysis, including pre-analytical (specimen collection and transport), analytical (reagents, equipment, procedures), and post-analytical (reporting and interpretation of results). A quality control officer oversees quality control in the department through regular monitoring, assessment, communication, and analysis of quality control data.
Reverse transcription polymerase chain reaction (RT-PCR) is a technique used to detect RNA expression and qualitatively detect gene expression by creating cDNA from RNA. RT-PCR involves reverse transcribing RNA into cDNA using reverse transcriptase, then amplifying the cDNA using PCR. It can be performed as a one-step or two-step process. RT-PCR is commonly used in research, genetic disease diagnosis, cancer detection, and studying viruses with RNA genomes.
This document discusses different types of polymerase chain reaction (PCR) techniques. It begins by providing background on PCR and its development. It then describes several types of PCR including multiplex PCR, which allows for simultaneous detection of multiple pathogens; nested PCR, which increases specificity; reverse transcription PCR (RT-PCR) and quantitative real-time PCR (qRT-PCR), which are used to detect RNA; quantitative PCR, which measures specific target DNA/RNA amounts; and other variants like hot-start PCR, touchdown PCR, and methylation-specific PCR. Each type is briefly explained along with its uses and applications in medical research.
2011 course on Molecular Diagnostic Automation - Part 1 - DNA ExtractionPatrick Merel
2011 course on Molecular Diagnostic Automation - Part 1 - Nucleic Acid Extraction.
This is from early 2011. Prices and Specifications of instruments may have changed.
Part 1 of 3
El documento describe el sistema GeneXpert, el laboratorio de diagnóstico molecular más pequeño del mundo. GeneXpert permite realizar pruebas moleculares en un cartucho cerrado de un solo uso en aproximadamente una hora, sin necesidad de equipos o personal especializado. El documento resume varias pruebas disponibles para GeneXpert como MTB/RIF para tuberculosis, C. difficile, GBS, influenza y más.
This document discusses various nucleic acid amplification tests (NAATs) for detecting Chlamydia trachomatis, including PCR, real-time PCR, transcription-mediated amplification (TMA), and strand displacement amplification (SDA). It provides details on commercially available tests like Cobas Amplicor, Roche cobas, Abbott RealTime, Gen-Probe Aptima Combo 2, and BD ProbeTec systems. The advantages and limitations of each method are outlined. Sensitivity and specificity rates for different sample types are generally high, ranging from 92-100% sensitivity and 95-100% specificity.
This document discusses conversion factors between international units (IU) and other measurement units for different assays that detect HIV, HCV, and HBV. It reports on analytical sensitivity studies comparing several assay systems. It finds that conversion factors between IU and other units like genotype-equivalent units (Geq) are assay-specific due to differences in extraction and detection methods between assays. The molecular composition and physical form of reference materials can also impact conversion factors.
The document describes the capabilities of the Maxwell 16 system, a cartridge-based automated nucleic acid purification system. It can purify genomic DNA, total RNA, and proteins from a variety of sample types, including cultured cells, tissues, blood, and food/plant samples. The system utilizes magnetic bead technology to rapidly and consistently isolate nucleic acids and proteins from samples in cartridges, providing high-quality purified material for downstream applications.
2011 course on Molecular Diagnostic Automation - Part 3 - DetectionPatrick Merel
2011 course on Molecular Diagnostic Automation - Part 3 - Detection.
This is from early 2011. Prices and Specifications of instruments may have changed a lot.
Part 3 of 3
The document discusses the history and development of the polymerase chain reaction (PCR) technique. It describes how Kary Mullis invented PCR in 1985 and was awarded the Nobel Prize for it. It then explains the basic steps of PCR including denaturation, annealing of primers, and extension. Finally, it discusses several variations and applications of PCR including real-time PCR, asymmetric PCR, and comparisons to cloning techniques.
Dokumen ini membahas tentang pemeriksaan infeksi Hepatitis C menggunakan metode chemiluminescence. Metode ini mendeteksi kehadiran antibodi anti-HCV di dalam serum pasien dengan menggunakan reaksi antigene-antibodi yang dilabel dengan acridinium ester untuk menghasilkan cahaya. Pemeriksaan dilakukan menggunakan alat ADVIA Centaur XP dengan prinsip indirect sandwich chemiluminescence.
An HPV sample collection kit contains a spatula, cyto-brush, and tube of sterile saline. A doctor uses the spatula to scrape cervical tissue and aid collection with the cyto-brush, which is rotated in the endometrial canal to collect a sample. The cyto-brush is then cut off into the saline tube and transported to the lab at 2-8 degrees Celsius for HPV DNA PCR testing.
The document summarizes algorithms and techniques for biochip design and optimization. It discusses physical design of DNA arrays, tag set design for universal tag arrays, and algorithms to optimize concurrent testing on digital microfluidic biochips. Key applications include gene expression analysis, SNP genotyping, and point-of-care medical diagnosis. Design challenges involve minimizing border length in DNA arrays, maximizing tag set size while avoiding unwanted hybridization, and routing droplets on biochips to test for defects in minimal time without merging or interference.
Technologies for Early Disease Detection and Rapid Disaster ResponseInSTEDD
The document discusses using text messaging and mobile phones to facilitate early detection of disease outbreaks and public health emergencies. It describes building a global system to detect emerging threats through frequent reporting from multiple data streams. Key approaches involve adopting social network and cognitive models, indicator-based and event-based surveillance, and integrating data visualization and analysis tools to identify signals and recommend response measures. The goal is to create a collaborative environment where automated systems interact with human experts to improve detection and response.
The document discusses various methods in molecular biology, including nucleic acid hybridization, DNA sequencing, real-time PCR, and DNA microarrays. Nucleic acid hybridization uses complementary base pairing between DNA or RNA probes and targets. DNA sequencing determines the nucleotide order using chain-terminating dideoxynucleotides. Real-time PCR quantifies DNA or RNA targets in real time using fluorescent probes. DNA microarrays allow analysis of gene expression patterns across thousands of genes.
The document discusses several clinical uses of HPV DNA testing, including:
1) Triaging women with abnormal cervical cytology results to determine who needs colposcopy.
2) Follow up of women treated for CIN II/III to monitor for recurrence.
3) Potential use as an adjunct to cytology for primary cervical cancer screening in women over 30.
