Serial Dilution Studies Research Articles

The efficacy of targeted next-generation sequencing for detection of clinically actionable mutations in cancer.

10598 Background: The emergence of next-generation sequencing (NGS) technologies has significantly accelerated the identification of cancer-causing mutations and the development of personalized cancer care. However, the clinical application of these technologies to detect cancer gene mutations has been extremely limited due to the long turn around time, the high cost, and large amount of input DNA required by existing NGS-based tests. Methods: We have assessed the performance of a novel NGS technology that merges multiplex PCR with ion semiconductor sequencing (AmpliSeq, Life Technologies, Inc.) in our clinical diagnostic laboratory. The test interrogates 739 common mutations in 46 cancer genes including many clinically actionable mutations concurrently. First, we studied 12 tumor samples including 4 archived FFPE, 4 blood/bone marrow, and 4 cell line samples with known mutations to evaluate the sensitivity and specificity of the test. We then studied 34 de-identified, archived FFPE tumor samples of unknown genotype to further evaluate the efficacy of the test. Results: We successfully identified all known mutations previously detected by Pyposequencing or Sanger sequencing technologies. Multiple serial dilution studies showed that the test could detect mutations at frequencies as low as 5% with 99% confidence. For the samples of unknown genotype, we detected 23 COSMIC mutations in 16 samples including HRAS, BRAF, MET, TP53 mutations in lung cancer, KRAS, PIK3CA, TP53, APC, BRAF, ERBB2 mutations in colon cancer, TP53 and KRAS mutations in breast cancer, and KIT and PDGFRA mutations in GIST. Analysis of the variant call data showed that a minimum of 100X coverage is required in order to detect mutations at 10% frequency or above; a minimum 300K final library reads are necessary in order to minimize/eliminate amplicon dropout. Conclusions: The targeted NGS test can effectively detect cancer gene mutation with input DNA as low as a few nanograms, turn around time can be as short as two days, and can significantly lower cost compared to traditional Sanger sequencing. Our experience demonstrates that this technology holds great potential for clinical use, including diagnostic and therapeutic applications.

Evaluation of 25-hydroxy vitamin D assay on the immunodiagnostic systems iSYS analyser

We evaluated the recently released chemiluminescence assay for 25-hydroxy vitamin D (25-OHD) on the Immunodiagnostic Systems iSYS (IDS-iSYS) automated analyser. The IDS-iSYS comparison was performed using patient samples previously measured for 25-OHD by a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method (n = 119) and an IDS enzyme immunoassy (IDS-EIA) method (n = 64). Limit of detection and limit of quantification were determined from a precision profile. Imprecision was assessed using quality control material and pooled serum. External QAP material (Vitamin D External Quality Assessment Scheme, UK) was analysed to establish inaccuracy. Linearity was assessed by two dilution studies. Cross-reactivity was determined by three serial dilution studies of patient samples with known 25-OHD(2) concentrations. The IDS-iSYS correlated well with both established methods (iSYS = 1.03LC-MS/MS - 6.53, R(2) = 0.82 and iSYS = 1.07IDS-EIA - 1.61, R(2) = 0.86). Imprecision of the iSYS assay for IDS control material was 13.4% at 32 nmol/L, 10% at 78 nmol/L, 9.4% at 161 nmol/L, and for the pooled material 9.3% at 72 nmol/L and 5.6% at 158 nmol/L. The evaluation found the assay to be highly accurate (IDS-iSYS = 0.93ALTM + 3.79, R(2) = 0.94) and linear (obs(1) = 0.93exp(1) - 5.05, R(2) = 0.99 (P = 0.256); and obs(2) = 0.97exp(2) + 6.07, R(2) = 0.97 (P = 0.654); ALTM, all-laboratory trimmed mean). Cross-reactivity studies demonstrated no significant difference to the calculated total 25-OHD as measured by LC-MS/MS. Even though the imprecision of the iSYS was found to be greater than that of the LC-MS/MS and EIA methods, the performance characteristics of the IDS-iSYS 25-OHD assay are suitable for routine diagnostic purposes on a high throughput automated analyser.

