Nucleic Acid Amplification Techniques
Sensitivity and Specificity
Polymerase Chain Reaction
Gene Amplification
Self-Sustained Sequence Replication
Ligase Chain Reaction
Gonorrhea
Neisseria gonorrhoeae
Keratin-19
DNA Primers
Base Sequence
Urine
Clinical significance of expression of human cytomegalovirus pp67 late transcript in heart, lung, and bone marrow transplant recipients as determined by nucleic acid sequence-based amplification. (1/1844)
Human cytomegalovirus (HCMV) infection was monitored retrospectively by qualitative determination of pp67 mRNA (a late viral transcript) by nucleic acid sequence-based amplification (NASBA) in a series of 50 transplant recipients, including 26 solid-organ (11 heart and 15 lung) transplant recipients (SOTRs) and 24 bone marrow transplant recipients (BMTRs). NASBA results were compared with those obtained by prospective quantitation of HCMV viremia and antigenemia and retrospective quantitation of DNA in leukocytes (leukoDNAemia). On the whole, 29 patients were NASBA positive, whereas 10 were NASBA negative, and the blood of 11 patients remained HCMV negative. NASBA detected HCMV infection before quantitation of viremia did but after quantitation of leukoDNAemia and antigenemia did. In NASBA-positive blood samples, median levels of viremia, antigenemia, and leukoDNAemia were significantly higher than the relevant levels detected in NASBA-negative HCMV-positive blood samples. By using the quantitation of leukoDNAemia as the "gold standard," the analytical sensitivity (47.3%), as well as the negative predictive value (68. 3%), of NASBA for the diagnosis of HCMV infection intermediate between that of antigenemia quantitation (analytical sensitivity, 72. 3%) and that of viremia quantitation (analytical sensitivity, 28.7%), while the specificity and the positive predictive value were high (90 to 100%). However, with respect to the clinically relevant antigenemia cutoff of >/=100 used in this study for the initiation of preemptive therapy in SOTRs with reactivated HCMV infection, the clinical sensitivity of NASBA reached 100%, with a specificity of 68. 9%. Upon the initiation of antigenemia quantitation-guided treatment, the actual median antigenemia level was 158 (range, 124 to 580) in SOTRs who had reactivated infection and who presented with NASBA positivity 3.5 +/- 2.6 days in advance and 13.5 (range, 1 to 270) in the group that included BMTRs and SOTRs who had primary infection (in whom treatment was initiated upon the first confirmation of detection of HCMV in blood) and who presented with NASBA positivity 2.0 +/- 5.1 days later. Following antiviral treatment, the durations of the presence of antigenemia and pp67 mRNA in blood were found to be similar. In conclusion, monitoring of the expression of HCMV pp67 mRNA appears to be a promising, well-standardized tool for determination of the need for the initiation and termination of preemptive therapy. Its overall clinical impact should be analyzed in future prospective studies. (+info)Comparison of levels of human immunodeficiency virus type 1 RNA in plasma as measured by the NucliSens nucleic acid sequence-based amplification and Quantiplex branched-DNA assays. (2/1844)
This study compared levels of human immunodeficiency virus type 1 RNA in plasma as measured by the Quantiplex branched-DNA and NucliSens nucleic acid sequence-based amplification assays. RNA was detectable in 118 of 184 samples (64.13%) by the Quantiplex assay and in 171 of 184 samples (92.94%) by the NucliSens assay. Regression analysis indicated that a linear relationship existed between the two sets of values (P < 0.0001), although the Quantiplex and NucliSens values were significantly different (P < 0.001), with the NucliSens values being approximately 0.323 log higher. Spearman correlation analysis indicated that the overall changes in patient viral load patterns were highly correlative between the two assays: r = 0.912, P < 0.0001. The lower limits of sensitivity were determined to be approximately 100 copies/ml and 1,200 to 1,400 copies/ml for the NucliSens and Quantiplex assays, respectively. (+info)Prospective comparison of the Gen-probe PACE 2 assay and the Abbott ligase chain reaction for the direct detection of Chlamydia trachomatis in a low prevalence population. (3/1844)
In a prospective study, the Gen-Probe PACE 2 (GP) assay was compared with Abbott Laboratories' ligase chain reaction (LCR) assay for the detection of Chlamydia trachomatis. A total of 493 female patients consented to collection of two cervical samples; a first-void urine (FVU) sample was collected also from 446 of the participants. Cervical samples were tested by both GP and LCR; 16 samples (3.1%) tested positive by both methods and no discrepant results were observed. All but one of the FVU samples collected from patients with a positive cervical sample was positive for C. trachomatis by LCR. The stability of FVU samples over time in the LCR test was also evaluated and proved to be significantly longer than the 4 days stated by the manufacturer. While LCR proved to be highly sensitive in detecting chlamydial infection in FVU samples, no difference was noted between LCR and GP in the detection of cervical C. trachomatis infection in this study population. (+info)Design and evaluation of a human immunodeficiency virus type 1 RNA assay using nucleic acid sequence-based amplification technology able to quantify both group M and O viruses by using the long terminal repeat as target. (4/1844)
Currently available human immunodeficiency virus type 1 (HIV-1) RNA quantification assays can detect most viruses of the group M subtypes, but a substantial number are missed or not quantified reliably. Viruses of HIV-1 group O cannot be detected by any commercially available assay. We developed and evaluated a quantitative assay based on nucleic acid sequence-based amplification (NASBA) technology, with primers and probes located in the conserved long terminal repeat (LTR) region of the HIV-1 genome. In 68 of 72 serum samples from individuals infected with HIV-1 subtypes A to H of group M, viruses could be detected and quantified. In serum samples from two patients infected with HIV-1 group O viruses, these viruses as well could be detected and quantified. In contrast, the currently used gag-based assay underestimated the presence of subtype A viruses and could not detect subtype G and group O viruses. The discrepancy between the results of the two assays may be explained by the number of mismatches found within and among the probe and primer regions of the subtype isolates. These data indicate that LTR-based assays, including the NASBA format chosen here, are better suited to monitoring HIV-1 therapy than are gag-based assays in an era in which multiple HIV-1 subtypes and groups are spreading worldwide. (+info)High-resolution genotyping of Streptococcus pyogenes serotype M1 isolates by fluorescent amplified-fragment length polymorphism analysis. (5/1844)