HPV testing was found to be an effective triage method in the ALTS study, detecting 96% of CIN 2/3 with 56% colposcopy referral compared to cytology methods.
2017 Oregon Wine Sympoisum| Daniel Sweeney- Red Blotch Disease: Detection, Ve...Oregon Wine Board
As red blotch continues to encroach upon more and more Oregon vineyards, knowledge of the latest research and trends has never been more critical. Scientists from UC Davis, ARS and Oregon State University will share their latest research on detection, vectors and the spread of grapevine red blotch associated virus. From ARS, Mysore Sudarshana will share his research on detection, from UC Davis, Frank Zalom will share his research on the vectors and spread of red blotch in California. Vaughn Walton and Rick Hilton will share their latest research on the vectors and spread in Oregon. Attendees will also hear from a Southern Oregon grower about his personal trials and tribulations at controlling the virus.
1. Specific tests for diagnosing HIV infection include detecting viral antigens like p24, isolating the live virus, detecting viral nucleic acids through PCR, and detecting antibodies through ELISA and Western blot tests.
2. ELISA and rapid tests are used as initial screening tests to detect antibodies, while Western blot is a supplemental test used to confirm positive ELISA results.
3. In addition to specific tests, nonspecific tests like complete blood counts can provide clues about HIV infection by detecting signs of immune deficiency like low CD4+ T cell and platelet counts.
DNA microarrays contain thousands of DNA probes attached to a solid surface that allow for the simultaneous analysis of gene expression across many genes. The core principle is based on DNA hybridization, where fluorescently labeled cDNA or RNA samples are hybridized to complementary probes on the array. By detecting which probes light up after hybridization and washing, researchers can determine which genes are expressed or detect genetic variations in the sample. Microarrays have numerous applications, including gene expression analysis, disease diagnosis, drug discovery, and toxicology research. They provide a fast way to study thousands of genes but results require further validation and correlations do not necessarily indicate causation.
Plasmid Manufacturing Service from GenScript ProBioGenScript ProBio
GenScript ProBio offers the best Plasmid Manufacturing Service and employs a GMP-compliant plasmid production process that allows customers to replicate DNA used in experiments with minimal additional effort. By employing this process, Genscript can provide plasmids produced at the highest quality standards. For more information, visit our website. https://www.genscriptprobio.com/gct-proplasmid.html
Microbial S.L. is a biotechnological company devoted to the design and production of products for the rapid detection of pathogen microorganisms in environmental and food samples.
The document describes STRATEC Molecular's portfolio of nucleic acid purification kits and sample preparation solutions. It highlights the InviGenius automated nucleic acid purification system, which can process 12 samples directly from primary tubes to PCR-ready DNA/RNA. It also discusses the PSP SalivaGene DNA Kit for non-invasive saliva collection and DNA stabilization at room temperature for 12 months, and the PSP Spin Stool DNA Plus Kit for integrated stool sample collection, transport, and DNA purification.
Next-generation sequencing course, part 1: technologiesJan Aerts
This document provides an overview of next-generation sequencing technologies and their applications. It discusses genome enrichment techniques to isolate targeted regions for sequencing. It also describes template preparation methods like emulsion PCR and solid-phase amplification. Finally, it reviews various sequencing platforms like Illumina, SOLiD, 454 and details the sequencing and imaging processes. There are exercises proposed to work with sequencing data files in Galaxy.
Target enrichment enables researchers to focus their next generation sequencing (NGS) efforts on regions of interest, allowing them to obtain more sequencing data relevant to their study. In-solution target capture is a method of enrichment using oligonucleotide probes directed to specific regions within a genome. Target capture can be used to enrich multiple samples simultaneously, reducing the cost per sample, while using individually synthesized probes allows researchers to construct gene panels that can be optimized over time.
This document summarizes rapid detection methods for foodborne pathogen bacteria. It discusses how foodborne illnesses are a major public health problem and rapid detection of pathogens is needed. Several detection methods are outlined, including traditional culturing as well as newer techniques like PCR, real-time PCR, LAMP, and immunoassays. LAMP is highlighted as a new method that can rapidly detect pathogens under isothermal conditions. The document concludes that LAMP is a promising technique for pathogen detection due to its speed, simplicity and accuracy.
Polymerase chain reaction (PCR) is a technique used to amplify specific DNA sequences. It involves cycling between high and low temperatures to separate DNA strands and allow for replication. This allows for targeted amplification of millions of copies of a particular DNA sequence. Real-time quantitative PCR (qPCR) allows for detection and quantification of DNA during amplification through the use of fluorescent probes. Reverse transcription PCR (RT-PCR) first converts RNA to DNA before amplification. PCR techniques like qRT-PCR are currently used for accurate diagnosis of COVID-19 by detecting the SARS-CoV-2 virus from samples.
The Future of RNA Therapies Produced with LinearDNA™ IVT TemplatesLineaRx
Proprietary, highly efficient and scalable linDNA (linear DNA, the product of PCR) manufacturing process for use in nucleic acid-based therapies. Learn how LineaRx is the common denominator of next-generation therapies.
CIMNA, the unique center for Immune monitoring. CRO / Central Lab / Services in Cytometry, ELISpot, Luminex, Miccroarrays, biostatistics, clinical management, medical writing...
Apac distributor training series 3 swift product for cancer studySwift Biosciences
This document provides an overview of Swift Biosciences' product training series for their APAC distributors on using Swift products for cancer studies. It summarizes different Swift library preparation and sequencing kits that can be used for various cancer applications, including genomic sequencing, RNA sequencing, amplicon panels, hybridization capture, and DNA methylation. The document also reviews types of mutations found in cancer, considerations for cancer clinical workflows, and provides an example of using Swift's 2S Turbo kit for targeted sequencing of formalin-fixed, paraffin-embedded tissue samples.
One-Stop Antibody Drug Discovery Services from GenScript ProBioGenScript ProBio
GenScript ProBio is the biopharmaceutical division of GenScript, a leading biotech company. GenScript ProBio provides end-to-end services from drug discovery to commercialization, including antibody discovery and development, cell line development, process development, and clinical manufacturing. Key services include antibody humanization, developability assessment, and affinity maturation to improve antibody candidates for preclinical and clinical development.
