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Molecular detection of low-level disease in patients with cancer.

The accurate detection of low-level disease in patients with cancer is essential to improve the staging of disease and consequently to define appropriate treatment strategies. Most methods currently used for staging are based on imaging studies and histological and immunocytochemical analysis of tissues such as bone marrow aspirates, or antibody assays for marker proteins secreted into the circulation. These methods have limited sensitivity. However, assays for nucleic acid-based markers may be valuable tools for the sensitive detection, assessment, and monitoring of disease status in asymptomatic cancer patients. Application of these methods may allow the early detection of cancer, when the tumour burden is smaller and the disease potentially more curable. The last decade has seen the application of polymerase chain reaction (PCR)-based methods to the detection of tumour in a wide variety of compartments, including peripheral blood, bone marrow, lymph nodes, urine, sputum, faeces, pancreatic juice, and more recently plasma. Molecular detection of disease by PCR has targeted DNA and RNA markers, including mutations, microsatellites, and tissue-specific gene expression. It is likely that these molecular methods will provide important clinical information, though their current clinical utility remains unclear. The current status of nucleic acid-based assays for the detection and assessment of disease status in the management of patients with solid tumours is reviewed.

Adult↗

Use of FTA filter paper for the molecular detection of Newcastle disease virus.

The feasibility of using Flinders Technology Associates filter papers (FTA cards) to collect allantoic fluid and chicken tissue samples for Newcastle disease virus (NDV) molecular detection was evaluated. Trizol RNA extraction and one-step reverse transcriptase-polymerase chain reaction (RT-PCR) were used. FTA cards allowed NDV identification from allantoic fluid with a titre of 10(5.8) median embryo lethal doses/ml. The inactivated virus remained stable on the cards for 15 days. NDV was detected from FTA imprints of the trachea, lung, caecal tonsil and cloacal faeces of experimentally infected birds. RT-PCR detection from FTA cards was confirmed by homologous frozen-tissue RT-PCR and virus isolation. Direct nucleotide sequence of the amplified F gene allowed prediction of NDV virulence. No virus isolation was possible from the FTA inactivated samples, indicating viral inactivation upon contact. The FTA cards are suitable for collecting and transporting NDV-positive samples, providing a reliable source of RNA for molecular characterization and a hazard-free sample.

Animals↗

Accurate molecular detection of melanoma nodal metastases: an assessment of multimarker assay specificity, sensitivity, and detection rate.

BACKGROUND: The application of lymphoscintigraphy followed by sentinel lymph node (SN) biopsy to patients with primary melanoma has revolutionised the ability to identify accurately, yet conservatively, those patients who harbour occult nodal metastases. The molecular detection of SN micrometastases facilitates the cost effective analysis of the entire SN using multiple markers. Currently, a lack of marker specificity is the main barrier preventing the molecular evaluation of SN tissue from becoming clinically applicable. AIMS: To develop a reproducible multimarker reverse transcription-polymerase chain reaction (RT-PCR) assay, with the emphasis on achieving high specificity for the accurate detection of melanoma metastases in nodal tissue. METHODS: Three pigment cell specific (PCS) markers-tyrosinase, Pmel-17, and MART-1-and one cancer testis antigen (CTA)-MAGE-3-were selected for use in a multimarker RT-PCR assay. The conditions for this assay were optimised. RESULTS: High specificity was achievable for each marker by optimising the PCR cycle number such that unwanted transcripts (that is, illegitimate transcripts and/or specific transcripts from other low abundance nodal cell types) remained undetectable in appropriate controls (normal visceral nodes). Tyrosinase was 100% specific at 40 PCR cycles, MAGE-3 and MART-1 at 35 PCR cycles, and Pmel-17 at 30 PCR cycles. Tyrosinase proved to be the most sensitive marker, detecting 10 melanoma cells in 0.1 g of nodal tissue. CONCLUSIONS: Excellent reproducibility of the entire nodal processing and RT-PCR protocol for the detection of very low numbers of melanoma cells in nodal tissue was shown, although there is a risk of false positives using the PCS markers alone, because of an approximate 4-8.5% incidence rate of nodal nevi in melanoma draining SNs (these nevi being absent in all other normal nodes). MAGE-3 was shown to be the only marker that is not expressed by melanocytes. However, because not all melanomas express MAGE-3, it is recommended that more emphasis should be placed on the development of a panel of CTA markers to ensure a zero false positive rate and to provide optimum detection.

