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Fluid composition impacts standardized testing protocols in ultrahigh molecular weight polyethylene knee wear testing.

Wear of total knee replacements is determined gravimetrically in simulator studies. A mix of bovine serum, distilled water, and additives is intended to replicate the lubrication conditions in vivo. Weight gain due to fluid absorption during testing is corrected using a load soak station. In this study, three sets of ultrahigh molecular weight polyethylene tibial plateau were tested against highly polished titanium condyles. Test 1 was performed in two different institutions on the same simulator according to the standard ISO 14243-1, using two testing lubricants. Test 2 and test 3 repeated both previous test sections. The wear and load soak rates changed significantly with the lubricant. The wear rate decreased from 16.9 to 7.9 mg weight loss per million cycles when switching from fluid A to fluid B. The weight gain of the load soak specimen submersed in fluid A was 6.1 mg after 5 x 10(6) cycles, compared with 31.6 mg for the implant in fluid B after the same time period. Both lubricants were mixed in accordance with ISO 14243 (Implants for surgery - wear of total knee-joint prostheses), suggesting that calf serum should be diluted to 25 +/- 2 per cent with deionized water and a protein mass concentration of not less than 17 g/l. The main differences were the type and amount of additives that chemically stabilize the lubricant throughout the test. The results suggest that wear rates can only be compared if exactly the same testing conditions are applied. An agreement on detailed lubricant specifications is desirable.

Body Fluids↗

Phylogenetic test of the molecular clock and linearized trees.

To estimate approximate divergence times of species or species groups with molecular data, we have developed a method of constructing a linearized tree under the assumption of a molecular clock. We present two tests of the molecular clock for a given topology: two-cluster test and branch-length test. The two-cluster test examines the hypothesis of the molecular clock for the two lineages created by an interior node of the tree, whereas the branch-length test examines the deviation of the branch length between the tree root and a tip from the average length. Sequences evolving excessively fast or slow at a high significance level may be eliminated. A linearized tree will then be constructed for a given topology for the remaining sequences under the assumption of rate constancy. We have used these methods to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.

Alcohol Dehydrogenase↗

Gene expression fingerprints in human tubulointerstitial inflammation and fibrosis as prognostic markers of disease progression.

BACKGROUND: Gene expression profiling of nephropathies may facilitate development of diagnostic strategies for complex renal diseases as well as provide insight into the molecular pathogenesis of kidney diseases. To test molecular based renal disease categorization, differential gene expression profiles were compared between control and hydronephrotic kidneys showing varying degrees of inflammation and fibrosis. METHODS: RNA expression profiles from 9 hydronephrotic and 3 control kidneys were analyzed using small macroarrays dedicated to genes involved in cell-cell contact, matrix turnover, and inflammation. In parallel, the degree of tubulointerstitial inflammation, fibrosis, and tubular atrophy using light microscopy and quantitative immunohistochemical parameters was determined. RESULTS: Hierarchic clustering and self-organizing maps led to a gene expression dendrogram with three distinct nodes representing the control group, four kidneys with high inflammation, and five kidneys giving high fibrosis scores. To evaluate the clinical applicability of the marker set, the expression of nine genes (6Ckine, IL-8, MMP-9, MMP-3, MMP-7, urokinase R, CXCR5, integrin-beta4, and pleiotrophin) was tested in tubulointerstitial samples from routine renal biopsies. Seven mRNA markers showed differential regulation in inflammation and fibrosis in the biopsy population. Clinical follow-up revealed stringent correlation between gene expression data and progression of renal disease, and allowed segregation of the biopsies into progressive or stable disease course based on gene expression profiles. CONCLUSION: This study suggests the feasibility of gene expression-based disease categorization in human nephropathies based on the extraction of marker gene sets.

Adult↗

Facioscapulohumeral muscular dystrophy with EcoRI/BlnI fragment size of more than 32 kb.

Facioscapulohumeral muscular dystrophy (FSHD) is associated with the deletion of a variable number of 3.3-kb subunits of a tandemly arranged repeat (D4Z4) on chromosome 4q35. EcoRI/BlnI fragments in the range of 10-35 kb are currently defined as disease-associated. Diagnosis of FSHD is frequently complicated by interchromosomal exchange with a homologous locus on 10q26. We present clinical and laboratory data of six subjects from two unrelated families with a marked FSHD phenotype and EcoRI/BlnI fragments of 39 and 33 kb, respectively. Origin on chromosome 4q35 was confirmed by haplotype analysis in the first family and was supported by pulsed field gel electrophoresis data in the second family. Our data further confirm the existence of a region of overlap of normal and pathological fragments. Fragments from this region can obviously be associated with marked FSHD phenotypes. Furthermore, application of linked markers and resolution of all EcoRI/BlnI fragments by pulsed field gel electrophoresis in addition to routine laboratory tests considerably augments the information obtained from molecular tests, upon which genetic counselling can then be based.