We have used fluorescent amplified-fragment length polymorphism (FAFLP) analysis to subtype clinical isolates of Streptococcus pyogenes serotype M1. Established typing methods define most M1 isolates as members of a clone that has a worldwide distribution and that is strongly associated with invasive diseases. FAFLP analysis simultaneously sampled 90 to 120 loci throughout the M1 genome. Its discriminatory power, precision, and reproducibility were compared with those of other molecular typing methods. Irrespective of disease symptomatology or geographic origin, the majority of the clinical M1 isolates shared a single ribotype, pulsed-field gel electrophoresis macrorestriction profile, and emm1 gene sequence. Nonetheless, among these isolates, FAFLP analysis could differentiate 17 distinct profiles, including seven multi-isolate groups. The FAFLP profiles of M1 isolates reproducibly exhibited between 1 and more than 20 amplified fragment differences. The high discriminatory power of genotyping by FAFLP analysis revealed genetic microheterogeneity and differentiated otherwise "identical" M1 isolates as members of a clone complex. (+info)Amplified-fragment length polymorphism analysis versus macro-restriction fragment analysis for molecular typing of Streptococcus pneumoniae isolates. (6/1844)
Forty-eight pneumococci were genotyped by on-line laser fluorescence amplified-fragment length polymorphism (AFLP) and pulsed-field gel electrophoresis (PFGE) analysis of chromosomal restriction fragments. Overall, the data generated by the two methods corresponded well. However, with AFLP, clusters were delineated at a higher similarity level, and isolate differentiation was more pronounced. AFLP and PFGE were equally efficient for assessing intraserotype diversity. We conclude that AFLP is a useful alternative to PFGE. (+info)Loss of heterozygosity analysis using whole genome amplification, cell sorting, and fluorescence-based PCR. (7/1844)
Loss of heterozygosity (LOH) is a common genetic lesion found in many human neoplasms. Extending investigation of LOH to large-scale clinical and public health science studies has proven difficult because of the small size and cellular and genetic heterogeneity of human neoplasms, in addition to the challenges associated with increasing throughput. Our approach to LOH analysis was developed using clinical biopsy samples from patients with Barrett's esophagus (BE) and uses flow cytometric cell sorting to increase sample purity, whole genome amplification to increase sample amount, and automated fluorescent genotyping to increase sample throughput. This approach allows LOH assessment at 20 loci in DNA extracted from 1000 flow-purified cells while maintaining accurate and reproducible allele ratios compared with the standard method of using genomic DNA. This method of analysis should allow accurate, reproducible determination of allele ratios in a variety of human tumors and premalignant conditions. (+info)Comparison of the PACE 2 assay, two amplification assays, and Clearview EIA for detection of Chlamydia trachomatis in female endocervical and urine specimens. (8/1844)
Screening for sexually transmitted diseases (STDs) in a greater proportion of sexually active patients has become an accepted protocol by most health care providers. The purpose of this study was to compare the current test methods for detection of Chlamydia trachomatis used at the University of South Alabama, the PACE 2 assay (Gen-Probe) and the Clearview EIA (Wampole Laboratories), with two amplification technologies, the AMP CT (Gen-Probe) and LCx (Abbott) assays. In addition, a number of demographic parameters were ascertained by asking questions at the time of examination as well as for health care provider concerns and preferences. One urine and four endocervical swab specimens were collected in random order from 787 female patients attending one of four obstetrics-gynecology clinics. Eighty-seven percent of patients had no STD-related symptoms. Patients were considered positive for C. trachomatis if three or more assays (swab and/or urine) were positive. Abbott and Gen-Probe confirmed discrepant results by alternate amplified assays. A total of 66 true-positive specimens were detected by use of the combination of endocervical swabs and urine specimens. After discrepant analysis, sensitivities for endocervical swab specimens for the EIA and the PACE 2, LCx, and AMP CT assays were 50, 81, 97, and 100%, respectively. Sensitivities for the LCx and AMP CT assays with urine specimens were 98 and 81%, respectively. The prevalence of C. trachomatis was 8.4%, as determined by amplification technology. Overall, the amplification technologies were the most sensitive methods with either swab (AMP CT assay) or urine (LCx assay) specimens. The PACE 2 assay offered the advantage of a simpler and less expensive assay with acceptable sensitivity. The clearview CT EIA, while yielding a rapid in-office result, had unacceptably low sensitivity. The wide variation in performance with amplification assays with urine specimens as reported in both this study and the literature obviates the need to clarify optimal parameters for this specimen type. (+info)Nucleic acid amplification techniques (NAATs) are medical laboratory methods used to increase the number of copies of a specific DNA or RNA sequence. These techniques are widely used in molecular biology and diagnostics, including the detection and diagnosis of infectious diseases, genetic disorders, and cancer.
The most commonly used NAAT is the polymerase chain reaction (PCR), which involves repeated cycles of heating and cooling to separate and replicate DNA strands. Other NAATs include loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), and transcription-mediated amplification (TMA).
NAATs offer several advantages over traditional culture methods for detecting pathogens, including faster turnaround times, increased sensitivity and specificity, and the ability to detect viable but non-culturable organisms. However, they also require specialized equipment and trained personnel, and there is a risk of contamination and false positive results if proper precautions are not taken.
Sensitivity and specificity are statistical measures used to describe the performance of a diagnostic test or screening tool in identifying true positive and true negative results.
* Sensitivity refers to the proportion of people who have a particular condition (true positives) who are correctly identified by the test. It is also known as the "true positive rate" or "recall." A highly sensitive test will identify most or all of the people with the condition, but may also produce more false positives.
* Specificity refers to the proportion of people who do not have a particular condition (true negatives) who are correctly identified by the test. It is also known as the "true negative rate." A highly specific test will identify most or all of the people without the condition, but may also produce more false negatives.