Antigens, Neoplasm↗

Clinical utility of molecular detection of human papillomavirus in cervical samples by hybrid capture technology.

High-risk human papillomaviruses (HPVs) are the primary risk factor for developing cervical carcinoma. Hybrid capture II HPV Test (HCII) is a standardized test for molecular detection of HPV DNA in cervical swabs. The aim of the study was to evaluate the clinical utility of the HCII when used in combination with conventional cytology in a group of 171 women who were followed-up with both, cytology and molecular testing for 3 years. At the end of the study, only women positive for high-risk HPV at baseline had retained or worsened cervical intraepithelial neoplasia (CIN). In most women who were negative for high-risk HPV, CIN had resolved within 3 years. These results are in concordance with earlier studies reporting the highly negative predictive value of high-risk HPV testing. Both cytology and high-risk HPV testing provide significant clinical information on the current cervical status of a woman. They should be used in combination for primary screening of CIN, which will provide a more selective and cost-effective follow-up.

Female↗

[Molecular detection and sequence analysis of hepatitis A virus (HAV) in two outbreaks in 2004 in North East Hungary].

INTRODUCTION: Hepatitis A virus (HAV) is the most important cause of acute infectious hepatitis worldwide. In Hungary, the reported number of HAV infections decreasing in the last decades, however, in every year approximately 500-800 new cases occur. In Hungary, particularly in North East region not only sporadic cases but also outbreaks of HAV are happen from time to time. Serology is routinely used laboratory method for diagnosis of HAV infections, although, there was no direct molecular detection and sequence analysis for the circulating HAV strains in Hungary. AIMS: Author's aims were to detection and genetic characterization of hepatitis A virus in outbreaks of hepatitis by molecular methods for reason of molecular epidemiology in Hungary. MATERIALS AND METHODS: Sera samples from symptomatic patients were tested from two acute hepatitis outbreaks in two settlements (Hajdúböszörmény and Kázsmárk) in North East Hungary in 2004 by enzim-immunoassay (EIA) and reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: Sera in 58 (100%) and 4 (28.6%) symptomatic patients were positive in outbreaks of Hajdúböszörmény and Kázsmárk by HAV IgM EIA, however, 4 (57.1%) and 2 (66.6%) HAV IgM positive samples were positive by RT-PCR. By sequence analysis, outbreaks caused by the same hepatitis A virus which belongs to genotype I, subtype IA. These viruses had 98.4% nucleotide identity to IT-SCH-00 virus detected in year 2000 in Italy the closest match in GenBank. CONCLUSIONS: Methods of molecular biology give new opportunity for surveillance of infectious diseases in public health. Firstly characterized hepatitis A viruses in Hungary show that the subtype IA have an important epidemiological role in outbreaks. It is also suggested that genotype IA HAV play a part in sporadic HAV cases in endemic region in Hungary, too.

Adolescent↗

Molecular detection of tumour DNA in serum and peritoneal fluid from ovarian cancer patients.

We have analysed DNA extracted from the serum and peritoneal fluid of 20 ovarian cancer patients for the presence of tumour-specific genetic alterations. The 20 patients included six with stage Ia disease. Using six polymorphic microsatellite loci we were able to detect novel alleles or loss of heterozygosity in 17/20 serum samples and 12/19 peritoneal fluid samples. Tumour-specific abnormalities were detected in the serum of all but one of the stage Ia cases. Half of the occurrences of loss of heterozygosity identified in primary tumour material were detectable in the serum samples. Novel alleles indicative of microsatellite instability were found in 3/6 patients with stage Ia disease but in only 1/14 of patients with more advanced disease. One of the eight patients in the control group displayed abnormalities in her serum DNA. The ease with which tumour-specific alterations were detected in serum and peritoneal samples from ovarian cancer patients, using a panel of only six polymorphic microsatellite markers on four chromosomes, suggests that molecular detection methods could prove useful in the staging, monitoring and screening of this disease.