Digital PCR for soybean GMO detection on the OpenArray Platform: a case study...Thermo Fisher Scientific
This document describes how digital PCR on the TaqMan OpenArray platform can be used as a sensitive tool for detecting genetically modified organisms (GMOs). [The summary describes:]
1) Custom TaqMan assays were designed to differentiate between GMO and wild-type soybean DNA. 2) The assays were validated for specificity using digital PCR. 3) Spike-in experiments were conducted adding GMO DNA at levels as low as 0.01% to wild-type DNA, and digital PCR accurately measured ratios matching estimated levels.
MOLECULAR TOOLS IN DIAGNOSIS AND CHARACTERIZATION OF INFECTIOUS DISEASES tawheedshafi
The future of the molecular diagnostics of infectious diseases will undoubtedly be focused on a marked increase in the amount of information detected with remarkably simplified, rapid platforms that will need complex software analysis to resolve the data for use in clinical decision-making.
Sequential Automation of RNA and DNA preps on the same QIAcube instrumentQIAGEN
Automation of QIAGEN spin-column kits on the QIAcube saves valuable time and ensures standardized results. Since the same QIAcube may be used by multiple researchers for different applications, cross-contamination between samples and preparation technologies must be avoided (e.g., when nucleases are used). The unique instrument design and features minimize contamination between sequential preps, allowing both RNA and DNA preps to be performed on the same instrument. To show the process safety and robustness, we performed alternating automated RNA preps (requiring a DNase step) and DNA plasmid preps (requiring an RNase step). The preps were sequentially performed on the same QIAcube instrument using the RNeasy® Mini Kit and the QIAprep® Spin Miniprep Kit, respectively.
Independently, we performed a series of manually processed preps to compare with the automated preps. RNA and DNA quality and yields were similar between the two methods, showing the absence of carryover of nucleases.
PCR is a technique used to amplify DNA. There are several types of PCR including multiplex PCR, nested PCR, RT-PCR, quantitative PCR, hot-start PCR, touchdown PCR, assembly PCR, colony PCR, methylation-specific PCR, and LAMP assay. Each type has a specific application or mechanism. For example, multiplex PCR allows simultaneous analysis of multiple targets, nested PCR increases specificity, RT-PCR converts RNA to cDNA, and quantitative PCR measures the amount of target DNA or RNA.
This document discusses various types of polymerase chain reaction (PCR). It begins with an introduction to PCR and its history of being invented by Kary Mullis. It then describes different types of PCR including multiplex PCR, nested PCR, reverse transcriptase PCR, real-time PCR, touchdown PCR, hot start PCR, and colony PCR. Each type is defined and its applications and advantages are outlined. The document provides an overview of the various techniques derived from standard PCR that are used for different purposes.
RT-PCR by Arnab Kumar Samanta(sen-4^J2020)[133].pptxArnabSamanta26
1) RT-PCR is the primary method for detecting SARS-CoV-2, the virus that causes COVID-19. It works by extracting the viral RNA from samples and amplifying specific DNA targets.
2) The RT-PCR process involves reverse transcribing the viral RNA into cDNA, then amplifying the cDNA using PCR. If the virus is present, fluorescent probes will bind to the amplified DNA and be detected in real time.
3) RT-PCR is highly sensitive and specific for detecting SARS-CoV-2, but it also requires specialized equipment and reagents, making it an expensive testing method.
New Progress in Pyrosequencing for Automated Quantitative Analysis of Bi- or ...QIAGEN
Pyrosequencing is a highly flexible technology based on sequencing-by-synthesis for the rapid and quantitative analysis of any type of sequence variation. The real-time output delivers high-resolution sequence information, making pyrosequencing highly suitable for applications ranging from biallelic or multiallelic SNP analysis, DNA methylation quantification to complex mutation analysis of multiple sequence variations in a single run.
In this slideeck, we introduce the new PyroMark Q48 Autoprep system which enables fully automated template preparation integrated in the pyrosequencing workflow. In addition, a new Multiple Primer Dispensation (MPD) strategy is presented which allows fully automated dispensation of sequencing primer, offering a seamless workflow from samples to quantitative genotyping results.
This slidedeck focuses on the following topics
• Pyrosequencing technology and workflow in genotyping analysis
• Introduction into the new PyroMark Q48 Autoprep
• MPD strategy for a seamless automated pyrosequencing workflow
Join us and learn how you can apply the new pyrosequencing system and protocol to your variant analysis or genotyping research
Similar to 2011 course on Molecular Diagnostic Automation - Part 2 - Amplification (20)
The skin is the largest organ and its health plays a vital role among the other sense organs. The skin concerns like acne breakout, psoriasis, or anything similar along the lines, finding a qualified and experienced dermatologist becomes paramount.
Discover the benefits of homeopathic medicine for irregular periods with our guide on 5 common remedies. Learn how these natural treatments can help regulate menstrual cycles and improve overall menstrual health.
Visit Us: https://drdeepikashomeopathy.com/service/irregular-periods-treatment/
Computer in pharmaceutical research and development-Mpharm(Pharmaceutics)MuskanShingari
Statistics- Statistics is the science of collecting, organizing, presenting, analyzing and interpreting numerical data to assist in making more effective decisions.
A statistics is a measure which is used to estimate the population parameter
Parameters-It is used to describe the properties of an entire population.
Examples-Measures of central tendency Dispersion, Variance, Standard Deviation (SD), Absolute Error, Mean Absolute Error (MAE), Eigen Value
Osvaldo Bernardo Muchanga-GASTROINTESTINAL INFECTIONS AND GASTRITIS-2024.pdfOsvaldo Bernardo Muchanga
GASTROINTESTINAL INFECTIONS AND GASTRITIS
Osvaldo Bernardo Muchanga
Gastrointestinal Infections
GASTROINTESTINAL INFECTIONS result from the ingestion of pathogens that cause infections at the level of this tract, generally being transmitted by food, water and hands contaminated by microorganisms such as E. coli, Salmonella, Shigella, Vibrio cholerae, Campylobacter, Staphylococcus, Rotavirus among others that are generally contained in feces, thus configuring a FECAL-ORAL type of transmission.
Among the factors that lead to the occurrence of gastrointestinal infections are the hygienic and sanitary deficiencies that characterize our markets and other places where raw or cooked food is sold, poor environmental sanitation in communities, deficiencies in water treatment (or in the process of its plumbing), risky hygienic-sanitary habits (not washing hands after major and/or minor needs), among others.