Analysis of cutoffs for screening sensitized blood donors for HLA alloantibodies using a cytometric microbead assay

Cytometric-based microbead assays for HLA alloantibodies may be effective tools for transfusion-related acute lung injury (TRALI) risk reduction. However, the optimal cutoff for donor screening is unclear. To optimize the screening test cutoff in sensitized donors, sera were screened with a cytometric microbead assay. Confirmatory testing was performed on samples with a normalized background (NBG) ratio of 2.4 or more. Sera with a NBG of 2.4 to 9.9 had positive predictive values (PPVs) of 78.2% (95% confidence interval [CI], 67.8%-86.0%) and 71.1% (95% CI, 56.5%-82.4%) for Class I and II antibodies, respectively. Sera with a NBG of 10 or more had PPVs of 98.9% (95% CI, 93.3%-100%) and 99.1 (95% CIs, 94.7%-100%) for Class I and II, respectively. The percent panel-reactive antibody (PRA) of confirmed HLA alloantibodies from sera with a NBG of 2.4 to 9.9 was 29.3±17% (mean±standard deviation) for Class I and 22.3±16.7% for Class II, but for antibodies from sera with a NBG of 10 or more the PRAs were 65.3±24.0 and 64.1±25.2% for Class I and II, respectively (p<0.00001). Serial dilution studies comparing the screening test with antiglobulin-enhanced lymphocytotoxicity suggested that NBG correlated with antibody titer. In our center, deferral for prior pregnancy or transfusion would result in loss of 28.8% of apheresis platelet (PLT) donors. Using the screening test at a cutoff of 2.4 or more or 10 or more would reduce the fraction of donors lost to 12.7 or 8.0%, respectively. A screening cutoff of 10 or more predicts HLA alloimmunization in sensitized donors and is associated with higher PRAs and titers. Implementation of this cutoff may reduce TRALI risk while limiting unnecessary deferral of PLT donors.

Multiplex real-time quantitative PCR, microscopy and rapid diagnostic immuno-chromatographic tests for the detection of Plasmodium spp: performance, limit of detection analysis and quality assurance

BackgroundAccurate laboratory diagnosis of malaria species in returning travelers is paramount in the treatment of this potentially fatal infectious disease.Materials and methodsA total of 466 blood specimens from returning travelers to Africa, Asia, and South/Central America with suspected malaria infection were collected between 2007 and 2009 at the reference public health laboratory. These specimens were assessed by reference microscopy, multipex real-time quantitative polymerase chain reaction (QPCR), and two rapid diagnostic immuno-chromatographic tests (ICT) in a blinded manner. Key clinical laboratory parameters such as limit of detection (LOD) analysis on clinical specimens by parasite stage, inter-reader variability of ICTs, staffing implications, quality assurance and cost analysis were evaluated.ResultsQPCR is the most analytically sensitive method (sensitivity 99.41%), followed by CARESTART (sensitivity 88.24%), and BINAXNOW (sensitivity 86.47%) for the diagnosis of malaria in returning travelers when compared to reference microscopy. However, microscopy was unable to specifically identify Plasmodia spp. in 18 out of 170 positive samples by QPCR. Moreover, the 17 samples that were negative by microscopy and positive by QPCR were also positive by ICTs. Quality assurance was achieved for QPCR by exchanging a blinded proficiency panel with another reference laboratory. The Kappa value of inter-reader variability among three readers for BINAXNOW and CARESTART was calculated to be 0.872 and 0.898 respectively. Serial dilution studies demonstrated that the QPCR cycle threshold correlates linearly with parasitemia (R2 = 0.9746) in a clinically relevant dynamic range and retains a LOD of 11 rDNA copies/μl for P. falciparum, which was several log lower than reference microscopy and ICTs. LOD for QPCR is affected not only by parasitemia but the parasite stage distribution of each clinical specimen. QPCR was approximately 6-fold more costly than reference microscopy.DiscussionThese data suggest that multiplex QPCR although more costly confers a significant diagnostic advantage in terms of LOD compared to reference microscopy and ICTs for all four species. Quality assurance of QPCR is essential to the maintenance of proficiency in the clinical laboratory. ICTs showed good concordance between readers however lacked sensitivity for non-falciparum species due to antigenic differences and low parasitemia.ConclusionMultiplex QPCR but not ICTs is an essential adjunct to microscopy in the reference laboratory detection of malaria species specifically due to the superior LOD. ICTs are better suited to the non-reference laboratory where lower specimen volumes challenge microscopy proficiency in the non-endemic setting.