Alleles↗

Surgical maneuvers enhance molecular detection of circulating tumor cells during gastric cancer surgery.

OBJECTIVE: To evaluate the relation between the presence of cancer cells in blood according to the time course during a surgical procedure and liver metastases in patients with gastric cancer. SUMMARY BACKGROUND DATA: Several studies have reported on the detection of circulating cancer cells in blood by reverse transcriptase-polymerase chain reaction (RT-PCR). However, few reports have examined the relation between molecular detection of circulating cancer cells according to the time course during a surgical procedure and blood-borne metastases. METHODS: Blood samples from 57 patients with gastric cancer were obtained from the portal vein, peripheral artery, and superior vena cava before and after tumor dissection. After total RNA was extracted from each blood sample, carcinoembryonic antigen (CEA)-specific RT-PCR was performed. RESULTS: CEA-mRNA was detected in the blood of 21 (36.8%) of the 57 patients. CEA-mRNA was not detected in the blood obtained from 15 healthy volunteers and 15 patients with benign disease. The positive rate increased in proportion to the depth of tumor. The incidence of positive CEA-mRNA did not differ among the various sites of blood sampling. The appearance of circulating cancer cells was related to the surgical maneuver. A significant relation was found between the detection of CEA-mRNA and blood-borne metastases. CONCLUSIONS: A high incidence of positive CEA-mRNA was found in the blood during gastric cancer surgery. Surgical maneuvers are a possible cause of hematogenous metastasis. The authors found that patients with positive CEA-mRNA had a high risk of blood-borne metastasis even after curative resection.

Aged↗

Molecular detection of micrometastatic breast cancer in histopathology-negative axillary lymph nodes correlates with traditional predictors of prognosis: an interim analysis of a prospective multi-institutional cohort study.

OBJECTIVE: We sought to establish the clinical relevance of micrometastatic disease detected by reverse transcription polymerase chain reaction (RT-PCR) in axillary lymph nodes (ALN) of breast cancer patients. BACKGROUND: The presence of ALN metastases remains one of the most valuable prognostic indicators in women with breast cancer. However, the clinical relevance of molecular detection of micrometastatic breast cancer in sentinel lymph nodes (SLN) and nonsentinel ALN has not been established. METHODS: Four hundred eighty-nine patients with T1-T3 primary breast cancers were analyzed in a prospective, multi-institutional cohort study. ALN were analyzed by standard histopathology (H&E staining) and by multimarker, real-time RT-PCR analysis (mam, mamB, muc1, CEA, PSE, CK19, and PIP) designed to detect breast cancer micrometastases. RESULTS: A positive marker signal was observed in 126 (87%) of 145 subjects with pathology-positive ALN, and in 112 (33%) of 344 subjects with pathology-negative ALN. In subjects with pathology-negative ALN, a positive marker signal was significantly associated with traditional indicators of prognosis, such as histologic grade (P = 0.0255) and St. Gallen risk category (P = 0.022). Mammaglobin was the most informative marker in the panel. CONCLUSION: This is the first report to show that overexpression of breast cancer-associated genes in breast cancer subjects with pathology-negative ALN correlates with traditional indicators of disease prognosis. These interim results provide strong evidence that molecular markers could serve as valid surrogates for the detection of occult micrometastases in ALN. Correlation of real-time RT-PCR analyses with disease-free survival in this patient cohort will help to define the clinical relevance of micrometastatic disease in this patient population.

Adult↗

Molecular detection of GES-2 extended spectrum Beta-lactamase producing Pseudomonas aeruginosa in Pretoria, South Africa.