These are generally consequences (signs and symptoms) resulting from gastrointestinal infections: diarrhea, vomiting, fever and malaise, among others.
The treatment consists of replacing lost liquids and electrolytes (drinking drinking water and other recommended liquids, including consumption of juicy fruits such as papayas, apples, pears, among others that contain water in their composition).
To prevent this, it is necessary to promote health education, improve the hygienic-sanitary conditions of markets and communities in general as a way of promoting, preserving and prolonging PUBLIC HEALTH.
Gastritis and Gastric Health
Gastric Health is one of the most relevant concerns in human health, with gastrointestinal infections being among the main illnesses that affect humans.
Among gastric problems, we have GASTRITIS AND GASTRIC ULCERS as the main public health problems. Gastritis and gastric ulcers normally result from inflammation and corrosion of the walls of the stomach (gastric mucosa) and are generally associated (caused) by the bacterium Helicobacter pylor, which, according to the literature, this bacterium settles on these walls (of the stomach) and starts to release urease that ends up altering the normal pH of the stomach (acid), which leads to inflammation and corrosion of the mucous membranes and consequent gastritis or ulcers, respectively.
In addition to bacterial infections, gastritis and gastric ulcers are associated with several factors, with emphasis on prolonged fasting, chemical substances including drugs, alcohol, foods with strong seasonings including chilli, which ends up causing inflammation of the stomach walls and/or corrosion. of the same, resulting in the appearance of wounds and consequent gastritis or ulcers, respectively.
Among patients with gastritis and/or ulcers, one of the dilemmas is associated with the foods to consume in order to minimize the sensation of pain and discomfort.
The biomechanics of running involves the study of the mechanical principles underlying running movements. It includes the analysis of the running gait cycle, which consists of the stance phase (foot contact to push-off) and the swing phase (foot lift-off to next contact). Key aspects include kinematics (joint angles and movements, stride length and frequency) and kinetics (forces involved in running, including ground reaction and muscle forces). Understanding these factors helps in improving running performance, optimizing technique, and preventing injuries.
Travel vaccination in Manchester offers comprehensive immunization services for individuals planning international trips. Expert healthcare providers administer vaccines tailored to your destination, ensuring you stay protected against various diseases. Conveniently located clinics and flexible appointment options make it easy to get the necessary shots before your journey. Stay healthy and travel with confidence by getting vaccinated in Manchester. Visit us: www.nxhealthcare.co.uk
Breast cancer: Post menopausal endocrine therapyDr. Sumit KUMAR
Breast cancer in postmenopausal women with hormone receptor-positive (HR+) status is a common and complex condition that necessitates a multifaceted approach to management. HR+ breast cancer means that the cancer cells grow in response to hormones such as estrogen and progesterone. This subtype is prevalent among postmenopausal women and typically exhibits a more indolent course compared to other forms of breast cancer, which allows for a variety of treatment options.
Diagnosis and Staging
The diagnosis of HR+ breast cancer begins with clinical evaluation, imaging, and biopsy. Imaging modalities such as mammography, ultrasound, and MRI help in assessing the extent of the disease. Histopathological examination and immunohistochemical staining of the biopsy sample confirm the diagnosis and hormone receptor status by identifying the presence of estrogen receptors (ER) and progesterone receptors (PR) on the tumor cells.
Staging involves determining the size of the tumor (T), the involvement of regional lymph nodes (N), and the presence of distant metastasis (M). The American Joint Committee on Cancer (AJCC) staging system is commonly used. Accurate staging is critical as it guides treatment decisions.
Treatment Options
Endocrine Therapy
Endocrine therapy is the cornerstone of treatment for HR+ breast cancer in postmenopausal women. The primary goal is to reduce the levels of estrogen or block its effects on cancer cells. Commonly used agents include:
Selective Estrogen Receptor Modulators (SERMs): Tamoxifen is a SERM that binds to estrogen receptors, blocking estrogen from stimulating breast cancer cells. It is effective but may have side effects such as increased risk of endometrial cancer and thromboembolic events.
Aromatase Inhibitors (AIs): These drugs, including anastrozole, letrozole, and exemestane, lower estrogen levels by inhibiting the aromatase enzyme, which converts androgens to estrogen in peripheral tissues. AIs are generally preferred in postmenopausal women due to their efficacy and safety profile compared to tamoxifen.
Selective Estrogen Receptor Downregulators (SERDs): Fulvestrant is a SERD that degrades estrogen receptors and is used in cases where resistance to other endocrine therapies develops.
Combination Therapies
Combining endocrine therapy with other treatments enhances efficacy. Examples include:
Endocrine Therapy with CDK4/6 Inhibitors: Palbociclib, ribociclib, and abemaciclib are CDK4/6 inhibitors that, when combined with endocrine therapy, significantly improve progression-free survival in advanced HR+ breast cancer.
Endocrine Therapy with mTOR Inhibitors: Everolimus, an mTOR inhibitor, can be added to endocrine therapy for patients who have developed resistance to aromatase inhibitors.
Chemotherapy
Chemotherapy is generally reserved for patients with high-risk features, such as large tumor size, high-grade histology, or extensive lymph node involvement. Regimens often include anthracyclines and taxanes.
Spontaneous Bacterial Peritonitis - Pathogenesis , Clinical Features & Manage...Jim Jacob Roy
In this presentation , SBP ( spontaneous bacterial peritonitis ) , which is a common complication in patients with cirrhosis and ascites is described in detail.
The reference for this presentation is Sleisenger and Fordtran's Gastrointestinal and Liver Disease Textbook ( 11th edition ).
acne vulgaris -Mpharm (2nd semester) Cosmetics and cosmeceuticals
2011 course on Molecular Diagnostic Automation - Part 2 - Amplification
1. Patrick Merel
Biomedical Innovation Platform (PTIB), Pessac, France
pmerel@mac.com
PCR Automation in Molecular Diagnostic
part 2
1
1
2. From Waterbath to PCR Chips
DNA diagnostic mostly PCR diagnostic
PCR challengers: small market share but robust alternatives
Automation of PCR: Automation of PCR setup
Robotic friendly
thermocyclers
Thermocyclers evolution
integration into fully automated platforms
microfluidics? PCR chips?
no PCR at all?