In medical testing, both sensitivity and specificity are important considerations when evaluating a diagnostic test. High sensitivity is desirable for screening tests that aim to identify as many cases of a condition as possible, while high specificity is desirable for confirmatory tests that aim to rule out the condition in people who do not have it.
It's worth noting that sensitivity and specificity are often influenced by factors such as the prevalence of the condition in the population being tested, the threshold used to define a positive result, and the reliability and validity of the test itself. Therefore, it's important to consider these factors when interpreting the results of a diagnostic test.
Polymerase Chain Reaction (PCR) is a laboratory technique used to amplify specific regions of DNA. It enables the production of thousands to millions of copies of a particular DNA sequence in a rapid and efficient manner, making it an essential tool in various fields such as molecular biology, medical diagnostics, forensic science, and research.
The PCR process involves repeated cycles of heating and cooling to separate the DNA strands, allow primers (short sequences of single-stranded DNA) to attach to the target regions, and extend these primers using an enzyme called Taq polymerase, resulting in the exponential amplification of the desired DNA segment.
In a medical context, PCR is often used for detecting and quantifying specific pathogens (viruses, bacteria, fungi, or parasites) in clinical samples, identifying genetic mutations or polymorphisms associated with diseases, monitoring disease progression, and evaluating treatment effectiveness.
Molecular diagnostic techniques are a group of laboratory methods used to analyze biological markers in DNA, RNA, and proteins to identify specific health conditions or diseases at the molecular level. These techniques include various methods such as polymerase chain reaction (PCR), DNA sequencing, gene expression analysis, fluorescence in situ hybridization (FISH), and mass spectrometry.
Molecular diagnostic techniques are used to detect genetic mutations, chromosomal abnormalities, viral and bacterial infections, and other molecular changes associated with various diseases, including cancer, genetic disorders, infectious diseases, and neurological disorders. These techniques provide valuable information for disease diagnosis, prognosis, treatment planning, and monitoring of treatment response.
Compared to traditional diagnostic methods, molecular diagnostic techniques offer several advantages, such as higher sensitivity, specificity, and speed. They can detect small amounts of genetic material or proteins, even in early stages of the disease, and provide accurate results with a lower risk of false positives or negatives. Additionally, molecular diagnostic techniques can be automated, standardized, and performed in high-throughput formats, making them suitable for large-scale screening and research applications.
Gene amplification is a process in molecular biology where a specific gene or set of genes are copied multiple times, leading to an increased number of copies of that gene within the genome. This can occur naturally in cells as a response to various stimuli, such as stress or exposure to certain chemicals, but it can also be induced artificially through laboratory techniques for research purposes.
In cancer biology, gene amplification is often associated with tumor development and progression, where the amplified genes can contribute to increased cell growth, survival, and drug resistance. For example, the overamplification of the HER2/neu gene in breast cancer has been linked to more aggressive tumors and poorer patient outcomes.
In diagnostic and research settings, gene amplification techniques like polymerase chain reaction (PCR) are commonly used to detect and analyze specific genes or genetic sequences of interest. These methods allow researchers to quickly and efficiently generate many copies of a particular DNA sequence, facilitating downstream analysis and detection of low-abundance targets.
"Self-Sustained Sequence Replication" is not a recognized medical term. It appears to be related to the field of molecular biology, specifically in the study of DNA replication and gene expression. However, I am an assistant trained to assist with general knowledge questions and not a medical professional. Therefore, I would recommend consulting a reliable medical source or speaking with a healthcare provider for accurate information regarding this term.
Ligase Chain Reaction (LCR) is a highly specific and sensitive method used in molecular biology for the detection of point mutations or small deletions or insertions in DNA. It is an enzymatic reaction-based technique that relies on the repeated ligation of adjacent oligonucleotide probes to form a continuous strand, followed by thermal denaturation and reannealing of the strands.
The LCR process involves the use of a thermostable ligase enzyme, which catalyzes the formation of a phosphodiester bond between two adjacent oligonucleotide probes that are hybridized to complementary sequences in the target DNA. The oligonucleotides are designed to have a gap at the site of the mutation or deletion/insertion, such that ligation can only occur if the probe sequences match perfectly with the target DNA.
After each round of ligation and denaturation, the reaction mixture is subjected to PCR amplification using primers flanking the region of interest. The amplified products are then analyzed for the presence or absence of ligated probes, indicating the presence or absence of the mutation or deletion/insertion in the target DNA.
LCR has been widely used in diagnostic and research applications, including the detection of genetic diseases, infectious agents, and cancer-associated mutations. However, it has largely been replaced by other more sensitive and high-throughput methods such as real-time PCR and next-generation sequencing.
'Chlamydia trachomatis' is a species of bacterium that is the causative agent of several infectious diseases in humans. It is an obligate intracellular pathogen, meaning it can only survive and reproduce inside host cells. The bacteria are transmitted through sexual contact, and can cause a range of genital tract infections, including urethritis, cervicitis, pelvic inflammatory disease, and epididymitis. In women, chlamydial infection can also lead to serious complications such as ectopic pregnancy and infertility.
In addition to genital infections, 'Chlamydia trachomatis' is also responsible for two other diseases: trachoma and lymphogranuloma venereum (LGV). Trachoma is a leading cause of preventable blindness worldwide, affecting mostly children in developing countries. It is spread through contact with contaminated hands, clothing, or eye secretions. LGV is a sexually transmitted infection that can cause inflammation of the lymph nodes, rectum, and genitals.
'Chlamydia trachomatis' infections are often asymptomatic, making them difficult to diagnose and treat. However, they can be detected through laboratory tests such as nucleic acid amplification tests (NAATs) or culture. Treatment typically involves antibiotics such as azithromycin or doxycycline. Prevention measures include safe sex practices, regular screening for STIs, and good hygiene.
Chlamydia infections are caused by the bacterium Chlamydia trachomatis and can affect multiple body sites, including the genitals, eyes, and respiratory system. The most common type of chlamydia infection is a sexually transmitted infection (STI) that affects the genitals.