A Serial Dilution Study of Gadolinium-Based MR Imaging Contrast Agents

With the approval of gadobenate dimeglumine, higher relaxivity MR contrast agents were introduced into the clinical environment, and multiple in vivo studies compared the efficacy and safety with the previously approved agents. An in vitro study was conducted to demonstrate differences between the various agents to confirm published values and for imaging-sequence optimization. A contrast phantom was made with serial dilutions of commercially available formulations of 5 US Food and Drug Administration-approved gadolinium-based MR imaging contrast agents in human serum substitute. Dilution factors ranging from 1:8 to 1:4096 were included in the phantom. Spin-echo sequences were performed at 1.5T and 3T with varying TRs and TEs. At physiologic concentrations and by using short TRs and TEs, gadobenate demonstrated the highest signal intensities, confirming greater R1 relaxivity. At higher concentrations and with longer TR and TE values, the greatest signal intensity loss was appreciated for gadobenate, confirming greater R2 relaxivity. Using rigorous in vitro methodology and serial dilution techniques, this study confirms the reported higher R1 and R2 relaxivities of gadobenate relative to the other agents at 1.5T and 3T.

Hemocompatibility of Hydrophilic Antimicrobial Copolymers of Alkylated 4-Vinylpyridine

Quaternized poly(vinylpyridine) (PVP) is a polymer with inherent antimicrobial properties that is effective against Gram-positive bacteria, Gram-negative bacteria, viruses, and yeast cells. However, quaternized PVP has poor biocompatibility, which prevents its use in biomaterial applications. Copolymerization was examined as a method of modifying the structure to incorporate biocompatibility. Polyethyleneglycol methyl ether methacrylate (PEGMA) and hydroxyethyl methacrylate (HEMA) are polymers generally known to be biocompatible and thus were chosen as comonomers. Random copolymers of 4-vinylpyridine and PEGMA or HEMA were synthesized via free radical polymerization and quaternized with bromohexane. Copolymer biocompatibility was characterized by interaction with human red blood cells to analyze hemolysis. Hemolysis of human red blood cells was conducted on insoluble films and on water-soluble polymers in a serial dilution study. Hemolysis results demonstrated that blood compatibility does not depend on PEG chain length in PEGMA incorporated copolymers. Results indicate a critical weight ratio of PEGMA to VP in copolymers separating the no-hemolysis regime from 100% hemolysis.

Rapid Detection of Epidermal Growth Factor Receptor Mutations in Lung Cancer by the SMart-Amplification Process

A positive response to gefitinib in non-small cell lung cancer (NSCLC) has been correlated to mutations in epidermal growth factor receptor (EGFR) gene. Previous reports have been based mainly on diagnostic screening by sequencing. However, sequencing is a time-consuming and complicated procedure, not suitable for routine clinical use. We have developed rapid, simple, and sensitive mutation detection assays based on the SMart Amplification Process (SMAP) and applied it for analyzing EGFR gene mutations in clinical samples. By using SMAP, we can detect mutations within 30 min including sample preparation. To validate the assay system for potential use in clinical diagnostics, we examined 45 NSCLC patients for EGFR mutations using sequencing and SMAP. The outcomes of the SMAP assay perfectly matched the sequencing results, except in one case where SMAP was able to identify a mutation that was not detected by sequencing. We also evaluated the sensitivity and specificity of SMAP in mutation detection for EGFR. In a serial dilution study, SMAP was able to find a mutation in a sample containing only 0.1% of the mutant allele in a mixture of wild-type genomic DNA. We also could show amplification of mutated DNA with only 30 copies per reaction. The SMAP method offers higher sensitivity and specificity than alternative technologies, while eliminating the need for sequencing to identify mutations in the EGFR gene of NSCLC. It provides a robust and point-of-care accessible approach for a rapid identification of most patients likely to respond to gefitinib.