Adult↗

Carrier screening for cystic fibrosis: a perinatal perspective.

Cystic fibrosis (CF) is one of the most common autosomal recessive disorders in the United States today. One in 29 Americans, greater than 10 million people of Caucasian ethnicity, is a carrier for this genetic condition. Although it has been 10 years since the discovery of the gene for CF, carrier screening is not yet a standard of practice. The ultimate goal of carrier testing is to provide individuals at risk with information and guidance that will permit them to make informed and independent decisions. It can be anticipated that perinatal nurses will be part of the process of carrier screening of CF for prenatal patients. This article describes the nature of CF, the options for testing, and the basics of the molecular testing so nurses can be instrumental in the education process when this becomes standard practice.

Adult↗

Methicillin-resistant Staphylococcus aureus producing Panton-Valentine leukocidin in a retrospective case series from 12 French hospital laboratories, 2000-2003.

A retrospective analysis of hospital laboratory databases for 2000-2003 found that 0.4-1.0% of methicillin-resistant Staphylococcus aureus isolates had an antibiotic susceptibility pattern associated previously with the production of Panton-Valentine leukocidin (PVL). Of 81 isolates of this type, 35 were available for molecular testing. Each of the 35 available isolates carried the PVL genes, and 33 of these 35 isolates had an identical SmaI pulsed-field gel electrophoresis pattern.

Adolescent↗

Evaluation of the research methodology in genetic, molecular and proteomic tests.

INTRODUCTION: The advances in genomic analysis technologies have conducted to the development of new diagnostic tests in the clinical practice. As well as it happened in other diagnostic fields, the knowledge of the main flaws affecting genetic investigation will facilitate the application of the results. METHODS: We included 44 original articles that evaluate diagnostic exactitude of genetic and molecular tests (including proteomic), published from 2002 to June 2005 in five international publications: JAMA, Lancet, New England Journal of Medicine, Cancer Research and Clinical Cancer Research. We examined adherence to 24 methodological criteria included in the guide STARD (Standards for Reporting of Diagnostic Accuracy. RESULTS: The mean number of methodological criteria satisfied was 9.8 (95% CI 8.8-10.6); the greater deficiencies were in aspects related to the description of patient's selection 9 (20%), the treatment of indeterminate results 5 (11%) and the determination of test reproducibility 6 (13%). It was observed a high fulfillment in the description of the gold standard 39 (87%) and in the methodology of the test 28 (62%). DISCUSSION: The methodologic quality of the evaluated articles is lower than the quality observed in other research fields. The methodologic aspects that most need improvement are those linked to the clinical information of the populations studied and the reproducibility of the tests. The research and development of new genetic-molecular technologies requires a better fulfillment of the epidemiological and clinical criteria already followed by other diagnostic fields.

Genetic Testing↗

[The bacteriology of tuberculosis and non-tuberculosis mycobacterial infections].

Changing incidence and nature of mycobacterial infections subsequent to the historical regression of tuberculosis and the acquired human immunodeficiency syndrome (AIDS) epidemic, as well as the development of new technical tools for molecular biology, have profoundly modified the methods used for the bacteriological diagnosis of mycobacteria infections. Although microscopic search for acid-fast bacilli, culture and antibiotic resistance tests on Löwenstein-Jensen medium remain the reference methods, more rapid and sophisticated methods are now available. Culture on radiolabeled media using the Bactec system has shortened the delay for positive culture and interpretable antibiotic sensitivity tests. Molecular techniques allow: 1) rapid identification of the most frequently isolated mycobacteria strains, including the most frequent laboratory contaminant M. gordonae, with genome probes; 2) genome typing of M. tuberculosis strains to trace interhuman transmission, detect recurrence or exogenous reinfection or demonstrate laboratory contamination; 3) rapid detection of rifampicin resistance; and 4) direct detection of M. tuberculosis and M. avium in pathological specimens. The role of mycobacteria in the environment causing opportunistic infections, atypical mycobacteria or non-tuberculosis mycobacteria (NTM), particularly the aviaire complex, has grown considerably. Isolation and identification relies on methods used to detect bacilli as well as blood cultures and analysis of fecal matter. NTM are naturally resistant to most of the antituberculosis antibiotics but are sometimes sensitive to aminoglycosides, fluoroquinolones or new macrolides.