In women, chlamydia infections can cause symptoms such as abnormal vaginal discharge, burning during urination, and pain in the lower abdomen. In men, symptoms may include discharge from the penis, painful urination, and testicular pain or swelling. However, many people with chlamydia infections do not experience any symptoms at all.
If left untreated, chlamydia infections can lead to serious complications, such as pelvic inflammatory disease (PID) in women, which can cause infertility and ectopic pregnancy. In men, chlamydia infections can cause epididymitis, an inflammation of the tube that carries sperm from the testicles, which can also lead to infertility.
Chlamydia infections are diagnosed through a variety of tests, including urine tests and swabs taken from the affected area. Once diagnosed, chlamydia infections can be treated with antibiotics such as azithromycin or doxycycline. It is important to note that treatment only clears the infection and does not repair any damage caused by the infection.
Prevention measures include practicing safe sex, getting regular STI screenings, and avoiding sharing towels or other personal items that may come into contact with infected bodily fluids.
Gonorrhea is a sexually transmitted infection (STI) caused by the bacterium Neisseria gonorrhoeae, also known as "gono" bacteria. It can infect various parts of the body including the genitals, rectum, and throat. The bacteria are typically transmitted through sexual contact with an infected person.
Symptoms may vary but often include abnormal discharge from the genitals or rectum, painful or burning sensations during urination, and in women, vaginal bleeding between periods. However, many people with gonorrhea do not develop symptoms, making it essential to get tested regularly if you are sexually active with multiple partners or have unprotected sex.
If left untreated, gonorrhea can lead to severe complications such as pelvic inflammatory disease (PID) in women and epididymitis in men, which may result in infertility. In rare cases, it can spread to the bloodstream and cause life-threatening conditions like sepsis.
Gonorrhea is curable with appropriate antibiotic treatment; however, drug-resistant strains of the bacteria have emerged, making accurate diagnosis and effective treatment increasingly challenging. Prevention methods include using condoms during sexual activity and practicing safe sex habits.
Neisseria gonorrhoeae is a species of gram-negative, aerobic diplococcus that is the etiologic agent of gonorrhea, a sexually transmitted infection. It is commonly found in the mucous membranes of the reproductive tract, including the cervix, urethra, and rectum, as well as the throat and eyes. The bacterium can cause a range of symptoms, including discharge, burning during urination, and, in women, abnormal menstrual bleeding. If left untreated, it can lead to more serious complications, such as pelvic inflammatory disease and infertility. It is important to note that N. gonorrhoeae has developed resistance to many antibiotics over time, making treatment more challenging. A culture or nucleic acid amplification test (NAAT) is used for the diagnosis of this infection.
Bacterial DNA refers to the genetic material found in bacteria. It is composed of a double-stranded helix containing four nucleotide bases - adenine (A), thymine (T), guanine (G), and cytosine (C) - that are linked together by phosphodiester bonds. The sequence of these bases in the DNA molecule carries the genetic information necessary for the growth, development, and reproduction of bacteria.
Bacterial DNA is circular in most bacterial species, although some have linear chromosomes. In addition to the main chromosome, many bacteria also contain small circular pieces of DNA called plasmids that can carry additional genes and provide resistance to antibiotics or other environmental stressors.
Unlike eukaryotic cells, which have their DNA enclosed within a nucleus, bacterial DNA is present in the cytoplasm of the cell, where it is in direct contact with the cell's metabolic machinery. This allows for rapid gene expression and regulation in response to changing environmental conditions.
Keratin-19 is a type I acidic keratin that is primarily expressed in simple epithelia, such as the gastrointestinal tract, respiratory tract, and epidermal appendages (e.g., hair follicles, sweat glands). It plays an essential role in maintaining the structure and integrity of these tissues by forming intermediate filaments that provide mechanical support to cells.
Keratin-19 is often used as a marker for simple epithelial differentiation and has been implicated in various pathological conditions, including cancer progression and metastasis. Mutations in the KRT19 gene, which encodes keratin-19, have been associated with certain genetic disorders, such as epidermolysis bullosa simplex, a blistering skin disorder.
In summary, Keratin-19 is an important structural protein expressed in simple epithelia that plays a crucial role in maintaining tissue integrity and has implications in various pathological conditions.
DNA primers are short single-stranded DNA molecules that serve as a starting point for DNA synthesis. They are typically used in laboratory techniques such as the polymerase chain reaction (PCR) and DNA sequencing. The primer binds to a complementary sequence on the DNA template through base pairing, providing a free 3'-hydroxyl group for the DNA polymerase enzyme to add nucleotides and synthesize a new strand of DNA. This allows for specific and targeted amplification or analysis of a particular region of interest within a larger DNA molecule.
A base sequence in the context of molecular biology refers to the specific order of nucleotides in a DNA or RNA molecule. In DNA, these nucleotides are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, uracil (U) takes the place of thymine. The base sequence contains genetic information that is transcribed into RNA and ultimately translated into proteins. It is the exact order of these bases that determines the genetic code and thus the function of the DNA or RNA molecule.
Bacteriological techniques refer to the various methods and procedures used in the laboratory for the cultivation, identification, and study of bacteria. These techniques are essential in fields such as medicine, biotechnology, and research. Here are some common bacteriological techniques:
1. **Sterilization**: This is a process that eliminates or kills all forms of life, including bacteria, viruses, fungi, and spores. Common sterilization methods include autoclaving (using steam under pressure), dry heat (in an oven), chemical sterilants, and radiation.
2. **Aseptic Technique**: This refers to practices used to prevent contamination of sterile materials or environments with microorganisms. It includes the use of sterile equipment, gloves, and lab coats, as well as techniques such as flaming, alcohol swabbing, and using aseptic transfer devices.
3. **Media Preparation**: This involves the preparation of nutrient-rich substances that support bacterial growth. There are various types of media, including solid (agar), liquid (broth), and semi-solid (e.g., stab agar). The choice of medium depends on the type of bacteria being cultured and the purpose of the investigation.
4. **Inoculation**: This is the process of introducing a bacterial culture into a medium. It can be done using a loop, swab, or needle. The inoculum should be taken from a pure culture to avoid contamination.