A sensitive method for detection of EGFR gene mutations in plasma

18027 Background: Somatic mutations in the tyrosine kinase (TK) domain of the EGFR gene are associated with clinical response to TK inhibitors in patients with non-small cell lung cancer. An assay that detects such mutations in the plasma would provide a noninvasive technique to assess suitability for TK inhibitor therapy. Here we describe: 1) the development of a sensitive assay to detect the E746-A750 deletion in the TK domain of EGFR in plasma; and 2) optimization of the method for plasma DNA extraction. Methods: Our assay uses Mse I to specifically digest wild-type (WT) genomic DNA (gDNA) to reduce non-specific amplification. After digestion, samples are PCR- amplified using 1 unlabeled primer and 1 FAM-labeled primer spanning the E746-A750 deletion region and fluorescence detected with an automated analyzer. Serial dilution studies were conducted using H1650 gDNA (del E746-A750 cell line) diluted in WT gDNA after Mse I digestion. To assess detection of the deletion in plasma, 3–4 mL whole blood was spiked with 1–37 ng H1650 gDNA; gDNA from the separated plasma was then extracted (silica column/2-propanol precipitation), digested with Mse I, and amplified as above. Several extraction methods were evaluated using pooled plasma samples and PBS spiked with 10–350 ng gDNA: silica column, magnetic bead, phenol:chloroform, and 2-propanol precipitation. Results: Digestion of the WT EGFR allele followed by deletion-specific fluorescent PCR allowed detection of caof ca. 1 copy of the del E746-A750 EGFR gene (10 pg gDNA) diluted to 0.001%. Furthermore, del E746-A750 was successfully detected in 1/5 the final DNA volume (5 μl) in all spiked blood samples. Magnetic bead-based DNA extraction yielded the highest percent recovery of gDNA from PBS (69% recovery of the 10-ng sample). Phenol:chloroform extraction gave the highest yield with pooled plasma samples. Conclusions: The combination of an optimized DNA extraction method, clearing the plasma DNA sample of amplifiable WT DNA by restriction digestion, and mutation-specific fluorescent PCR provides a highly sensitive assay for detection of somatic mutations in plasma. No significant financial relationships to disclose.

Evaluation of denaturing high‐performance liquid chromatography as a rapid detection method for identification of epidermal growth factor receptor mutations in nonsmall‐cell lung cancer

Somatic mutations of the epidermal growth factor receptor (EGFR) gene in nonsmall-cell lung cancer (NSCLC) may predict responsiveness to tyrosine kinase inhibitors. These mutations are commonly identified using DNA sequencing methods. Although considered the gold standard, this approach is time-consuming. In addition, this approach requires large diagnostic specimens and a high ratio of tumor-to-normal-tissue DNA for optimal results. The use of denaturing high-performance liquid chromatography (dHPLC) as a method to screen for the 2 predominant EGFR mutations is reported. Clinical specimens from 104 NSCLC patients were analyzed for EGFR mutations in exons 19 and 21. After DNA extraction and polymerase chain reaction (PCR), both direct sequencing and dHPLC were performed and the results were compared. Sequencing revealed a total of 7 mutations: 3 deletion mutations in exon 19 and 4 missense mutations in exon 21. dHPLC showed the presence of genomic alterations in 23 samples, including the 7 identified by sequencing plus 16 additional samples (10 in exon 19 and 1 in exon 21). dHPLC fractions were isolated, reamplified, and sequenced to confirm the results. In serial dilution studies, dHPLC was able to detect mutations in samples containing as little as 1.6% to 6.25% mutated DNA, whereas direct sequencing required at least 30%. dHPLC is an efficient and more sensitive method for screening for genomic alterations in exons 19 and 21 of the EGFR gene compared with direct sequence analysis. These data suggest that dHPLC should be implemented as a screening tool for detection of EGFR mutations.

Use of denaturing high performance liquid chromatography (dHPLC) for detection of EGFR mutations in patients with NSCLC