AIDS-Related Opportunistic Infections↗

Using expanded genetic alphabets to simplify high-throughput genetic testing.

DNA is the only chemistry that allows for molecular recognition on demand. Unlike any other molecular recognition chemistry, DNA enables the simple design and rapid synthesis of molecule sets that will recognize each other and self-assemble into nanostructures. In molecular diagnostics, DNA is used to capture complementary sequences in order to decode complex mixes. Expanding DNA chemistry to include additional base pairs enables a more precise manipulation of nanostructures constructed with DNA. MultiCode technology is that type of expanded DNA chemistry. The technology exploits DNA hydrogen bonding patterns that differ from natural DNA, thereby enabling a simple means of transcending problems that are otherwise unsolvable. Made up of additional base pairs (not simply single bases), MultiCode technology is used today to decode sequences in an orthogonal manner to natural DNA. This review will discuss MultiCode technology and specifically focus on how the technology can be used to build molecular testing platforms.

CpG Islands↗

Use and interpretation of HCV diagnostic tests in the clinical setting.

The rapidly emerging and sometimes complicated field of HCV diagnostics can be simplified by classification of tests into two general categories: serologic tests which screen for anti-HCV antibodies, and molecular tests which are used to assess HCV viremia and characterize viral infection at the genetic level. Antibody tests include the highly sensitive screening enzyme immunoassays (current versions: EIA-2 and EIA-3), and supplemental tests such as the recombinant immunoblot assay (RIBA-2). Molecular assays such as HCV RNA polymerase chain reaction (PCR) may play an important role in confirming HCV infection in several clinical situations, such as immunosuppressed patients with chronic hepatitis C, patients with acute hepatitis who might be in the diagnostic "window" period prior to seroconversion, and seropositive patients with normal ALT values. Quantitative HCV-RNA tests, such as quantitative PCR (Q-PCR) and branched DNA (bDNA), provide valuable tools for assessing the level of HCV viremia prior to and during therapy. Genotype tests allow classification of HCV infection in one of six distinct HCV genotypes, although the clinical relevance of HCV genotype tests has not been established.

False Positive Reactions↗

Genetic defects causing mitochondrial respiratory chain disorders and disease.

Genetic mitochondrial defects of the respiratory chain show marked phenotypic variability. Laboratory diagnosis is complicated and includes biochemical screening tests, tissue histopathology, functional enzyme studies, and molecular tests where available. Normal respiratory chain function necessitates the co-ordinated expression of over 100 different gene loci, and the interaction of two genetic systems, the nuclear and mitochondrial genomes. Thus genetic counselling for the mitochondrial disorders is extremely challenging. In this review, the classes of mitochondrial and nuclear defects that give rise to functional abnormalities of the mitochondrial respiratory chain are discussed, with specific instructive examples described in some detail.

DNA Replication↗

Long Range Polymerase Chain Reaction-Based Diagnosis of Friedreich Ataxia in the Clinical Molecular Diagnostics Laboratory.

Background: Friedreich ataxia, an autosomal recessive neurodegenerative disease, is one of the recently identified trinucleotide repeat disorders. Approximately 94% of affected individuals are homozygous for an intronic GAA repeat within the frataxin gene. The identification of this trinucleotide expansion as the causative mutation in the majority of affected individuals has resulted in the availability of molecular testing for Friedreich ataxia in the clinical molecular diagnostics laboratory. Methods and Results: A Friedreich ataxia protocol has been implemented using two long-range polymerase chain reaction-based assays primed with the GAA-F/GAA-R and Bam/2500F primer sets [1]. The amplified products are analyzed on precast minigels and visualized by Sybr Green staining. The GAA primer set, which produces a normal product of approximately 500 bp and an expanded product of greater than 800 bp, is used to approximate the size range of expanded repeats. Because the GAA primer set occasionally demonstrates preferential amplification of the normal allele in heterozygotes, the Bam/2500F primer set is used to verify results. Conclusions: This protocol has been used to analyze 42 specimens from patients about whom we had detailed clinical information. Concordant results obtained from the GAA and Bam/2500F primer sets, as well as correlations between clinical information and molecular results, indicate that, for the majority of patient specimens, this protocol allows rapid analysis and sizing of GAA repeats in normal and expanded alleles.

Journal Article↗

Candida spp. morphotype differentiation on Sabouraud-Triphenyltetrazolium-Agar (STTZ-Agar) under three different experimental conditions.