2
2
7. Digene’s Hybrid Capture Technology
•Same day, objective results using a microplate test format.
•High throughput automation for handling increasing test volumes.
•Sensitivity comparable to many other target amplification technologies, without the
complexity of these other test methods.
•Minimal required specimen preparation, allowing samples to be processed quickly
and efficiently.
•Protection against cross contamination problems that can occur with some target
amplification assays.
•Hybrid Capture tests are available to detect human papillomavirus (HPV), chlamydia
trachomatis (CT), neisseria gonorrhea (GC), and cytomegalovirus (CMV); the latter is
available in tube format only.
7
7
11. Signal Amplification with the Invader reaction
IF the variation or sequence in question is present, an
In the first reaction, two oligonucleotides
overlapping structure is created with the mutant probe
- a primary probe and an Invader® oligo -
and the Invader® oligo on the target. The patented
associate with a specific region of DNA to
Cleavase® enzymes specifically cleave the primary probes
generate a one-base overlapping
that form overlapping structures with the Invader® oligo,
structure at the nucleotide being
releasing the 5' flaps plus one nucleotide. In the absence
interrogated.
of the specific target, no flap is released.
11
11
12. Signal Amplification with the Invader reaction
Released flaps from the primary reaction B e c a u s e t h e s e t w o c l e ava g e
serve as Invader® oligos in a second, reactions occur simultaneously,
simultaneous invasive cleavage reaction on they can produce 1 million to 10
a labeled, synthetic oligo, the fluorescence million labeled cleavage products
resonance energy transfer (FRET) probe. per target sequence. A standard 4-
Cleavage of this FRET probe results in the hour reaction produces over 10
generation of a fluorescent signal. million-fold signal amplification.
12
12
13. Signal Amplification with the Invader reaction
IVD products ASRs
InPlex CF FII FV
UGT1A1 MTHFR 677 MTHFR 1298
HPV
HPV 16/18 HCVg
HR-16/18
4hrs incubation
13
13
14. Invader Signal Amplification Evolution
Invader Plus® methodology Invader® InPlex™ Technology
•Utilizes basic PCR amplification •Partnership with 3M, a world leader in health care innovation
•Coupling PCR with Invader® chemistry •Combines performance, ease of use of Invader® chemistry
brings the best of both worlds with 3M microfluidic technology
•Enhances and extends the Invader® chemistry
•Speed to result, Efficiency,Ease of use
•Utilizes existing laboratory equipment
14
14
18. PCR and Diagnostic
...in just 25 years
■ 1984 : presented by K. Mullis
■ 1988 : 1st PCR by RK. Saiki
■ 1991 : 1st TaqMan PCR by PM. Hollan and PCR
patent rights acquired by Roche
■ 1992 : Realtime PCR concept by R. Higuchi
■ 1996 : Lightcycler launched by Idaho Tech.
■ 1997 : LLightcycler launched by Roche
■ 2003 : HRM methods introduced by Idaho Tech.
■ 2009 : LightCycler1536 introduced by Roche
18
18
19. Automating PCR Operations
Plasticware options
Tubes and plates format
Sealing plates
Instrumentation for regular PCR
robotic friendly?
integration friendly?
Instrumentation for realtime PCR
robotic friendly?
integration friendly?
PCR offering in the IVD market
19
19
20. Microtiterplate formats for PCR
Various format of 96 well plate format
Up to 384 and 1536 well plate format 20
20
21. Fluidigm, Illumina, LifeTech: New Formats?
Fuidigm EP1
or BioMArk
96.96 Dynamic Array IFC
48.770 Digital Array IFC
Digital Array
Producing up to 9,216 real-time qPCR reactions in
the same amount of time as a single 384-well plate,
while using just 1/200th the amount of reagents.
21
21
22. Fluidigm, Illumina, LifeTech: New Formats?
48-well
polypropylene
reaction
plates
and
Optically clear
pressure-
sensitive
adhesive film
Back to the 48’s
The Eco thermal system incorporates a precisely electroformed hollow silver block that is heated and cooled by a
single Peltier device. The hermetically sealed hollow block contains a conductive fluid and two opposing agitators
driven by electromagnetic motors. During PCR cycling, these agitators rapidly circulate the fluid throughout the
hollow block, transferring heat from the Peltier device evenly across the block. This unique design virtually
eliminates thermal non-uniformity and block edge effects, providing a new level of thermal performance of ±
0.1°C well-to-well uniformity across the 48-well plate.
22
22
23. Fluidigm, Illumina, LifeTech: New Formats?
OpenArray
The OpenArray® Real-Time PCR Instrument and OpenArray AccuFill™
System combination enables the processing of hundreds to thousands of
samples per day enabling mid-density, high-throughput results with ease
of use. Reliable multiple sample loading— fill 3,072 through-holes (33 nL
each) without cross-contamination and with minimal hands-on time.
Economical, highly scalable approach—run up to three OpenArray Plates
simultaneously on the OpenArray Real-Time PCR Instrument
23
23
24. Innovation in ‘regular’ PCR
AlphaHelix AmpXpress:
a very rapid thermal cycler utilizing
SuperConvection™ technology that
make the instrument significantly faster
than conventional thermal cyclers. 40
ycles in 20 minutes.
Compared to conventional thermal
cyclers, where thermal homogenization in-tube temperature measurements
occurs by convection at normal gravity of reaction temperature
(1 x g), AmpXpress utilizes
SuperConvection, at 3000 x g, together
with extreme heating and cooling, to
enable previously unachievable Capillette is a small cartridge
temperature ramping rates (measured containing four chambers that we
fill with your reagents for one
in-tube!) and instant thermal
complete PCR.
homogenization within the samples,
that lead to more efficient amplification Simply add your DNA template to
and time savings. a PCR tube, place Capillette in
the top and spin it in a centrifuge
to empty the reagents into the
tube.
24
24
25. Innovation in ‘regular’ PCR
Icubate:
iCubate Cassettes are custom made to
automate molecular protocols such as
PCR, ligation, hybridization and detection.
Possible applications include pathogen
identification from various sample sources.
An iCubate system includes one Reader,
one Processor (4 units), and a computer
with preinstalled software. The internal and
external barcode scanners located
throughout the system will ensure error free
processing and tracking of your samples.