10068 Background: Somatic mutations of the epidermal growth factor receptor (EGFR) gene may predict responsiveness to tyrosine kinase inhibitors in patients with non-small cell lung cancer (NSCLC). These mutations are commonly identified using DNA sequencing methods. Although considered the gold standard, this approach is expensive and time-consuming. In addition, a high ratio of tumour to normal tissue DNA is required for optimal results which is not often available in biopsies obtained from these patients. The primary objective of this study was to develop a rapid and sensitive method for screening of EGFR mutations. Materials and Methods: Clinical specimens from 110 NSCLC patients were analysed for EGFR mutations in exons 19 and 21. After DNA extraction and PCR, both dHPLC and direct sequencing were performed and results were compared. Results: Sequencing revealed a total of 7 (6%) mutations: 4 missense mutations in exon 21 and 3 deletion mutations in exon 19. dHPLC showed the presence of genomic alterations in 18 (16%) samples, including the 7 identified by sequencing plus 11 additional samples (10 in exon 19 and one in exon 21). dHPLC fractions were isolated, reamplified, and sequenced to confirm these results. In serial dilution studies, dHPLC was able to detect mutations in samples containing as little as 10% mutated DNA whereas direct sequencing required at least 30%. Conclusions: dHPLC is an efficient and accurate, as well as a a more sensitive method for screening of genomic alterations in exons 19 and 21 of the EGFR gene compared to direct sequencing. This data suggests that dHPLC should be implemented as a screening tool for detection of EGFR mutations. No significant financial relationships to disclose.

Detection of occult tumor cells in lymph nodes from non-small cell lung cancer patients using reverse transcription-polymerase chain reaction for carcinoembryonic antigen mRNA with the evaluation of its sensitivity

We evaluated the usefulness of a real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) method for detecting occult tumor cells in histologically malignant-negative lymph nodes resected from patients with non-small cell lung cancer. First, we examined the relationship between tumor cell number and carcinoembryonic antigen (CEA) mRNA copy number using a PCR method with a cancer cell line (A549) in a serial dilution study. Next, we evaluated the relationship between nodal metastatic area size and CEA mRNA copy number using lymph nodes with histologically proven metastasis in a serial slice study. On the basis of those results, we performed RT-PCR analyses with 28 primary tumors and 211 lymph nodes from 28 patients who underwent a lobectomy with systematic node dissection. Our results in the serial dilution study showed that the detectable limitation by quantitative RT-PCR was 25-100 neoplastic cells and 20-100 CEA mRNA copy numbers. In the serial slice study, we found a correlation between CEA mRNA copy number and nodal metastatic area. In the clinical samples, amplification of CEA mRNA was obtained with all 28 primary tumors and 13 of the lymph nodes with metastasis shown by hematoxylin-eosin staining. Furthermore, 52 (25%) of 211 histologically negative lymph nodes and the specimens from 14 (64%) of the 22 pN0 patients revealed a significant level of CEA mRNA. These results indicate that micrometastases, which are not detectable with conventional examinations, can be detected by the present method of RT-PCR for CEA mRNA in a proportion of patients with resected pN0 non-small cell lung cancer.

Epidermal growth factor receptor gene mutation in non-small cell lung cancer using highly sensitive and fast TaqMan PCR assay

Epidermal growth factor receptor (EGFR) gene mutations have been found in a subset of non-small cell lung cancer (NSCLC) with good clinical response to gefitinib therapy. A quick and sensitive method with large throughput is required to utilize the information to determine whether the molecular targeted therapy should be applied for the particular NSCLC patients. Using probes for the 13 different mutations including 11 that have already been reported, we have genotyped the EGFR mutation status in 94 NSCLC patients using the TaqMan PCR assay. We have also genotyped the EGFR mutations status in additional 182 NSCLC patients, as well as 63 gastric, 95 esophagus and 70 colon carcinoma patients. In 94 NSCLC samples, the result of the TaqMan PCR assay perfectly matched with that of the sequencing excluding one patient. In one sample in which no EGFR mutation was detected by direct sequencing, the TaqMan PCR assay detected a mutation. This patient was a gefitinib responder. In a serial dilution study, the assay could detect a mutant sample diluted in 1/10 with a wild-type sample. Of 182 NSCLC samples, 46 mutations were detected. EGFR mutation was significantly correlated with gender, smoking status, pathological subtypes, and differentiation of lung cancers. There was no mutation detected by the TaqMan PCR assay in gastric, esophagus and colon carcinomas. TaqMan PCR assay is a rapid and sensitive method of detection of EGFR mutations with high throughput, and may be useful to determine whether gefitinib should be offered for the treatment of NSCLC patients. The TaqMan PCR assay can offer us a complementary and confirmative test.