One hundred and thirty-two strains of Candida spp. were cultured on STTZ-Agar at 37 degrees C for 6 days and at 25 degrees C for 6 and 21 days to determine the culture conditions that would ensure maximum reproducibility in the discrimination of the strains of the same species. Standardization is of utmost importance, as varying experimental conditions can alter the results of the tests. Further studies are needed also implementing molecular tests to establish possible relationships between morphotype, genotype and virulence.

Agar↗

Approaches to thyroid nodules in paediatric cancer predisposition syndromes.

OBJECTIVE: The objective of this work was to summarize current evidence and practical management considerations for thyroid nodules in children and adolescents with cancer predisposition syndromes (CPSs), focusing on follicular cell-derived nodules and non-medullary thyroid carcinoma (NMTC). METHODS: We synthesized current paediatric guideline recommendations and recent cohort, pathology, and molecular studies addressing CPS-associated nodular thyroid disease, including PTEN hamartoma tumour syndrome (PHTS), DICER1 syndrome, familial adenomatous polyposis, and related endocrine neoplasia syndromes. RESULTS: Evidence quantifying syndrome-stratified malignancy risk among paediatric CPS patients presenting with nodules remains limited and is largely derived from mixed-age or retrospectively ascertained cohorts with surveillance and verification bias. High-resolution ultrasound (US) is central to risk stratification. US-guided fine-needle aspiration (FNA) is a cornerstone of evaluation yet frequently yields indeterminate results, particularly in follicular-patterned and encapsulated lesions (e.g. PHTS and DICER1 syndrome), and sampling error is accentuated in polyclonal multinodular disease. Molecular testing may aid aetiologic clarification and, in selected settings, risk refinement. However, panels optimized for sporadic adult disease may have reduced 'rule-out' utility in CPSs. Biochemical assessment (TSH ± free thyroxine) complements imaging, while routine thyroglobulin is not recommended, and thyroid autoantibodies should be viewed as adjunctive rather than directive markers in CPSs. CONCLUSION: Management of thyroid nodules in paediatric CPSs is best approached through integrated, multidisciplinary risk assessment that combines expert ultrasound, context-aware cytology and molecular interpretation, and shared decision-making. This review proposes a CPS-adapted, multidisciplinary risk assessment framework and highlights the need for prospective multicentre registries and harmonized protocols to define syndrome-specific outcomes and evidence-based thresholds for surveillance and intervention.

Humans↗

Molecular analysis and predictive testing in retinoblastoma.

Predictive testing using molecular analysis is an integral part of contemporary retinoblastoma management. We have made extensive use of segregation analysis for risk assessment in both familial and sporadic disease. Investigation of loss of heterozygosity in tumor samples proved to be invaluable for the identification of linkage phase. In many families, however, accurate carrier risk assessment depends on direct identification of the causative R B I mutation. Consequently, we have developed methods for rapid mutation screening. Using these techniques, mutation analysis can now be offered to an increasing number of individuals.

DNA Mutational Analysis↗

[Fragile X syndrome is still unrecognized: efficacy of molecular diagnosis in mentally retarded probands].

BACKGROUND: The fragile X mental retardation syndrome is the most common cause of inherited mental retardation. Identification of the unstable mutation responsible for the disease has allowed the design of a fully reliable molecular test for the diagnosis of the disease and for genetic counselling (identification of clinically normal carriers and prenatal diagnosis). We started in July 1991 to search for the mutation in mentally retarded probands, with no known cause for their phenotype. We present the results of a 42-month experience. POPULATION AND METHODS: One thousand and one hundred fourty-nine probands were analysed. In case of a positive diagnosis, an extension of the molecular study to relatives was proposed. DNA samples were studied by Southern blot following EcoRI or EcoRI + EagI digestion. Clinical data were collected from referring clinicians. RESULTS: Seventy-three carriers of a full mutation were identified, belonging to 52 families. The mean age of the fragile X probands was 16 +/- 14 years, which is very surprising for a disease that causes significant manifestations by the age of 2 to 3 years. This indicates an insufficient knowledge about this disease in France. Most of the demands for the test were from clinical geneticists. This diagnosis is of major importance for genetic counselling, as illustrated by the following study of 108 women at risk in these families. CONCLUSIONS: The importance of an early diagnosis followed by an extended family study, for carrier screening and prevention of this severe disease, justifies molecular testing on any child with mental retardation or significant language delay of unknown cause, in the absence of clinical signs formally excluding a fragile X diagnosis.

Adolescent↗

Packaging cell line DNA contamination of vector supernatants: implication for laboratory and clinical research.