Screening for and detection of the novel extended spectrum Beta-lactamase (ESBL), GES-2 produced by Pseudomonas aeruginosa remains a problem in the clinical microbiology laboratory. This study aimed to compare the normally used ESBL screening agent ceftazidime, with molecular detection, to demonstrate the presence of GES-2 ESBL production in clinical isolates of P. aeruginosa. Ceftazidime was found unreliable as an ESBL screening agent, with a specificity of 34.4%, when National Committee for Clinical Laboratory Standards resistance criteria for P. aeruginosa were employed. An improved PCR detection method was devised, that amplified a 371 bp segment of bla(GES-2). This should lead to more cost-effective DNA sequencing and sequence interpretation in the laboratory.

Base Sequence↗

Genetic diversity and molecular detection of three toxic dinoflagellate genera (Alexandrium, Dinophysis, and Karenia) from French coasts.

The objectives of this study were 1) to study the genetic diversity of the Alexandrium, Dinophysis and Karenia genera along the French coasts in order to design probes targeting specific DNA regions, and 2) to apply PCR-based detection to detect these three toxic dinoflagellate genera in natural samples. Genetic diversity of these toxic taxa was first studied from either cultures or cells isolated from Lugol-fixed field samples. By this way, partial sequences of the large ribosomal subunit (LSU rDNA) including the variable domains D1 and D2 of A. minutum, Alexandrium species inside the tamarensis complex, the D. acuminata complex and K. mikimotoi were obtained. Next, specific primers were designed for a selection of toxic algae and used during semi-nested PCR detection. This method was tested over a 3-month period on water samples from the Bay of Concarneau (Brittany, France) and on sediment from the Antifer harbor (The English Channel, France). Specificity and sensitivity of this molecular detection were evaluated using the occurrence of target taxa reported by the IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) monitoring network based on conventional microscopic examination. This work presents the first results obtained on the biogeographical distribution of genotypes of these three toxic genera along the French coasts.

Animals↗

Molecular detection of codon 12 K-RAS mutations in circulating DNA from serum of colorectal cancer patients.

Point mutations of the K-RAS gene at codon 12 are found in about 40% of cases with colorectal cancer. The diagnostic implications of the detection of these mutations and their clinical utility are still unclear. The aim of this study was to test both the feasibility of the detection of the mutated K-RAS gene in serum and its potential role in colorectal cancer detection and monitoring. Codon 12 K-RAS mutations were examined in DNA extracted from the serum of 35 patients with colorectal cancer and were compared with the K-RAS status in the corresponding primary tumor. Molecular detection was performed by the mutant-enriched PCR (ME-PCR) assay, a sensitive method capable of distinguishing a small quantity of mutated DNA in the presence of abundant wild-type DNA. The occurrence of mutations was compared with clinicopathological parameters as well as CEA and CA19.9 serum levels. We found codon 12 K-RAS mutations in the tissue of 13/35 (37%) patients. Serum mutations were detected in 5/13 (38.5%) patients with mutated K-RAS in the tissue. 26/35 (74%) patients showed an identical K-RAS pattern in tissue and serum. No codon 12 K-RAS alterations were found in serum samples of 22 patients with benign gastrointestinal diseases. Elevated serum CEA levels were detected in 16 patients, four of whom also presented serum RAS mutations. Our results confirm that K-RAS mutations can be found in circulating DNA extracted from serum samples of patients with colorectal cancer and show that there is a correspondence between serum and tissue K-RAS patterns.

Adult↗

Clinical course of human T-lymphotropic virus type I carriers with molecularly detectable monoclonal proliferation of T lymphocytes: defining a low- and high-risk population.