Detection of disseminated lung cancer cells in regional lymph nodes by assay of CK19 reverse transcriptase polymerase chain reaction and its clinical significance

To set up a molecular method (i.e. RT-PCR) that can be used to detect disseminated tumor cells (DTCs) in regional lymph nodes (LNs) in patients with lung cancer and to evaluate its clinical significance. Cytokeratin 19 (CK(19)) was used as marker. Serial dilution study for LC-5 cells (a lung squamous cell line) was performed to detect sensitivity of the molecular protocol. Regional LNs (n = 261) and primary lung cancer tissue (n = 40) were obtained from 40 patients with lung cancer who underwent lobectomy or pneumonectomy. They were randomly categorized into two groups: group I (LN-based study, n = 20) and group II (patient-based study, n = 20). Each LN was halved. One half of a LN was subjected to histological examination (HE) and the other half was subjected to RT-PCR amplification of CK(19) mRNA. The effect on survival was analyzed. The cumulative survival was calculated by the Kaplan-Meier method and compared by the log rank test. The Cox model analyzed the prognostic factors. CK(19) mRNA expressed in all tumor tissues as well as LC-5, PAa cells (a lung adenocarcinoma cell line), but not in normal control LNs. Serial dilution study for LC-5 cells demonstrated that CK(19) mRNA was detectable at a concentration as low as 10 LC-5 cells in 1x10(7) LN cells. There was no significant difference between the detecting result of single LN and that of mixed LNs (P > 0.05). In 18 of 40 patients, the metastasis in regional LNs was found by both HE and RT-PCR. Of 22 patients without pathologically involved nodes, six (27%) were found to express CK(19) mRNA in regional LNs. According to the results of regional LNs in 40 patients by molecular assay, the presence of the CK(19) product in LNs was related to tumor size (chi(2) = 5.76, P < 0.025) as well as cell differentiation of the tumor (chi(2) = 7.08, P < 0.01). Following a median observation time of 26 months (range, 4 to 60 months), patients with DTCs in nodes showed significant shorter disease-free survival duration than node-negative patients (log-rank test, P = 0.001). The independence of this prognostic significance was demonstrated by a multivariate analysis (Cox regression model, P = 0.004). The results diagnosed by HE had no significant effect on prognoses (P = 0.455). Comparing with HE, RT-PCR can make more accurate assessment of metastatic status in LNs, which is helpful for screening the patients in whom the early subclinical metastasis exists and disclosing the intrinsic regulation of malignant metastasis. The presence of DTCs in LNs is an independent factor for prognosis. Molecular detection of DTCs in LNs is a supplement for current tumor staging in lung carcinoma.

Detection of nonmelanoma skin cancer micrometastases in lymph nodes by using reverse transcriptase-polymerase chain reaction for keratin 19 mRNA.

A new sensitive method for the detection of skin cancer micrometastases in lymph nodes is based on amplification of keratin 19 (K19) mRNA by reverse transcriptase-polymerase chain reaction (RT-PCR). To compare results of RT-PCR with those of histological examination in terms of the detection rate of skin cancer micrometastases. Twenty-six lymph nodes obtained from 13 patients with squamous cell carcinoma (SCC), eccrine porocarcinoma and Paget's disease were investigated by histological examination (haematoxylin and eosin sections) and RT-PCR. RT-PCR was performed on extracted RNA by using K19 primer pairs. RT-PCR products were visualized by ethidium bromide staining and confirmed by non-radioactive hybridization with K19-specific probes. All of 10 histologically positive lymph nodes yielded the expected 460-bp band. Of the 16 histologically negative lymph nodes, one (6%) was found by RT-PCR to express K19 mRNA, indicating the presence of micrometastases which could not be detected by histological examination. A serial dilution study using RNA extracted from SCC cells mixed with RNA extracted from normal lymph node cells showed a detection sensitivity of K19 RT-PCR of 10-5 micro g cancer cell RNA in 1 micro g lymph node RNA. Nested RT-PCR showed a detection sensitivity of one tumour cell in 106 lymphocytes. These results demonstrate the usefulness of K19 RT-PCR for the detection of skin cancer micrometastases in lymph nodes.