Investigators conducting retroviral gene therapy trials are required to monitor for the presence of replication-competent retrovirus (RCR). The required testing utilizes a combination of biologic assays and molecular tests using PCR. In the course of a human clinical gene therapy trial, we detected 4070A viral envelope sequences in CD34(+) peripheral blood stem cells 2 days after transduction using a PCR-based assay, suggesting the presence of RCR. The supernatant and producer cells used for vector generation had been negative in extensive screening using the extended S(+)/L(-) assay. The presence of a replication-competent virus was subsequently excluded by a combination of biologic and PCR analyses. The source of the 4070A viral envelope sequences was determined to be packaging cell line DNA in the vector supernatant. The analysis of a variety of vector supernatants by quantitative real-time PCR revealed 4070A envelope DNA sequences from the packaging cell line in concentrations equivalent to approximately 50-500 focus-forming units per milliliter of wild-type 4070A virus. When PCR was performed after reverse transcriptase treatment of supernatant (i.e., assessing both RNA and DNA content), 4070A envelope sequence concentrations ranged from 10(2) to 3.5 x 10(3) focus-forming units per milliliter of wild-type 4070A virus. Our data indicate that PCR should not be used to analyze transduced cells for RCR within the first 2 weeks of vector exposure. Furthermore, investigators using PCR to analyze transduction efficiency shortly after vector exposure may experience false-positive findings.

Cell Line↗

Molecular biology of colorectal cancer.

Colorectal cancer is a significant cause of morbidity and mortality in Western populations. This cancer develops as a result of the pathologic transformation of normal colonic epithelium to an adenomatous polyp and ultimately an invasive cancer. The multistep progression requires years and possibly decades and is accompanied by a number of recently characterized genetic alterations. Mutations in two classes of genes, tumor-suppressor genes and proto-oncogenes, are thought to impart a proliferative advantage to cells and contribute to development of the malignant phenotype. Inactivating mutations of both copies (alleles) of the adenomatous polyposis coli (APC) gene--a tumor-suppressor gene on chromosome 5q--mark one of the earliest events in colorectal carcinogenesis. Germline mutation of the APC gene and subsequent somatic mutation of the second APC allele cause the inherited familial adenomatous polyposis syndrome. This syndrome is characterized by the presence of hundreds to thousands of colonic adenomatous polyps. If these polyps are left untreated, colorectal cancer develops. Mutation leading to dysregulation of the K-ras protooncogene is also thought to be an early event in colon cancer formation. Conversely, loss of heterozygosity on the long arm of chromosome 18 (18q) occurs later in the sequence of development from adenoma to carcinoma, and this mutation may predict poor prognosis. Loss of the 18q region is thought to contribute to inactivation of the DCC tumor-suppressor gene. More recent evidence suggests that other tumor-suppressor genes--DPC4 and MADR2 of the transforming growth factor beta (TGF-beta) pathway--also may be inactivated by allelic loss on chromosome 18q. In addition, mutation of the tumor-suppressor gene p53 on chromosome 17p appears to be a late phenomenon in colorectal carcinogenesis. This mutation may allow the growing tumor with multiple genetic alterations to evade cell cycle arrest and apoptosis. Neoplastic progression is probably accompanied by additional, undiscovered genetic events, which are indicated by allelic loss on chromosomes 1q, 4p, 6p, 8p, 9q, and 22q in 25% to 50% of colorectal cancers. Recently, a third class of genes, DNA repair genes, has been implicated in tumorigenesis of colorectal cancer. Study findings suggest that DNA mismatch repair deficiency, due to germline mutation of the hMSH2, hMLH1, hPMS1, or hPMS2 genes, contributes to development of hereditary nonpolyposis colorectal cancer. The majority of tumors in patients with this disease and 10% to 15% of sporadic colon cancers display microsatellite instability, also know as the replication error positive (RER+) phenotype. This molecular marker of DNA mismatch repair deficiency may predict improved patient survival. Mismatch repair deficiency is thought to lead to mutation and inactivation of the genes for type II TGF-beta receptor and insulin-like growth-factor II receptor. Individuals from families at high risk for colorectal cancer (hereditary nonpolyposis colorectal cancer or familial adenomatous polyposis) should be offered genetic counseling, predictive molecular testing, and when indicated, endoscopic surveillance at appropriate intervals. Recent studies have examined colorectal carcinogenesis in the light of other genetic processes. Telomerase activity is present in almost all cancers, including colorectal cancer, but rarely in benign lesions such as adenomatous polyps or normal tissues. Furthermore, genetic alterations that allow transformed colorectal epithelial cells to escape cell cycle arrest or apoptosis also have been recognized. In addition, hypomethylation or hypermethylation of DNA sequences may alter gene expression without nucleic acid mutation.

Colorectal Neoplasms↗