5. **Incubation**: After inoculation, the bacteria are allowed to grow under controlled conditions of temperature, humidity, and atmospheric composition. This process is called incubation.
6. **Staining and Microscopy**: Bacteria are too small to be seen with the naked eye. Therefore, they need to be stained and observed under a microscope. Gram staining is a common method used to differentiate between two major groups of bacteria based on their cell wall composition.
7. **Biochemical Tests**: These are tests used to identify specific bacterial species based on their biochemical characteristics, such as their ability to ferment certain sugars, produce particular enzymes, or resist certain antibiotics.
8. **Molecular Techniques**: Advanced techniques like PCR and DNA sequencing can provide more precise identification of bacteria. They can also be used for genetic analysis and epidemiological studies.
Remember, handling microorganisms requires careful attention to biosafety procedures to prevent accidental infection or environmental contamination.
Urine is a physiological excretory product that is primarily composed of water, urea, and various ions (such as sodium, potassium, chloride, and others) that are the byproducts of protein metabolism. It also contains small amounts of other substances like uric acid, creatinine, ammonia, and various organic compounds. Urine is produced by the kidneys through a process called urination or micturition, where it is filtered from the blood and then stored in the bladder until it is excreted from the body through the urethra. The color, volume, and composition of urine can provide important diagnostic information about various medical conditions.
Specimen handling is a set of procedures and practices followed in the collection, storage, transportation, and processing of medical samples or specimens (e.g., blood, tissue, urine, etc.) for laboratory analysis. Proper specimen handling ensures accurate test results, patient safety, and data integrity. It includes:
1. Correct labeling of the specimen container with required patient information.
2. Using appropriate containers and materials to collect, store, and transport the specimen.
3. Following proper collection techniques to avoid contamination or damage to the specimen.
4. Adhering to specific storage conditions (temperature, time, etc.) before testing.
5. Ensuring secure and timely transportation of the specimen to the laboratory.
6. Properly documenting all steps in the handling process for traceability and quality assurance.
Group B streptococcal infection
Loop-mediated isothermal amplification
Viability PCR
Nicking enzyme amplification reaction
NASBA (molecular biology)
Bartonella quintana
Aminoallyl nucleotide
Epidemiology of Hepatitis D
Cycling probe technology
Richard A. Collins
Karenia brevis
Polymerase chain reaction inhibitors
Female genital disease
Naat (disambiguation)
Recombinase polymerase amplification
NAA
Gardnerella vaginalis
Rolling circle replication
Primer dimer
Transcription-mediated amplification
Chlamydia antibodies
Respiratory syncytial virus
Touchdown polymerase chain reaction
Multiple displacement amplification
National TB Elimination Program (India)
Nucleic acid test
Branched DNA assay
Microbial ecology
Bio-MEMS
Nucleic acid methods
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Polymerase Chain Reaction ProtocolLoop-mediated isot5
- If we take loop-mediated isothermal amplification (LAMP) as an example, again we find much development towards compatibility with diagnostic applications over the years. (ttp.com)
- Loop-mediated isothermal amplification (LAMP), an isothermal nucleic acid amplification technique, has been extensively used in many areas such as food safety and clinic diagnosis. (scirp.org)
- Advances in nucleic acid amplification techniques mean that it is now possible to test for Neisseria meningitidis DNA using Loop-mediated-isothermal AMPlification (LAMP). (qub.ac.uk)
- Ms. Pennisi, a PhD student working as part of a multidisciplinary at the department of infectious disease and Centre for Bioinspired Technology at Imperial College, London, developed loop-mediated isothermal amplification (LAMP) assays to detect for the first time host RNA signatures on a nucleic acid-based point-of-care handheld system to discriminate bacterial from viral infection. (the-hospitalist.org)
- Tests which detect active infection, such as quantitative real-time polymerase chain reaction (qPCR), loop-mediated isothermal amplification (LAMP), or antigen ELISA, could be used as tools to monitor active asymptomatic infection and quickly identify areas with increasing active transmission. (holyexperiment.org)
Assays9
- This contractor will provide limited coverage for Gastrointestinal Pathogen (GIP) molecular assays identified by multiplex nucleic acid amplification tests (NAATs). (cms.gov)
- include light microscopy, immunochromatographic lateral flow assays (known as rapid diagnostic tests, RDTs), serology, fluorescence microscopy and nucleic acid amplification techniques (NATs), such as PCR and isothermal amplification. (biomedcentral.com)
- Standardization of hepatitis E virus (HEV) nucleic acid amplification technique-based assays: an initial study to evaluate a panel of HEV strains and investigate laboratory performance. (cdc.gov)
- For HPV testing, self-sampling instead of clinician-sampling has proven to be equally accurate, in particular for assays that use nucleic acid amplification techniques. (frontiersin.org)
- Because of the improved culture methods and sensitive nucleic acid amplification assays developed in recent years, Kingella kingae , a gram-negative coccobacillus of the Neisseriaceae family, is increasingly recognized as an invasive pathogen of early childhood. (cdc.gov)
- Sherlock Biosciences will integrate the method with its CRISPR-based Sherlock platform with the aim of developing diagnostic assays that can detect pathogen- or disease-related nucleic acids at the point-of-need without instruments. (labpulse.com)
- Many assays that are suitable for use in low-resource settings detect limiting amounts of target nucleic acids, but their results also need to be made visible to the naked eye to be useful at the point-of-need. (labpulse.com)
- Most nucleic acid-detecting diagnostic assays, including currently available SARS-CoV-2 PCR tests, are performed on qPCR instruments that cycle between defined temperatures. (labpulse.com)
- The Wyss Institute noted that its ambient amplification method now could introduce an unprecedented robustness into molecular detection assays because it enables maximum amplification without heat activation and in a range of temperatures, opening up various opportunities for point-of-need testing in different temperature and geographical settings. (labpulse.com)
NAAT3