Detection of Sporothrix schenckii in Clinical Samples by a Nested PCR Assay

Cutaneous sporotrichosis is a chronic granulomatous fungal infection caused by Sporothrix schenckii with worldwide distribution. Its traditional diagnosis is time-consuming and difficult to differentiate from that of a clinical sporotrichoid lesion caused by various pathogens. In this study, a nested PCR assay for the detection of S. schenckii was evaluated by using a sequence of 18S rRNA gene as a target. For the examination of specificity and sensitivity, five clinical isolates with 1 ATCC 10213 strain of S. schenckii, 10 strains of clinical common fungi, 3 strains of Mycobacterium spp., Staphylococcus aureus, and normal human skin tissue were used. The expected fragment was amplified from six S. schenckii isolates in the first round and nested PCR but not from other microorganisms and human DNA. Their sequences were 100% identical to the S. schenckii 18S rRNA gene sequence deposited in GenBank. A detection limit of 40 fg of S. schenckii DNA extract was determined with ethidium bromide staining. Serial dilution studies demonstrated that the nested PCR could detect a DNA amount of 1 CFU of S. schenckii in tissue samples. We further investigated the nested PCR assay for the detection of S. schenckii from the tail tissues of 5 experimentally infected mice and from the clinical biopsy specimens of 12 patients with sporotrichosis confirmed by culture or histochemical staining. The nested PCR assay was positive in all 5 infected mice and in 11 of the 12 clinical specimens. The high sensitivity and specificity of this nested PCR indicate that the assay can provide rapid diagnosis with sufficient accuracy to be clinically useful for patients with sporotrichosis.

Studies on neurosteroids XIV. Levels of dehydroepiandrosterone sulfate in rat brain and serum determined with newly developed enzyme-linked immunosorbent assay.

An enzyme-linked immunosorbent assay (ELISA) of dehydroepiandrosterone sulfate (DHEAS), one of the neurosteroids, has been developed for measuring its brain and serum levels in rats without deconjugation. 11 alpha-Hemiglutaryloxy-DHEAS was newly synthesized, conjugated with bovine serum albumin (BSA), and immunized to rabbits for the production of anti-DHEAS antibodies. A bridge-heterologous ELISA system employing the sequential saturation method exhibited a high sensitivity with a midpoint of 100 pg. Although the antibody significantly cross-reacted with epiandrosterone sulfate, it easily discriminated the unconjugated steroids and pregnenolone sulfate, which is reported to exist in the brain at a much higher level when compared with DHEAS. The brain homogenate or serum was treated with hexane to remove the lipophilic compounds and purified with an OASIS HLB cartridge. The DHEAS levels were then determined by ELISA. The overall recovery rate through the pretreatment was a satisfactory and constant (81.8 +/- 3.4% for brain, 89.3 +/- 3.0% for serum, mean +/- standard deviation). This ELISA afforded a satisfactory serial dilution study and recovery test. The intra- and inter-assay coefficients of variation were lower than 13%, which showed the precision of the proposed method. The applied method showed that DHEAS was not detected in some brain samples and its levels were much lower than those previously reported and than its serum levels.

A monoclonal antibody-based enzyme-linked immunosorbent assay of ursodeoxycholic acid 3-sulfates in human urine

Sulfation of the 3-hydroxy group is assumed to be a major metabolic route of ursodeoxycholic acid (UDCA) which is used for treating various hepatobiliary diseases. We have developed a sensitive enzyme-linked immunosorbent assay (ELISA) for determining the total amount of nonamidated, glycine- and taurine-amidated ursodeoxycholic acid 3-sulfates (UDCA 3-Suls) using a newly established monoclonal antibody. In this study, 12 kinds of antibody-secreting hybridoma clones were generated by a fusion experiment between P3/NS1/1-Ag4-1 myeloma cells and the spleen cells from a BALB/c or an A/J mouse which had been immunized with a conjugate of nonamidated UDCA 3-Sul and bovine serum albumin. One of the monoclonal antibodies, Ba-10 (γ2a, κ), had suitable binding properties for clinical application, which was group-specific to the UDCA 3-Suls, and showed negligible cross-reactivities with various related bile acids including potentially interfering compounds, namely, the unconjugated UDCA, UDCA 7- N-acetylglucosaminide, the 3-sulfates of cholic acid, chenodeoxycholic acid and deoxycholic acid. The antibody Ba-10 allowed us to develop a sensitive competitive ELISA system whose measurable range was approximately 2–200 pg per assay. A serial dilution study indicated that the ELISA enables the direct measurement of the UDCA 3-Suls in human urine before and after the administration of exogenous UDCA. The daily urinary excretion rate of UDCA 3-Suls from healthy male volunteers ( n = 5) was determined to be a mean of 131 ± 61.2 (SD) μg as the nonamidated UDCA 3-Sul equivalent.