To characterize the prodromal phase of adult T-cell leukemia (ATL), a prospective follow-up study was conducted on 50 carriers in a putative pre-ATL state. This state was defined by the presence of molecularly-detectable monoclonal proliferation of human T-lymphotropic virus type I (HTLV-I)-infected T lymphocytes, and the absence of clinical symptoms of leukemia. The median observation time was 50 months. The pre-ATL subjects were divided into two groups according to initial white blood cell (WBC) counts: group A, those with a normal WBC count (9,000/microL) (n = 30), and group B, those with an increased WBC count (9,000 to 15,000) (n = 20). Comparisons were made between the two groups and with a group of 25 patients with chronic ATL (group C) who had WBC counts of more than 15,000. Significant differences in survival rate were found between groups A and B (10-year survival 65.7%) and group C (32.8%) (P < .01), and between group A (10-year survival 90.0%) and group B (52.1%) (P < .05). The incidence of transformation to overt ATL was 10% (3 of 30) in group A and 50% (10 of 20) in group B (P < .01). In six transformed cases (one in A and five in B) we found exactly the same integration sites in pre-ATL and overt ATL phases, confirming the multistep leukemogenesis hypothesized for this disease. However, the pre-ATL subjects could be divided into two distinct prognostic groups based on the initial WBC count; those with good and those with poor prognosis. Although the 10% transformation rate (2.5% annually) in group A seemed to be extremely high compared with that in the general population of HTLV-I carriers (around 0.06% to 0.4% annually), the majority of group A subjects and some in group B showed stable clinical courses without transformation. Further, development of ATL was not observed in four group A subjects with HTLV-I-associated myelopathy (HAM), which is rarely associated with ATL. We propose to call this group of rather benign HTLV-I carriers "HTLV-I carriers with monoclonal proliferation of T lymphocytes (HCMPT)." Thus far we have been unable to identify reliable parameters other than WBC counts that prospectively distinguish HCMPT from the true pre-ATL state, in which there is a high probability of developing ATL. Further clinical and biologic approaches should elucidate the natural history of the HTLV-I carrier state and early events in ATL leukemogenesis.

Adult↗

Molecular detection of dengue viruses in field caught Aedes aegypti mosquitoes from northeastern Argentina.

Most molecular protocols for Dengue virus detection described so far are time consuming and cumbersome with mosquito samples. In order to count with a sensitive and specific molecular detection system for monitoring possible Dengue outbreaks and circulating viral serotypes in field-caught Aedes aegypti populations from Northeastern Argentina, a RT-PCR and RFLP assay was developed. The original RT-PCR assay proposed by Sudiro et al. for human serum was optimized for mosquito samples. Modifications were done at the RNA extraction-purification and at the thermal profile steps. The generic 230 bp amplicon was validated by RFLP assay and cycle sequencing. Results showed that, due to the generic characteristic of the primers used, certain mosquito genome regions could be co-amplified, making confirmation of the Dengue specific amplicon by RFLP assay a required step. Under these conditions, the proposed method can be employed as a Dengue viral generic screening procedure in Aedes aegypti mosquito samples, giving in our hands an estimated 99.52% of confirmed negatives (207/208 tested samples).

Aedes↗

Molecular detection of bean common mosaic and bean common mosaic necrosis potyviruses and pathogroups.

Partial nucleotide sequences of selected isolates of bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) were determined. Based on these sequences and previously published sequence data, a reverse transcription, polymerase chain reaction (RT-PCR) in combination with restriction endonuclease analyses, was developed for molecular detection of BCMV, BCMNV and some viral pathogroups (PG). Specific detection of the two viruses was accomplished by constructing two virus-specific primer pairs that amplified a PCR product specific for each virus. By application of RT-PCR, four BCMV-PG-V isolates were differentiated from isolates of BCMV pathogroups I, II, IV and VII. Distinction of two BCMNV pathogroups (PG-III and PG-VI) was achieved by restriction enzyme XbaI digestion of BCMNV PCR products. However, no combination of tested restriction enzymes distinguished all five recognized BCMV pathogroups. A primer pair Dts/Uny15 proved to be specific for BCMV pathogroup PG-V. Thus, by a combination of RT-PCR and restriction enzyme analyses, it was possible to differentiate both viruses, two pathogroups of BCMNV, and one pathogroup of BCMV from the others.