- There has been a gradual shift toward new techniques and methods of diagnosis of viral infections, including nucleic acid amplification test (NAAT), which have shown promising results with improved accuracy and reduced time of diagnosis. (transparencymarketresearch.com)
- In terms of test, the global virus diagnostic test kits market can be categorized into traditional tests (cell culture test, complement fixation test (CFT), Haemagglutination inhibition test, and others) and rapid tests (nucleic acid amplification test (NAAT), immunoassay test, next generation sequencing (NGS), and mass spectrometry). (transparencymarketresearch.com)
- C. trachomatis can be isolated in culture or identified by nucleic acid amplification tests (NAAT) and immunofluorescence techniques, and testing should be done when it is readily available. (msdmanuals.com)
Detection20
- On September 30, 1999, the Food and Drug Administration approved a reformulated Amplified Mycobacterium Tuberculosis Direct Test* (MTD) (Gen-Probe ® , San Diego, California) for detection of Mycobacterium tuberculosis in acid-fast bacilli (AFB) smear-positive and smear-negative respiratory specimens from patients suspected of having tuberculosis (TB). (cdc.gov)
- MTD and one other nucleic acid amplification (NAA) test, the Amplicor ® Mycobacterium Tuberculosis Test (Amplicor) (Roche ® Diagnostic Systems, Inc., Branchburg, New Jersey), previously had been approved for the direct detection of M. tuberculosis in respiratory specimens that have positive AFB smears. (cdc.gov)
- abstract = "Isothermal amplification-based techniques such as the rolling circle amplification have been successfully employed for the detection of nucleic acids, protein amounts, or other relevant molecules. (au.dk)
- Here, the rolling circle amplification method, termed rolling circle enhanced enzyme activity detection (REEAD) assay that allows for the quantitative measurement of topoisomerase 1 (TOP1) activity in a simple, fast, and gel-free manner is presented.By cleaving and ligating a specially designed DNA substrate, TOP1 converts a DNA oligonucleotide into a closed circle, which becomes the template for rolling circle amplification, yielding ~103 tandem repeat rolling circle products. (au.dk)
- We also discuss how robust, sensitive, and specific nucleic acid detection could be obtained when combined with the novel CRISPR/Cas system. (intechopen.com)
- PCR is still the go-to method in the molecular diagnostics industry but, with the rise of close-to-patient testing, isothermal amplification methods with their low power and potentially easier detection schemes look increasingly attractive. (ttp.com)
- Isothermal amplification methods can thus offer the same multiplexing possibilities and ease of diagnostic detection as PCR, and, perhaps surprisingly, a further development went back to basics and re-introduced a colorimetric version of pH-dependent detection, allowing a simple visual detection. (ttp.com)
- artus HBV Kits are based on the amplification and simultaneous detection of a specific region of the HBV genome using real-time PCR. (qiagen.com)
- Up to now, the most effective and sensitive techniques used for GMO detection are based on polymerase chain reaction (PCR). (scirp.org)
- Among them, mRNA typing with nucleic acid sequence based amplification (NASBA) [ 11 - 13 ] and flow cytometry (mRNA-Flow-FISH) techniques for E6/E7 HPV mRNA detection have been enrolled in cancer and precancerous lesions' detection with promising results in increasing PPV and reducing unnecessary recalls and referrals to colposcopy [ 14 - 18 ]. (hindawi.com)
- Recombinase Polymerase Amplification (RPA) for the Rapid Isothermal Detection of Spongospora subterranea f. sp. (oregonstate.edu)
- The amplification of specific nucleic acid sequences with high specificity and sensitivity is an essential technique for pathogen detection. (oregonstate.edu)
- Oligonucleotide primers were designed for amplification that target the internal transcribed spacer 1 (ITS1) region and the coat protein readthrough (CP-RT) domain for the detection of Sss and PMTV, respectively. (oregonstate.edu)
- The advent of the assay for nucleic acid amplification and detection enables clinicians to initiate and monitor antiviral therapy whilst allowing basic scientists to carry out studies on HBV biology. (degruyter.com)
- CSIC has developed a signal amplification method for single-stranded nucleic acids detection through self-sustained loop cleavage of DNA:DNA duplexes or RNA:DNA hybrids by the Fokl enzyme. (innoget.com)
- The design of new RNA direct detection approaches based on signal augmentation that avoids problems derived from nucleic acid amplification procedures in complex samples is still a challenge. (innoget.com)
- It improves the detection limit of target molecules by 2 to 4 orders of magnitude when coupled with isothermal amplification of nucleic acids techniques. (innoget.com)
- Understanding the comparative characteristics of different media in detection of mycobacteria from specimens treated with standard techniques in a single laboratory may help to explain differences in response to treatment found between different sites and different studies that use the different media. (case.edu)
- HIV infection can be diagnosed based on detection of antibodies that are directed against the proteins encoded by the 3 major genes, the detection of the p24 antigen, the viral nucleic acid, and, finally, by means of culturing the virus. (medscape.com)
- Since this test can amplify the small quantity of Nucleic acid it is considered the test of the high accuracy and high sensitivity for detection of the viral infection [4,5]. (biomedres.us)
Pathogen2
- Conventional technique is further segmented into gram-stain and pathogen culturing. (prnewswire.co.uk)
- Our newly engineered amplification method allows one to amplify pathogen or disease-reporting nucleic acid molecules at ambient temperatures, which is an important step in this direction. (labpulse.com)
Detect6
- Simple and Fast Rolling Circle Amplification-Based Detect. (au.dk)
- To date, many techniques have been developed to detect nucleic acids. (intechopen.com)
- Molecular Diagnostics: Molecular diagnostic techniques involve analyzing DNA, RNA, and proteins to detect genetic variations, identify infectious agents, and assess disease markers. (marketsandmarkets.com)
- Godbey said most lab-processed tests will detect the variants, and those tests that use a nucleic acid amplification technique apparently do detect known variants. (medpagetoday.com)
- Labs use nucleic acid amplification techniques to detect and quantify CMV and thereby enable timely treatment. (medtechdive.com)
- Polymerase chain reaction (PCR) is a relatively fast and simple laboratory technique that can detect a nucleic acid fragment by the amplification of small segments of DNA. (myhealth.gov.my)