Detection of lung cancer micrometastasis in regional lymph nodes by assays of CK19 reverse transcription-polymerase chain reaction.

To set up a molecular method(RT-PCR) which can be used to detect micrometastasis of regional lymph nodes (LNs) in patients with lung cancer. Primary lung cancer tissues ( n = 20) and regional LNs ( n = 159) were obtained from 20 patients with lung cancer who underwent lobectomy. Each LN was halved. One half of a LN was subjected to histological examination (HE) and the other half was subjected to RT-PCR amplification of CK19 mRNA. Serial dilution study using LC-5 cells was performed to detect sensitivity of the CK19 RT-PCR method. Serial dilution study for LC-5 cells demonstrated that CK19 mRNA was detectable at a concentration as low as 10 LC-5 cells in 1 *10(7) LN cells. CK19 mRNA was found in 42 LNs that were proved to have metastasis by HE. Of the other 117 LNs which were diagnosed as no metastasis by HE , however , twenty five LNs were found to express CK19 mRNA by RT-PCR. Comparing with HE method , the RT-PCR method can make more accurate assessment of metastatic status in LNs.

Detection of the pancreas-specific gene in the peripheral blood of patients with pancreatic carcinoma.

The prognosis of patients with pancreatic carcinoma remains very poor. To improve the therapeutic results, the early detection of this cancer is needed. The present study was performed to detect the pancreas-specific gene, chymotrypsinogen, in the peripheral blood from patients with pancreatic carcinoma by using reverse transcription polymerase chain reaction (RT-PCR) in order to evaluate the clinical significance of this gene. Ten patients with pancreatic carcinoma, two with acute pancreatitis, three with chronic pancreatitis and ten control subjects were examined for the presence of chymotrypsinogen using RT-PCR techniques in the peripheral blood. To confirm that the chymotrypsinogen gene was expressed in a pancreas-specific manner, the expression of chymotrypsinogen in various types of human adult tissue was evaluated by RT-PCR. The specific band of the chymotrypsinogen gene was detected in the pancreas. Serial dilution studies demonstrated the chymotrypsinogen gene to be detected at a concentration of one pancreatic cell per 106 peripheral blood cells. Seven out of the ten (70%) patients with pancreatic carcinoma were found to be positive based on the RT-PCR findings. In contrast, no pancreas-specific gene was detected in the peripheral blood of any patients with acute pancreatitis, chronic pancreatitis or the control subjects. Our observations show that the detection of the pancreatic specific gene, chymotrypsinogen, is therefore useful as a genetic diagnostic marker in pancreatic carcinoma. © 1999 Cancer Research Campaign

Semiautomated analysis of alkaline phosphatase isoenzymes in serum of normal cynomolgus monkeys (Macaca fascicularis).

Alkaline phosphatase (ALP) isoenzyme analysis, using a combination of wheat germ lectin (WGL) precipitation, levamisole inhibition and an automated p-nitrophenylphosphate assay was validated for use with serum from monkeys (Macaca fascicularis) and used to determine the activities of liver ALP (LALP), bone ALP (BALP) and intestinal ALP (IALP). Based on serial dilution studies and within-run and between-run coefficients of variation, each assay had excellent linearity and acceptable precision. In addition, liver and intestinal mucosa extracts for tissue specific alkaline phosphatases were used to confirm assay validations. Gender-specific differences for total ALP, LALP, and BALP activities were present in sera from normal monkeys between 2 and 4 years of age. Males had 1.3-fold higher total ALP and LALP activities, and 1.5-fold higher BALP activity compared with females. The majority of ALP activity in normal monkey serum was LALP isoenzyme activity, which ranged from 56.7% to 94.7% of total activity. Serum BALP activity ranged from 5.3% to 42.8%. There was negligible IALP activity in all serum samples.