Abstract:
BACKGROUND:Formalin-fixed paraffin-embedded (FFPE) tumor material represents a valuable resource for the analysis of RNA-based biomarkers, both in research laboratories and in routine clinical testing. A robust and automated RNA-extraction method with a high sample throughput is required. METHODS:We evaluated extraction performance for 4 silica-based RNA-extraction protocols: (a) a fully automated, bead-based RNA-isolation procedure; (b) its manual counterpart; (c) a semiautomated bead-based extraction system; and (d) a manual column-based extraction kit. RNA from 360 sections (90 sections per extraction method) of 30 FFPE tumor blocks up to 20 years of age was purified and analyzed by quantitative reverse-transcription PCR for ESR1 (estrogen receptor 1), PGR (progesterone receptor), ERBB2 [v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)], and RPL37A (ribosomal protein L37a). RESULTS:The semiautomated protocol gave the best yield. The 3 bead-based methods showed good across-method correlations in both yield and relative mRNA amounts (r = 0.86-0.95 and 0.98, respectively). In contrast, correlations between any of the bead-based methods and the manual column-based method were worse (r = 0.77-0.95 and 0.96, respectively). The fully automated method showed the lowest variation from section to section (root mean square error, 0.32-0.35 Cq, where Cq is the quantification cycle) and required the least hands-on time (1 h). CONCLUSIONS:The fully automated RNA-purification method showed the best reproducibility in gene expression analyses of neighboring sections of tissue blocks between 3 and 20 years of age and required the least overall and hands-on times. This method appears well suited for high-throughput RNA analyses in both routine clinical testing and translational research studies with archived FFPE material.
journal_name
Clin Chemjournal_title
Clinical chemistryauthors
Bohmann K,Hennig G,Rogel U,Poremba C,Mueller BM,Fritz P,Stoerkel S,Schaefer KLdoi
10.1373/clinchem.2008.122572subject
Has Abstractpub_date
2009-09-01 00:00:00pages
1719-27issue
9eissn
0009-9147issn
1530-8561pii
clinchem.2008.122572journal_volume
55pub_type
杂志文章abstract:BACKGROUND:The European Atherosclerosis Society-European Federation of Clinical Chemistry and Laboratory Medicine Consensus Panel aims to provide recommendations to optimize atherogenic lipoprotein quantification for cardiovascular risk management. CONTENT:We critically examined LDL cholesterol, non-HDL cholesterol, a...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:10.1373/clinchem.2018.287037
更新日期:2018-07-01 00:00:00
abstract:BACKGROUND:Because reference values for vitamin B(12) concentrations and vitamin B(12)-binding capacities for pregnant women have not been established, the reference values for nonpregnant women are often applied to assess vitamin B(12) status. The aim of the present study was to describe ranges of biochemical indices ...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:2002-06-01 00:00:00
abstract::In this method for serum and urinary urea determination, the same reagent is used without predilution of urine samples. The method is based on the pH increase resulting from the ammonia released by urease hydrolysis of urea. o-Cresolphthalein complexone is used to monitor the pH change colorimetrically. Urea concentra...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1992-05-01 00:00:00
abstract::The Center for Disease Control (CDC), the New York State Department of Health (NYSDH), the College of American Pathologists, and 23 manufacturers of diagnostic products participated in an interlaboratory study of aspartate aminotransferase (EC 2.6.1.1) methodologies. Six different lyophilized materials were prepared a...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1978-06-01 00:00:00
abstract::Patients' urines gave an unexpectedly high percentage of false-negative results for erythrocytes on a reagent strip, even when the test field for ascorbic acid indicated that none of this substance was present to inhibit the test reaction. By adding known amounts of erythrocytes to normal urines, we found that this ph...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1984-11-01 00:00:00
abstract:BACKGROUND:In vitro and animal studies suggest that tumor necrosis factor alpha (TNF-alpha) modulates intestinal iron transport. We hypothesized that the effect of TNF-alpha might be particularly relevant if iron absorption is not effectively controlled by the HFE gene. METHODS:In patients with homozygous C282Y hemoch...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:10.1373/clinchem.2005.065417
更新日期:2006-08-01 00:00:00
abstract::We describe the case of a three-year-old girl with Wilms' tumor, whose serum showed at least a fivefold increase in relative viscosity although concentrations of albumin and immunoglobulins were normal. An unusual electrophoretogram of serum protein prompted further investigation. The increased viscosity was caused by...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1984-06-01 00:00:00