NAATs3
- Several nucleic acid amplification tests (NAATs) are US Food and Drug Administration-cleared for detecting urogenital Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (GC) infection, but they have not been adequately evaluated for the relatively common oropharyngeal or rectal CT and GC infections in men who have sex with men (MSM). (nih.gov)
- and Nucleic Acid Amplification Techniques (NAATs). (wikipedia.org)
- The information in this article contains billing, coding or other guidelines that complement the Local Coverage Determination (LCD) for Foodborne Gastrointestinal Panels Identified by Multiplex Nucleic Acid Amplification (NAATs) (L37364). (cms.gov)
Isothermal amplification method1
- Recombinase polymerase amplification (RPA) is a rapid isothermal amplification method. (oregonstate.edu)
Polymerase chain re2
- Polymerase chain reaction (PCR), gene sequencing, microarrays, and other molecular techniques are used to identify specific genetic mutations, infectious agents, and biomarkers associated with diseases. (marketsandmarkets.com)
- Polymerase chain reaction (PCR) is an extremely useful technique for specific in vitro amplification of nucleic acids and has a large number of applications. (asm.org)
Strand displacement amplification2
- DNA strand displacement amplification is carried out under isothermal conditions and therefore does not need expensive instruments. (intechopen.com)
- NASBA (Nucleic Acid Sequence Based Amplification) and Strand Displacement Amplification were introduced at the same time, and the former multiplexed in 1999. (ttp.com)
Purification6
- Partitioning can improve the purification of one of two replicates, which in turn makes amplification more efficient. (ibtimes.com)
- Gentra is a privately held leading developer, manufacturer and supplier of non-solid phase nucleic acid purification products, providing both consumables and automated platforms. (webwire.com)
- Gentra is focused on the niche market of nucleic acid purification from large scale blood samples up to 10 ml. (webwire.com)
- In addition, Gentra has developed the Purescript , VersageneTM and Generation line of nucleic acid purification consumables. (webwire.com)
- Gentra is a well established leader in nucleic acid purification consumables and automation for important niche markets such as biobanking and DNA archiving, where larger sample volumes and long term stability are important for customers, said Peer M. Schatz, QIAGEN s Chief Executive Officer. (webwire.com)
- Gentra s portfolio of consumables and instruments for nucleic acid purification, as well as its strong reputation in an increasingly important market niche are a perfect fit for QIAGEN, he continued. (webwire.com)
Immunoassay1
- Biochemical technique is further segmented into enzyme immunoassay, agglutination and ELISA. (prnewswire.co.uk)
Hepatitis E vir1
- The reaction is stopped by adding a sulphuric acid solution and the OD of each well is read.The presence or absence of IgM antibodies to hepatitis E virus is determined by the ratio of the OD of each sample to the calculated cut-off value. (cdc.gov)
LAMP3
- Initially, LAMP was a pH-dependent precipitation assay, but the technique was later adapted for use with intercalating dye, allowing researchers to confirm specificity by post-reaction melting curve analysis. (ttp.com)
- In contrast, LAMP is considered difficult to design, requiring six primers for rapid amplification. (ttp.com)
- LAMP test is isothermal amplification technic uses single tube for amplification of DNAs and RNAs. (biomedres.us)
Diagnosis3
- These techniques provide detailed images that aid in the diagnosis and monitoring of various diseases and conditions. (marketsandmarkets.com)
- The invention, commercialized by Sequenom as its MaterniT21 test, created an alternative for prenatal diagnosis of fetal DNA that avoids the risks of widely-used techniques that took samples from the fetus or placenta. (justia.com)
- Highly sensitive qPCR was shown to be an effective technique for diagnosis of VL and monitoring of treatment response, and could be of value in an elimination setting [16]. (holyexperiment.org)
High specificity1
- The test has high sensitivity and high specificity because of the exponential amplification feature and 6 different sequences can be identified by 4 different primers simultaneously, respectively [11]. (biomedres.us)
Amplify2
- The RCA is able to amplify the nucleic acid 109 -fold signal amplification of each circle within 90 min. (biomedres.us)
- To eliminate the necessity for precise temperature cycling, biomedical researchers have developed so-called isothermal amplification methods that require heat to activate the amplifying enzymes, but then amplify nucleic acid sequences at a single tightly controlled temperature. (labpulse.com)
Vitro1
- In the early 1990s, Rolling Circle Amplification (RCA) was performed in vitro using small circular DNA amplification targets [2]. (ttp.com)
Sequence based1
- Molecular technique is further segmented into nucleic acid sequence based amplification and PCR. (prnewswire.co.uk)
Viral infections1
- First, transcription isothermal amplification techniques were employed to confirm bacterial and viral infections. (the-hospitalist.org)
Tests4
- Now that streamlined assay validation procedures and GMP-validated Nucleic Acid Amplification Techniques (NAT) tests are readily available, these methods provide manufacturers with the confidence required in production and batch release of products. (sgs.com)
- BioHelix, purchased by Quidel in 2013, offer a hand-held molecular test based in its proprietary Helicase-Dependent Amplification (HDA) while Abbott's Alere-I offer a panel of CLIA-waiver tests based on isothermal Nicking Enzyme Amplification Reaction (NEAR) technology. (ttp.com)
- Clinical diagnostics refers to the process of identifying, diagnosing, and monitoring diseases or medical conditions in patients through various laboratory tests, imaging techniques, and other diagnostic tools. (marketsandmarkets.com)
- This study evaluates routine microbiological and novel molecular markers of patient response to TB treatment, including several types of nucleic acid amplification (NAA) tests. (case.edu)
Methods6
- Depending on the nucleotide incorporation during the amplification, there is the possibility of different readout methods, from fluorescence to chemiluminescence to colorimetric. (au.dk)
- Indeed, in the years since, tens of isothermal amplification methods have not only been invented, but also developed towards diagnostic applicability. (ttp.com)
- Other isothermal amplification methods have been introduced since. (ttp.com)