Amino Acid Sequence↗

Surface plasmon resonance-based molecular detection of Hb S [beta6(A3)Glu-->Val, GAG-->GTG] at the gene level.

The surface plasmon resonance (SPR) approach, being a relatively novel biophysical method, is used to detect many different targets by biomolecular interaction. The SPR system uses optical and evanescent wave phenomenon. This approach does not need any labels, such as enzymes or isotopes, and the monitored interactions are in real time. In DNA-DNA interaction, the SPR approach is Tm-independent. Here we report our preliminary results for the molecular detection of the Hb S (GAG -->GTG) mutation at codon 6 of the human beta-globin gene. Our preliminary results show that the SPR approach could be applied as an inexpensive and fast routine test system for the molecular diagnosis of abnormal hemoglobins (Hbs), especially in premarital screening programs.

Genetic Counseling↗

Potential limitations of the 16S-23S rRNA intergenic region for molecular detection of Bartonella species.

PCR targeting the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region has been proposed as a rapid and reliable method for the detection of Bartonella species DNA in clinical samples. Because of variation in ITS sequences among Bartonella species, a single PCR amplification can be used to detect different species within this genus. Therefore, by targeting the ITS region, multiple PCRs or additional sample-processing steps beyond the primary amplification can be avoided when attempting to achieve molecular diagnostic detection of Bartonella species. Although PCR amplification targeting this region is considered highly sensitive, amplification specificity obviously depends on primer design. We report evidence of nonspecific PCR amplification of Mesorhizobium species with previously published primers that were designed to amplify the Bartonella consensus ITS region. Use of these or other, less species-specific, primers could lead to a false-positive diagnostic test result when evaluating clinical samples. We also report the presence of Mesorhizobium species DNA as a contaminant in molecular-grade water, a series of homologous sequences in the ITS region that are common to Bartonella and Mesorhizobium species, the amplification of Mesorhizobium DNA with unpublished primers designed in our laboratory targeting the ITS region, and the subsequent design of unambiguous ITS primers that avoid nonspecific amplification of Mesorhizobium species. Our results define some potential limitations associated with the molecular detection of Bartonella species in patient samples and indicate that primer specificity is of critical importance if the ITS region is used as a diagnostic target for detection of Bartonella species.

Bartonella↗

Clinical significance in molecular detection of p53 mutation in serum of patients with colorectal carcinoma.

Circulating DNA can be isolated from serum of patients with various carcinomas and p53 mutation can be observed in colorectal carcinoma. The aim of this study was to investigate the correlation between p53 mutation in DNA extracted from colorectal carcinoma and that in DNA extracted from serum of patients with colorectal carcinoma. The clinical significance in molecular detection of p53 mutation in serum of patients with colorectal carcinomas was also investigated. DNA was extracted from tumors and non-tumorous colorectal tissues of 46 patients with single sporadic colorectal carcinomas of stage I (n=6), stage II (n=18), stage III (n=15), and stage IV (n=7) according to the TNM classification. Circulating DNA was also extracted from the serum of the 46 patients with colorectal carcinoma and from 7 healthy volunteers for normal control. Mutations of the p53 gene were analyzed using a fluorescence-based polymerase chain reaction (PCR)-single-strand conformation polymorphism (SSCP) method. DNA sequences were determined in DNA fragments with shifted peaks by SSCP methods. Mutations in tumors were found in 22 (48%) of 46 patients, and mutations in serum were found in 3 (14%) of these 22 patients. Of 4 patients with stage IV disease, 3 (75%) had serum p53 mutation and the mutation pattern of these 3 patients was the same in both tumor and serum. No correlation was seen between p53 mutation in serum and the level of serum DNA. There was no significant difference between the presence of p53 mutation in serum and tumor size, depth of invasion, vascular invasion, or lymph node metastasis. However, liver metastasis showed significant difference (p=0.0026). The presence of p53 mutation in serum was associated with a clinically advanced stage accompanied by liver metastasis.

Adult↗