Concepts, principles, and applications of selected molecular biology techniques in clinical biochemistry

Prospective assessment of FilmArray® technology for the rapid identification of yeast isolated from blood cultures

We prospectively assessed the ability of FilmArray® device to identify fungal species involved in bloodstream infections. It succeeded in identifying 85.7% of isolates. The automated readout of results enabled the rapid initiation of appropriate antifungal therapy. Thus, FilmArray® appeared as a reliable alternative diagnostic method for the most common yeast-like species.

Rapid identification of pathogens from positive blood cultures by multiplex polymerase chain reaction using the FilmArray system

Sepsis is a leading cause of death. Rapid and accurate identification of pathogens and antimicrobial resistance directly from blood culture could improve patient outcomes. The FilmArray® (FA; Idaho Technology, Salt Lake City, UT, USA) Blood Culture (BC) panel can identify >25 pathogens and 4 antibiotic resistance genes from positive blood cultures in 1 h. We compared a development version of the panel to conventional culture and susceptibility testing on 102 archived blood cultures from adults and children with bacteremia. Of 109 pathogens identified by culture, 95% were identified by FA. Among 111 prospectively collected blood cultures, the FA identified 84 (91%) of 92 pathogens covered by the panel. Among 25 Staphylococcus aureus and 21 Enterococcus species detected, FA identified all culture-proven methicillin-resistant S. aureus and vancomycin-resistant enterococci. The FA BC panel is an accurate method for the rapid identification of pathogens and resistance genes from blood culture.

FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection

The ideal clinical diagnostic system should deliver rapid, sensitive, specific and reproducible results while minimizing the requirements for specialized laboratory facilities and skilled technicians. We describe an integrated diagnostic platform, the "FilmArray", which fully automates the detection and identification of multiple organisms from a single sample in about one hour. An unprocessed biologic/clinical sample is subjected to nucleic acid purification, reverse transcription, a high-order nested multiplex polymerase chain reaction and amplicon melt curve analysis. Biochemical reactions are enclosed in a disposable pouch, minimizing the PCR contamination risk. FilmArray has the potential to detect greater than 100 different nucleic acid targets at one time. These features make the system well-suited for molecular detection of infectious agents. Validation of the FilmArray technology was achieved through development of a panel of assays capable of identifying 21 common viral and bacterial respiratory pathogens. Initial testing of the system using both cultured organisms and clinical nasal aspirates obtained from children demonstrated an analytical and clinical sensitivity and specificity comparable to existing diagnostic platforms. We demonstrate that automated identification of pathogens from their corresponding target amplicon(s) can be accomplished by analysis of the DNA melting curve of the amplicon.

Rare cancer cell analyzer for whole blood applications: automated nucleic acid purification in a microfluidic disposable card

One current challenge facing point-of-care cancer detection is that existing methods make it difficult, time consuming and too costly to (1) collect relevant cell types directly from a patient sample, such as blood and (2) rapidly assay those cell types to determine the presence or absence of a particular type of cancer. We present a proof of principle method for an integrated, sample-to-result, point-of-care detection device that employs microfluidics technology, accepted assays, and a silica membrane for total RNA purification on a disposable, credit card sized laboratory-on-card ('lab card") device in which results are obtained in minutes. Both yield and quality of on-card purified total RNA, as determined by both LightCycler and standard reverse transcriptase amplification of G6PDH and BCR-ABL transcripts, were found to be better than or equal to accepted standard purification methods.

Micropillar array chip for integrated white blood cell isolation and PCR

We report the fabrication of silicon chips containing a row of 667 pillars, 10 by 20 microm in cross-section, etched to a depth of 80 microm with adjacent pillars being separated by 3.5 microm. The chips were used to separate white blood cells from whole blood in less than 2 min and for subsequent PCR of a genomic target (eNOS). Chip fluid dynamics were validated experimentally using CoventorWare microfluidic simulation software. The amplicon concentrations were determined using microchip capillary electrophoresis and were >40% of that observed in conventional PCR tubes for chips with and without pillars. Reproducible on-chip PCR was achieved using white blood cell preparations isolated from whole human blood pumped through the chip.

Validation of Sixteen Leukemia and Lymphoma Cell Lines as Controls for Molecular Gene Rearrangement Assays

Background: Assays for rearrangement of the immunoglobulin, T-cell receptor, bcr/abl, and bcl-2 genes are valuable tools to aid in the diagnosis of leukemias and lymphomas and are now offered by many pathology laboratories. However, there is a lack of well-characterized and validated calibrators and positive controls for these assays. We therefore evaluated 16 readily available leukemia and lymphoma cell lines for their potential use as controls.

Methods: DNA and RNA were isolated from each cell line and analyzed by Southern blot and PCR or reverse transcription-PCR (RT-PCR). Rearrangements in the IgJH, IgJκ, TcR-β or TcR-γ, bcr/abl, and bcl-2 genes were detected by commercially available probes and primers. Cell lineages were confirmed by immunophenotyping.

Results: Immunoglobulin and T-cell receptor gene rearrangements were identified in five B- and three T-cell lines, respectively. Two cell lines tested positive for the bcr/abl gene, and one was positive for the bcl-2 gene rearrangement by Southern blot.

Conclusions: The 16 cell lines studied can be used as positive controls in molecular detection assays for gene rearrangements. The parallel processing of these cell lines with clinical samples can serve to quality control the experimental procedures from the first step of DNA or RNA extraction to the final step of result analysis.

Impact of Ultra-Sensitive technology and contemporary therapy on laboratory results

The introduction of ultra-sensitive labels for immunoassays has exposed some of the limitations inherent in them. Thus, for instance a major problem with acridinium esters used, as chemiluminescence label is the formation of the so called "pseudobases" at an alkaline pH, which if not suppressed can affect the rate of the chemiluminescence reaction. Chemiluminescence labels such as luminol can also be problematic when attached to antibodies and small molecules to the extent that the sensitivity of the assay can be reduced by the decrease in the intensity of chemiluminescence. The increased use of molecular methods such as polymerase chain reaction (PCR) and post PCR methods to study mutations have various pittalls, which if unrecognized and uncontrolled can lead to incorrect results and misinterpretation. Patients who are exposed to mouse immunoglobulins through imaging or therapeutic techniques can develop antibodies to mouse immunoglobulins (human anti-mouse antibodies or HAMA) which can be a major problem for non optimized immunoassays using murine monoclonal antibodies. The types of therapy such as anticoagulant used in anticoagulant therapy, blood substitute and drug therapy can impact on the measurements of some of the biochemical and other analytes. One must separate the transient, physiological effects introduced by therapy from long-term biochemical alterations due to disease.

The relevance of apolipoprotein E polymorphism to Alzheimer's disease

The apo E gene located on chromosome 19 in humans is polymorphic. The three apo E isoforms E2, E3, and E4 are coded by three common alleles of the gene. The amyloid plaques in brains of Alzheimer disease (AD) patients are known to contain apo E. There is an increased prevalence of E4 allele in AD patients. apo E exhibits increased binding to a peptide Aβ deriving from amylold precursor protein. apo E, the risk factor for late AD disease is unable to prevent formation of paired helical filaments which in turn destabilizes neuronal microtubules.A variety of molecular techniques are available for apo E genotyping using DNA amplified by the polymerase chain reaction (PCR). The high guanine to cytosine content of apo E is problematic to the extent that the yield of PCR product and hybridization stringency can be compromised. The specificity of diagnosis of late-onset AD can be improved when results of apo E genotyping are evaluated together with clinical criteria.