Proprietary ARM-PCR technology
(Amplicon Rescued Multiplex PCR) allows
multiple targets to be amplified in one
reaction.
Proven array detection technology
analyzes multiple targets at once.
Plug and play operation, no need for Icubate:
extensive training.
Up to twelve units can be linked together
to run up to 48 samples simultaneously.
25
25
26. Innovation in ‘regular’ PCR
Idaho Technologies:
FilmArray: The FilmArray integrates
sample preparation, amplification,
detection, and analysis into one easy to
use system capable of massively
multiplexed PCR. Fully automated,
multiplex PCR capable of detecting
greater than 100 targets in one sample in
less than one hour.
Inject unprocessed sample and water, start the run Closed system prevents cross-contamination
and walk away Multiplexed testing analyzes up to 120 tests per
System integrates sample preparation, amplification, sample
detection and analysis Rapid results in 1 hour from sample injection
All necessary reagents are freeze dried in one pouch
and are stable at room temperature
26
26
27. Automation of PCR procedures
๏Automation of PCR setup
๏Automation through thermocycler integration
๏In house robotics
๏A new era for automated PCR: realtime PCR
27
27
28. High Throughput PCR wanted
๏Increasing number of tests
๏Increasing number of samples 28
28
30. Thermocyclers for a complete robotic integration
ü Automation of lid movements
ü Automation of PCR programs
ü Biorad Tetrad
ü AB 9700 AutoLid
ü MWG Primus HT
ü Biometra Trobot
ü ThermoHybaid
30
30
31. Closing the Tubes!
From silicone-like sheet
with a removable
plastic backing...
...to pre-cut, thin adhesive backed aluminum
foil with a roller as a simple and cost effective
system to seal PCR plate...to auto-sealing lids
and heat sealers
31
31
32. MWG-Biotech “no cross contamination” Patented Option
NCC-PCR ensures absolutely airtight sealing of each individual
cavity combined with the simplest, touch free operation and
compatibility with all current thermal cyclers (0.2ml Block).
In order to avoid contamination through aerosols every cavity in
the microplate is closed with individual seals. The opening and
closing of the reaction vessels takes place touch-free with the
patented "Deckel handler" - no hand contact.
32
32
33. Thermocyclers and “Low-End” Robotic Integration
Linking a generic workstation with a thermocyler + motorized lid, like here
with a BCI Biomek 2000 + Ptc200 from MJR
What is possible:
๏ PCR setup onto the workstation
(oil addition)
๏ manual transfer to the
thermocycler (plate sealing)
๏ or robotic transfer after reaction
setup (oil)
๏ Run the PCR
๏ Transfer the plate back
33
33
34. PCR Setup on the Biomek 2000 for generic HLA typing
1- the DNA+PCR mix is
transferred to PCR
tubes
2- the primers mixes are
then distributed in the
PCR tubes
34
34
35. Generic HLA-DRB1-DQB1 typing with the Biomek 2000
DRB1 PCR
Two times 40 PCRs (1 PE-9600
PCR control
plate) are setup for generic
HLA-DRB1 - DQB1 typing of Specific PCR
two patients. The PCR
reactions are prepared on the DQB1 PCR
Biomek 2000 in 9 minutes.
HLA- DRB1*03/07
Four PCR plates (8 patients) can be HLA-DQB1*02/02
managed simultaneously by the DRB1 PCR
Biomek 2000. (On the other hand 4
thermocyclers will be needed)
DQB1 PCR
HLA- DRB1*15/07
HLA-DQB1*02/0602
35
35
37. Automation of PCR procedures
๏Automation of PCR setup
๏Automation through thermocycler integration
๏In house robotics
๏A new era for automated PCR: realtime PCR
37
37
38. Thermocycler Modules and Robotic Integration
Integration of a remote PCR block on a MultiProbe robotic workstation
from Perkin Elmer
38
38
41. Thermocyclers and High-End Robotic Integration
Roche Diagnostic Cobas Taqman
96 integration through the Docking
Station to the Cobas Amplirep.
41
41
42. Automation of PCR procedures
๏Automation of PCR setup
๏Automation through thermocycler integration
๏In house robotics
๏A new era for automated PCR: realtime PCR
42
42
44. Full Robotic Integration
Automation of plate transportation
Automation of lid movements
Automation of PCR programs
ThermoHybaid, Bio-Rad
44
44
45. Full Robotic Integration
Automation of plate transportation
Automation of lid movements
Automation of PCR setup
Automation of PCR programs
Various robotic arms available
45
45
47. Accessories for Full Automation
Plate sealer
Plate piercer
Velocity11's PlateLoc Thermal Plate Sealer.
As a complementary machine to the PlateLoc, the
PlatePierce pierces a wide variety of seals on 96
or 384 well microplates in only 4 seconds of cycle
time.
Compatible plates: All SBS standard
microplates in 96 and 384 well formats
Compatible seals: A wide variety of both
pierceable and peelable seals. 47
47
48. Integration of PCR instrumentation
Integration of Beckman Coulter Inc. Biomek FX
with thermocyclers (AB-9700, MJR
Tetrad…etc) and plate sealer (ABGene).
48
48
50. Protedyne BioCube Workstation
The Protedyne PCR BioCube™ is
the first unit of its kind that services
up to eight PCR machines
(32 blocks) with a single robot.
Materials can enter
and exit the PCR BioCube™ via
input and output
conveyors for unattended operation.
50
50
51. Protedyne BioCube Workstation
Protedyne has also very recently The Protedyne PCR BioCube
announced the integration of with AB-9700 thermocyclers
Roche LC480 thermocycler in the
BioCube.
51
51
52. Automation of PCR procedures
๏Automation of PCR setup
๏Automation through thermocycler integration
๏In house robotics
๏A new era for automated PCR: realtime PCR
52
52
53. Fast PCR with integrated detection: the revolution
The Lightcycler integrates a 24 sample micro-
volume fluorimeter with an air thermal cycler
delivering accurate and high-speed temperature
control.
The Lightcycler is the fastest thermal cycler in the world. Thirty cycle reactions can
be run in as little as six minutes while an integrated fluorimeter monitors reactions
as they occur. The Lightcycler eliminates the need to perform both amplification and
separate product analysis allowing unprecedented throughput.
