Platforms.

The advent of DNA sequencing technologies and the various applications that can be performed will have a dramatic effect on medicine and healthcare in the near future. There are several DNA sequencing platforms available on the market for research and clinical use. Based on the medical laboratory scientist or researcher's needs and taking into consideration laboratory space and budget, one can chose which platform will be beneficial to their institution and their patient population. Although some of the instrument costs seem high, diagnosing a patient quickly and accurately will save hospitals money with fewer hospital stays and targeted treatment based on an individual's genetic make-up. By determining the type of disease an individual has, based on the mutations present or having the ability to prescribe the appropriate antimicrobials based on the knowledge of the organism's resistance patterns, the clinician will be better able to treat and diagnose a patient which ultimately will improve patient outcomes and prognosis.

Applications.

Next generation sequencing platforms and the applications that are offered have revolutionized the way a physician will treat and monitor a patient based on the individual's own genetic make-up. Whether whole genome sequencing, exome sequencing, or targeted sequencing is performed, the information generated must be analyzed, interpreted, and reported correctly. Since the various platforms and application panels are not FDA cleared (with the exception of the Illumina MiSeqDx Cystic Fibrosis Clinical Sequencing Assay and the Illumina MiSeqDx Cystic Fibrosis 139-Variant Assay) clinical laboratorians are faced with the challenge of standardizing and validating the various panels and platforms for appropriate quality management. Therefore, the American College of Medical Genetics and Genomics published guidelines for ordering, test development, validation and reporting of genetic information. These guidelines should be followed by all laboratorians performing NGS to ensure quality results and to provide proper interpretation of all genomic variants identified.

Personalized medicine and ethics.

An entire series could be dedicated to the topic of ethics in personalized medicine. Due to the advancements in NGS and genetic testing, personalized medicine is no longer something that will occur in the future, the reality is upon us now. Sequencing an individual's genome can have a substantial impact on the patient's treatment and overall quality of life. However, this can open "Pandora's box" especially if an individual does not want to know the information obtained. In addition, will insurance companies require genetic testing in order to pay for a targeted treatment? If the patient refuses to have the genetic testing, will they have to pay for their treatment out of pocket? In the human interest story presented, the researcher and his team discovered over activity of the FTL3 protein through RNA sequencing which resulted in rapid proliferation of his leukemic cells. He identified a drug marketed for advanced kidney cancer which was a FTL3 inhibitor. However, his insurance company refused to pay for the drug because it was not a known treatment for his condition of ALL. He incurred numerous out of pocket expenses in order to go into remission. Was it unethical for the insurance company to not pay for a treatment that ultimately worked but was not marketed or FDA cleared for his type of leukemia? There are so many questions and concerns when personalized medicine is implemented. Only time will tell the effects next generation sequencing and its role in personalized medicine will have in the future.

Updates in immunoassays: bacteriology.

There are many immunoassays available that provide rapid, accurate and sensitive results. The intent of this article was to provide a brief overview of some of the products and methodologies available for clinical use and to discuss some of the principles behind the methodology and instrumentation. In the area of infectious disease, the use of immunoassays ensures rapid turnaround times that will result in the administration of prompt, accurate treatment for the patient. Ultimately, this will improve overall patient outcomes while possibly decreasing the costs associated with increased hospital stay. In conclusion, immunoassays are essentially easy to perform, cost-effective, produce highly sensitive and specific results, and allow the medical laboratory professional the ability to report accurate results in a timely manner.

Updates in immunoassays: virology.

Virus identification is a challenge to the clinical microbiologist since growing viruses in traditional cell culture is labor intensive, time consuming, and subject to contamination. The advent of rapid and automated immunoassays has eliminated this problem by generating positive results in minutes to hours. For example, testing for infectious mononucleosis can yield a positive result in 3-8 minutes as seen with the Beckman Coulter, Inc. ICON Mono test or in 5-15 minutes with the MONO Mononucleosis Rapid Test Device marketed by ACON Laboratories, Inc. Fully automated immunoassay analyzers provide fast, accurate, sensitive results that aid in a prompt and accurate diagnosis for the patient. Turnaround times are shortened, allowing for timely medical intervention and treatment. The priority in any hospital or medical facility is to treat the patient as quickly and appropriately as possible. By using immunoassays, clinical laboratory professionals are able to report out correct results in a timely manner, ensuring overall positive patient outcomes and improved quality of healthcare.

Updates in immunoassays: parasitology.

Although most clinical laboratories use microscopy and routine O&P procedures when identifying parasitic infections, there are several parasites that are better detected through serological means. Toxoplasma, Giardia, and Cryptosporidium were discussed along with immunoassays used for their detection. Immunoassays provide quick results and are less labor intensive than specimen concentration and slide preparation for microscopic examination. These assays are easy to use and provide sensitive and specific results. Some clinical laboratories no longer perform O&Ps in house and refer specimens to reference laboratories for evaluation. By using immunoassays, some of the more common parasites can be identified in a timely manner reducing turn-around times. Some controversy exists over the use of IIF and EIA tests used for ANA testing along with measuring CRPs and PCT as predictors of bacterial sepsis and septic shock. Regardless of the methodology discussed in this series of articles, there are pros and cons to the various immunoassays available. Determining the most appropriate assay based on patient population and volume is governed by the institution and its patients' needs. In conclusion, immunoassays, whether manual or automated, are easy to use, cost effective and allow the medical laboratory professional to provide quick and accurate results to the clinician so the most appropriate treatment can be administered to the patient. The ultimate goal of healthcare professionals is to provide the highest quality of medical care in a timely manner. The use of immunoassays in the clinical laboratory allows the healthcare team to successfully achieve this goal.