- Imaging Techniques: Diagnostic imaging methods, such as X-rays, computed tomography (CT) scans, magnetic resonance imaging (MRI), ultrasound, and nuclear medicine scans, are used to visualize internal structures and identify abnormalities in the body. (marketsandmarkets.com)
- Each one of these techniques has its own performance, limitations and advantages, thus a combinatorial approach via computational intelligence methods could exploit the benefits of each method and produce more accurate results. (hindawi.com)
- Additionally, new techniques and recent developments in the methods applied for virus testing have led to the introduction of new rapid diagnostic test kits. (transparencymarketresearch.com)
Enzyme1
- PCR depends on amplification of the DNA strand using polymerase enzyme. (biomedres.us)
Diagnostics2
- Based on techniques, the infectious diagnostics disease market is segmented into conventional techniques, biochemical techniques and molecular techniques. (prnewswire.co.uk)
- Now, with the progression of diagnostics out of the lab and closer to the patient, the potential advantages of isothermal amplification techniques offer an increasingly interesting alternative. (ttp.com)
Enzymes2
- These biosensors are complexes of graphene oxide and biomacromolecules, including enzymes such as glucose oxidase, horseradish peroxidase, laccase, and nucleic acids such as DNA and RNA. (intechopen.com)
- Other techniques, such as RPA, contain additional enzymes, polyethylene glycol and a host of other additives. (ttp.com)
Samples2
- In addition, many customers in biobanking and DNA archiving use QIAGEN s whole genome amplification technology (WGA) to replicate and thereby immortalize precious samples. (webwire.com)
- This document provides evidence-based clinical practice guidelines on the diagnostic utility of nucleic acid-based testing of respiratory samples for viral pathogens other than influenza in adults with suspected community-acquired pneumonia (CAP). (guidelinecentral.com)
Enables2
- Sherlock Biosciences has inked a worldwide license agreement with Harvard University's Office of Technology Development for technology that enables the amplification of nucleic acid molecules at ambient temperatures, the organizations said on Monday. (labpulse.com)
- The acquisition enables Sherlock to combine its CRISPR, synthetic biology, and artificial intelligence technologies with Sense's instrument-free diagnostic hardware and rapid molecular amplification chemistries. (labpulse.com)
Genetic1
- Nucleic acid amplification has been the choice technique for detecting genetic markers for viruses and bacteria for years. (ibtimes.com)
Reaction4
- To test for inhibitors of MTD, spike an aliquot of the lysated sputum sample with lysed M. tuberculosis (approximately 10 organisms per reaction, or an equivalent amount of M. tuberculosis rRNA) and repeat the test starting with amplification. (cdc.gov)
- The reaction is stopped by adding a sulphuric acid solution and the OD of each well is read. (cdc.gov)
- As early as 1990, a review of target amplification systems for diagnostic applications concluded that techniques enjoying advantages such as "isothermal reaction … may eventually gain widespread use after further development" [1]. (ttp.com)
- The amplification reaction is then combined with microchip technology in the well of a portable point-of-care device named Lacewing. (the-hospitalist.org)
Method3
- Isothermal amplification is not a new concept or method. (ttp.com)
- So, why have isothermal approaches still not overtaken PCR as the go-to nucleic acid diagnostic method? (ttp.com)
- Applying a combination of known laboratory techniques to their discovery,they implemented a method for detecting the small fraction of paternally inherited cffDNA in maternal plasma or serum to determine fetal characteristics, such as gender. (justia.com)
Advantages2
Specific1
- 5'-monophosphate deaminase from Streptomyces murinus, D-allulose 3-epimerase from Arthrobacter globiformis expressed in Escherichia coli , carbohydrate-derived fulvic acid, jagua (genipin-glycine) blue (Jagua blue), lipase from Mucor javanicus and phosphatidylinositol-specific phospholipase C expressed in Pseudomonas fluorescens ). (who.int)
Successfully1
- Moreover, it has been successfully coupled with isothermal amplification of nucleic acids techniques. (innoget.com)
Inhibition1
- In addition, the kits contains a second heterologous amplification system to identify possible PCR inhibition. (qiagen.com)
Infectious2
- Market driving factors responsible for the growth of infectious disease diagnostic market include growing incidences of infectious disease, emphasis on advanced molecular techniques in underdeveloped regions. (prnewswire.co.uk)
- Additionally, advanced sterilization techniques, infection prevention measures, and outbreak management protocols are crucial in preventing the spread of highly infectious diseases, such as COVID-19. (cbinsights.com)
Microarrays2
- Nowadays, there are molecular biology techniques providing information related to cervical cancer and its cause: the human Papillomavirus (HPV), including DNA microarrays identifying HPV subtypes, mRNA techniques such as nucleic acid based amplification or flow cytometry identifying E6/E7 oncogenes, and immunocytochemistry techniques such as overexpression of p16. (hindawi.com)
- Results then were evaluated using microarrays, reverse transcriptase PCR (RT-PCR), and the eLAMP to confirm comparability with preferred techniques. (the-hospitalist.org)
Pathogens1
- Nucleic acids, as encoding information for all forms of life, are excellent biomarkers for detecting pathogens, hereditary diseases, and cancers. (intechopen.com)
Diagnostic accuracy1
- In this article we propose a clinical decision support system (CDSS), composed by artificial neural networks, intelligently combining the results of classic and ancillary techniques for diagnostic accuracy improvement. (hindawi.com)
Rapid1
- The rapid evolution of molecular biology techniques has a significant impact on laboratory medicine. (degruyter.com)
Sensitive1
- Nucleic acid amplification testing of a first-catch urine specimen is the most sensitive test (in a male) for gonorrhea or chlamydia. (medscape.com)
Laboratory techniques1
- A summary of the laboratory techniques for GBS identification is depicted in Ref 18. (wikipedia.org)
Culture1
- R.I. FRESHNEY: "Culture of Animal Cells: A Manual of Basic Technique", 1987, ALAN R. LISS, INC. (sumobrain.com)
Signal1
- It translates the nucleic acid amplification signal into a quantitative electrochemical signal without the need for a thermal cycler. (the-hospitalist.org)
Single1
- Once that's done, PCR amplification can follow , and all that's required is a single pipetting operation. (ibtimes.com)
Simple1
- This technique is quicker than traditional PCR techniques and can be performed using simple equipment. (qub.ac.uk)