53
53
56. Realtime PCR Instrument 1
Company Instrument Capacity; Labware Type of Thermocycler Robotic Friendly Web Address
(Yes, No, Not
Specified)
StepOne, StepOne+ 48, 96 fast block N
Peltier based, fast
7500 96 well plate N
block option
AB/Life Technologies 96, 384 well plate, or Peltier based, fast appliedbiosystems.com
7900HT Y
TaqMan array block option
96, 384 well plate, or
ViiA 7 fast block Y
TaqMan array
Y; Integration of
24 individually
sample preparation,
BD BD Max controlled chambers; fast cycler bd.com
amplification and
microfluidic cartridge
detection
Sandwich thermal-
Bioer Technology Line-Gene,2,K 33,66,48 tubes N bioer.com.cn/en
electronic Peltier
Biogene Insyte 96 well plate fast cycler NS biogene.com
Bioneer Exicycler 96 well plate Peltier based NS bioneer.com
MiniOpticon, MyIQ2,
Bio-rad 48,96,96,384 well plate Peltier based N bio-rad.com
CFX89, CFX384
16 independent units;
SmartCycler fast cycler N
proprietary tubes
Y; Integration of
1, 4, 16 independent
Cepheid sample preparation, cepheid.com
GeneXpert units; proprietary fast cycler
amplification and
cartridge
detection
48 independent units; Continuous flow fast
GeneXpert Infinity Y 56
proprietary cartridge cycler
56
57. Realtime PCR Instrument 2
Company Instrument Capacity; Labware Type of Robotic Friendly Web Address
Thermocycler (Yes, Not, Not
Specified)
Mastercyler ep
Eppendorf 96 well plate Peltier based N eppendorfna.com
realplex
Evogen Evocycler HD12 12 tubes-proprietary fast cycler N evogen.com
Focus 3M integrated Cycler 96 well disc fast cycler N integratedcycler.com
6 samples-6 tests;
GeneSystems GeneDisc Cycler fast cycler N genesystems.fr
CD format
Peltier based
Illumina Eco Real-Time 48 well plate N illumina.com
36 tubes; 72, 100 fast cycler
Qiagen Rotor-Gene Q N qiagen.com
proprietary tubes
LightCyler V1, V2 32 glass capillaries; N
96, 384 ; 1536 well fast cycler roche-applied-
LightCyler 480; 1536 Y science.com
plate
Roche Diagnostics 2x24 proprietary
Cobas Taqman 48 N
tubes
Peltier based roche.com
4x24 proprietary
Cobas Taqman 96 Y
tubes
Stratagene-Agilent
Mx3000, Mx3005P 96 well plate Peltier based N stratagene.com
Technologies
57
57
58. Innovation in realtime PCR
AlphaHelix QuanTyper
Superconvection and Capilette
Applied Biosystems/Life Technologies
ViiA 7 Realtime PCR with 96, 384 well plate and Taqman Array microfluidic cards
OpenArray with 3072 through hole plate
Fuidigm digital PCR
BioMark Realtime PCR with 48x48 (2304) or 96x96 (9216) Dynamic, Digital and Access
Array IFCs
Roche Applied Sciences
LightCycler 1536 Fast Realtime PCR
Small initiatives like
GeneSystems’s GeneDisc realtime PCR cycler
Enigma Diagnostics
58
58
59. AlphaHelix SuperConvection realtime PCR
AlphaHelix QuanTyper 48:
the first qPCR instrument to utilize
SuperConvection, making it the world's
most rapid qPCR instrument.
40 cycle qPCR including melt analysis in 15
minutes
48 samples per run
Quadruplex
20 - 200 µl volume range
Rapid and unique HRM analysis The rotating samples are heated using a circular
high-energy IR source.
Capillette is a small cartridge
containing four chambers that we
fill with your reagents for one
complete PCR.
Simply add your DNA template to
a PCR tube, place Capillette in
the top and spin it in a centrifuge
to empty the reagents into the
tube.
59
59
60. LifeTechnologies Open Array realtime PCR
OpenArray
The OpenArray® Real-Time PCR Instrument and OpenArray AccuFill™
System combination enables the processing of hundreds to thousands of
samples per day enabling mid-density, high-throughput results with ease
of use. Reliable multiple sample loading— fill 3,072 through-holes (33 nL
each) without cross-contamination and with minimal hands-on time.
Economical, highly scalable approach—run up to three OpenArray Plates
simultaneously on the OpenArray Real-Time PCR Instrument
60
60
61. Fluidigm Digital Array realtime PCR
96.96 Dynamic Array IFC IFC Controller HX BioMArk reader
Digital Array
Producing up to 9,216 real-time qPCR reactions in
the same amount of time as a single 384-well plate,
while using just 1/200th the amount of reagents.
61
61
62. Roche LC-1536 realtime PCR
1536 ‘regular’ realtime PCR
•Increase throughput fourfold
•Generate 1,536 data points in a single run in less than 50 min.
•Use significantly less reagent and sample with reaction vol. of
just 0.5-2.0 µl. 62
62
63. GeneSystems GeneDisc Cycler
The GeneDisc uses a hybrid technology between the DNA chip and real-time
PCR microplates that proves to be especially relevant for routine diagnostic
applications.
It is a single-use micro-laboratory of the size of a compact disc.
Its rim is engraved with 36 reaction microchambers preloaded with the reagents
necessary for detecting and quantifying the required targets.
Wells at its centre will be filled with the purified bacterial DNA.
A fine network of microchannels automatically and uniformly transfers the
bacterial DNA samples to the reaction chambers.
63
63
69. Fast PCR Instrument: Corbettnow part of Qiagen
Research
Rotor-Gene Q
๏30 µL x 100-wells: GeneDisc 100 (heat-sealed plate)
๏0.1 mL x 72-wells: GeneDisc 72 (heat-sealed plate)
๏0.1 mL x 72-wells: 0.1 mL strip tubes (strips of caps)
๏0.2 mL x 36-wells: 0.2 mL tube (attached cap)
69
69
71. QPCR robotic for 96-384 sample batch
Applied BioSystems PRISM®
7900HT
The ABI PRISM® 7900HT Sequence Detection System is a high-throughput real-time PCR system.
• An Automation Accessory combined with 384-well plate capability make the 7900HT system
ideally suited to meet the high-throughput requirements.