Molecular virology in the clinical laboratory.

As one can see by the tests listed at www.amp.org, molecular diagnostic techniques have enabled the laboratory professionals to play an integral role in the identification and quantitation of viral infectious agents. Viral loads can be determined for HIV, HBV, and HCV using a variety of molecular methods such as real-time PCR, TMA, NASBA, and bDNA. Determining the amount of viral particles in a sample can not only monitor the status and progression of the disease, but can also guide recommendations for antiviral therapy. Other assays listed include cytomegalovirus, enterovirus, and human metapneumovirus detection, HPV testing, influenza and respiratory virus panels, and West Nile virus detection in blood donations using a variety of molecular methodologies. The use of molecular methodologies in the detection of viral pathogens has grown at an astounding rate, especially in the past two decades. It is now widely accepted that PCR is the "gold standard" for nucleic acid detection in the clinical laboratory as well as in research facilities. This article only touched on some of the common, widely used assays and platforms used in the identification process. With more and more assays being developed, the cost behind molecular testing has decreased since there are more competitors on the market. At one point, laboratorians may have thought of routine molecular testing as the wave of the future. It is obvious the future is upon us. Molecular diagnostics has become part of the daily, routine workload in most clinical laboratories. The advent of fully automated systems with faster turn around times has given laboratory professionals the tools necessary to report out accurate and sensitive results to clinicians who can ultimately improve patient care and outcomes by rendering a correct and rapid diagnosis.

Molecular bacteriology in the clinical laboratory.

Identifying organisms in a timely manner has always been one of the greatest challenges for clinical microbiologists. Healthcare providers want rapid results in order to prescribe the appropriate antimicrobial therapy and improve patient care. Some of the more virulent pathogens such as MRSA, VRE, and MTB must be identified as quickly and accurately as possible in order to prevent the spread of the disease to other patients and employees. The need for rapid, molecular methodologies in the clinical bacteriology laboratory was essential to improve patient outcomes. Organisms that use to take days or weeks to identify are now detected in hours or within the same day. The advent of molecular assays has enabled clinical laboratory scientists to report out accurate, sensitive and timely results confirming the critical role they play on the healthcare team.

Molecular diagnostics in the public health laboratories.

At the New Jersey Department of Health and Senior Services laboratory, clinical laboratory scientists receive specimens from various health care facilities and clinics in the state, and identify and confirm organisms of particular health concern in a rapid and timely manner. Most of the assays performed are specialized tests that are not done routinely in the clinical laboratories. Identifying and monitoring infectious agents such as West Nile virus, Influenza 2009 A (H1N1) pdm, Mycobacterium tuberculosis, enteric organisms, etc. is part of the daily workload in the Public Health Laboratories. In addition, surveillance programs are in place to control the spread of various infectious agents and to aid in investigative epidemiologic purposes. The volume of samples and workload demands can be overwhelming especially in peak months such as summer (WNV) or winter (Influenza A) therefore, it was necessary to implement molecular diagnostics and robotic technology to aid in high throughput analysis. Molecular assays have become the "norm" not only in the public health laboratories but in most clinical microbiology laboratories as well. The use of molecular diagnostics has proven advantageous resulting in accurate results, decreased turn around times, and overall better patient care and outcomes.

Yersinia pestis: still a plague in the 21st century.

Yersinia pestis, the causative agent of plague, is an aerobic, non-motile, gram-negative bacillus belonging to the family Enterobacteriacea. It is a zoonotic infection transmitted to humans via the bite of a flea. Three clinical forms of human plague exist: bubonic, pneumonic, and septicemic. Many important virulence factors associated with this organism are responsible for its extreme pathogenicity and high mortality rates. The bubonic form of plague is usually not transmitted human to human but the pneumonic form is--through inhalation of contaminated aerosol droplets. The pneumonic plague would be the form most likely implicated in the event of an intentional attack. Inhalation of aerosols can cause devastating consequences resulting in many casualties. Unless antibiotics are administered within 24 hours of the initial symptoms, death is inevitable. Its potential for use as a biological weapon is of major concern to public health officials.

Botulin toxin: a weapon in terrorism.

Clostridium botulinum, the causative agent of botulism is an anaerobic, spore forming gram-positive bacillus. C. botulinum causes three types of botulism; foodborne botulism, wound botulism, and infant botulism. Most strains of the bacterium produce a potent, muscle-paralyzing neurotoxin. Respiratory failure secondary to paralysis of the respiratory muscles can lead to death unless appropriate therapy is promptly initiated. Due to the severity and potency of this neurotoxin, its importance as a biological weapon is of major concern to public health officials.

Francisella tularensis: possible agent in bioterrorism.

Francisella tularensis, the causative agent of tularemia, is a highly infectious gram-negative coccobacillus. Due to its high infectivity it is of major concern to public health officials as a possible biological weapon. Although accidental exposure can occur through arthropod bites, handling infected animals, or breathing in aerosols, cases are usually isolated and contained. In the event of an intentional exposure such as in a bioterrorist attack, inhalation of aerosols can result in devastating consequences with much causality. Although a vaccine is available, sufficient quantities may not be readily accessible in an actual attack. Therefore, it is very important for both medical professionals and public health officials to be prepared to contain and control the situation should it actually occur.