• Key applications include gene expression quantitation and the detection of single nucleotide
polymorphisms (SNPs) using the fluorogenic 5’ nuclease assay.
Key Features and Benefits
• Interchangeable formats provide improved throughput and flexibility
• Custom Automation Accessory provides 24-hour unattended operation
• Hand-held and integrated bar code readers simplify sample tracking
• Continuous wavelength detection from 500-660 nm allows the use of multiple fluorophores in a
single reaction
71
71
72. QPCR Robotic Integration
High Throughput Core Systems
already exist for PCR
automation
Combination of BCI core
system + Prism 7900 allows
configurations for:
NA extraction
PCR setup
Plate sealing
Prism 7900 loading
Up to 384 PCR every 2.5hrs
72
72
77. Biomek Nx-Sp8 / LC480 integration
The players: Beckman Coulter, Roche Diagnostics, AIG
An integration from The Biomedical Innovation Platform @
University Hospital of Bordeaux, France with the help of AIG,
Germany.
77
77
78. Very High Throughput QPCR with the LightCycler 1536
•Increase throughput fourfold.
•Generate 1,536 data points in a single
run in less than 50 minutes.
•Use significantly less reagent and
sample with reaction volumes of
just 0.5-2.0 µl.
78
78
80. Automation of PCR Setup with the MagnaPure LCs
MagnaPure LC2 MagnaPure LC
80
80
81. Automation of PCR Setup with the QIAgility
Automated PCR setup in all formats
The QIAgility uses a single-channel pipet to
automate PCR setup - up to 96 PCR reactions
can be set up in approximately 30 minutes.
Liquid-level sensing, facilitated by conductive
filtered tips, enables high-precision pipetting
81
81
82. Integration of PCR Setup with the QIAsymphony AS
Automated PCR setup in all formats
The QIAsymphony AS extends the capabilities of the
QIAsymphony SP to include automated assay setup.
The new module interfaces with the QIAsymphony SP
and is operated via the same easy-to-use, intuitive
software.
For integrated operation, samples processed on the
QIAsymphony SP can be transferred to the
QIAsymphony AS, reducing manual handling steps and
documentation.
The QIAsymphony AS provides active cooling of
reagents, eluates, and assays, enabling safe and
reproducible assay setup.
The QIAsymphony AS enables setup of multiple assays
per run or sample and supports artus® products and
other QIAGEN products for PCR.
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83. Robotic Friendly QPCR Instruments
The Parallab 350
(BioGene) is an
automated nano pipetter,
including a magnetic bead
station/separator and a
fast thermocycler
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85. Full Integration with the Cepheid GeneXpert
The GeneXpert cartridge-based PCR detection
system integrates automated sample preparation
with real-time PCR analysis. It can handle up to 5
mL of aqueous sample such as medical or
environmental swab extracts, bioaerosols, or
serum. Dry on-board reagents, easy sample
handling and setup, and a totally internally
controlled reagent system enable true random
access performance with results available in 30
minutes or less.
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86. Cepheid GeneXpert
The GeneXpert System is a 1 to 4-site, random access
instrument integrating real-time amplification and detection
features seen in the SmartCycler System, but delivering
results from unprocessed samples in less than 30 minutes.
The internal module is the common technology link between
the SmartCycler and GeneXpert, performing real-time
amplification and detection.
The GeneXpert automates sample preparation, integrating
the complex steps of DNA extraction in the microfluidic
cartridges.
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88. A New Step in MDx Automation
Cepheid Infinity / AACC 2008
Up to 2,074 test results in a mere 24 hour period. Less than 52
minutes time to first result. Less than 2 minutes sample prep time
per test. MRSA, EV, GBS tests available.
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89. Iquum Lab-in-a-Tube Platform
Liat Analyzer:
The Liat system, consisting of the Liat Analyzer and disposable Liat Tubes, automates
all nucleic acid testing processes, including reagent preparation, target enrichment,
inhibitor removal, nucleic acid extraction, amplification and real-time detection, in one
portable device.
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90. Iquum Lab-in-a-Tube Platforms
For example, a 50μl rapid
PCR can be accomplished in
as little as 7 min for 30 cycles.
Liat FlowCycler
The Liat FlowCycler can amplify 48 samples in parallel and is expandable to process 96 or more samples.
The system has 2 bays, each capable of accepting up to 3 Liat™ Tube Strips. Each Liat Tube Strip comprises 8
flexible PCR tubes for a system throughput of 48 samples.
The spacing of the individual flexible tubes of the Liat Tube Strip matches that of 8-well PCR tube strips or 8-
well columns of a 96 well plate, thus readily allowing integration of the FlowCycler system into existing liquid
handling system.
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91. Microfluidic based fully integrated platform
A microfluidic real time nucleic acid
analyzer, the BD-Max by HandyLab.
This system is capable of processing raw
patient samples, blood, urine, swab, CSF,
etc. to a result in about one hour.
It's PCR Real Time format will accept FDA
cleared, analyte specific reagents (ASR)
and/or your homebrew assays.
HandyLab's proprietary unitized reagents
and microfluidics cartridge radically reduce
the chance of a contamination event in
your laboratory.
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105. Realtime PCR Market Evolution
Major Diagnostic companies - Main molecular markers
(HIV, HBV, HCV, CT/GC)
- CE-IVD, FDA approved
- Instruments
Molecular Diagnostic reagents -Numerous minor markers
companies -Rarely major markers
-ASR, RUO
-Rarely instruments
Recently -Full menu
major diagnostic companies -CE-IVD
enhanced menu for minor -Instruments
makers
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106. MDX, PCR, Automation in conclusion
✓ PCR diagnostic switched from PCR to realtime PCR
✓ but still options for high-tech automated regular PCR+Arrays instruments
✓ Realtime PCR switched to Fast PCR
✓ from 96 well plates to capillaries to 96, 384 and 1536 well plates
✓ Realtime MDx assays on 2 instruments only
✓ NA extraction/PCR setup + Realtime PCR
✓ in house or MDx industry numerous solutions
✓Integration of realtime MDx assays on a single
instrument or expandable/connected instruments
✓ Roche Cobas, Qiagen QIAsymphony, Gen-Probe Panther instruments
✓ evolution through microfluidic instrumentation (Cepheid, BD/HandyLab..)
✓ Realtime PCR arrays and gene expression
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