abstract::We have developed and evaluated a new procedure for detecting trends in quality-control measurements and applied it to laboratory data. The method requires the use of sequential or "moving" slope estimates to identify trends. Formulae are derived to estimate the regression error for the moving slope directly from the ...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1991-03-01 00:00:00
abstract::This ultrafiltration technique allows determination of free drug in 50 microL of serum. We ultrafiltered sera containing the following drugs--valproic acid (and its major metabolites), phenobarbital, diazepam, indomethacin, phenytoin, furosemide, and chloramphenicol--using both the commercially available micropartitio...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1984-06-01 00:00:00
abstract::We have assessed Calbiochem single-vial enzymatic reagent systems for the analysis for cholesterol and triglycerides, using manual and centrifugal analyzer techniques. Analysis for cholesterol by both techniques had acceptable performance by the short-term criteria of the Center for Disease Control (CDC) during this s...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1978-11-01 00:00:00
abstract::We describe a gas--liquid-chromatographic method for determining the concentration of amantadine hydrochloride in urine with beta-phenylethylamine as internal standard. The urine sample is made alkaline and extracted with 0.5 mL of chloroform. After centrifugation the aqueous layer is aspirated, and an aliquot of the ...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1980-02-01 00:00:00
abstract::Hepatitis A virus (HAV) infection occurs worldwide and is an important cause of acute viral hepatitis in the US. In this review, I cover the epidemiology, course of infection, clinical manifestations, serological responses, and prevention of this infection. Although most patients completely recover from this disease, ...
journal_title:Clinical chemistry
pub_type: 杂志文章,评审
doi:
更新日期:1997-08-01 00:00:00
abstract::We modified the ISO-DALT two-dimensional gel electrophoresis system to allow the routine examination of serum specimens from patients with monoclonal gammopathies. This system, MC-Iso 1, is characterized by a broad pH gradient for resolving the basic immunoglobulin heavy and light chains. The increased resolution of b...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1982-04-01 00:00:00
abstract:BACKGROUND:ADB-PINACA and its 5-fluoropentyl analog 5F-ADB-PINACA are among the most potent synthetic cannabinoids tested to date, with several severe intoxication cases. ADB-PINACA and 5F-ADB-PINACA have a different legal status, depending on the country. Synthetic cannabinoid metabolites predominate in urine, making ...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:10.1373/clinchem.2016.267575
更新日期:2017-05-01 00:00:00
abstract::Problems encountered in the uroporphyrinogen I synthase assay were found to be due to the Triton reagent, slit-width and excitation wavelength settings of the spectrophotofluorometer, and leg-phase in the enzyme reaction. Of Triton X-100 from four suppliers, only three were found suitable. Differences in enzyme activi...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1980-08-01 00:00:00
abstract::A new method for the reliable identification of localized variations in DNA by detection of associated diagnostic products with matrix-assisted laser desorption ionization time-of-flight mass spectrometry is described. The diagnostic products are generated by the primer oligo base extension (PROBE) reaction, which req...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1997-07-01 00:00:00
abstract::Intra-erythrocytic pH, ATP concentrations, and 2,3-diphosphoglycerate relaxation times were studied in living erythrocytes by "high-resolution" 31P NMR spectroscopy to assess homeostasis within the cells. In uremic patients, intra-erythrocytic pH is significantly decreased before hemodialysis, but is corrected equally...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1987-01-01 00:00:00
abstract::We find lag phases exceeding 20 min in measuring creatine kinase activity, by using the kinetic creatin phosphate leads to creatine assay, in sera of some patients with carcinoma metastatic to the liver. Such long lag phases are accompanied by a decreased apparent enzyme activity. These problems are eliminated by addi...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1976-11-01 00:00:00
abstract:BACKGROUND:B-type natriuretic peptide (BNP), which is activated in heart failure (HF), is processed to an active form by corin. The corin gene is expressed in the human heart and kidney, but corin protein expression in the heart, kidney, and circulation, along with whether proBNP is processed by circulating corin, rema...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:10.1373/clinchem.2010.153908
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:The sex differential in coronary heart disease (CHD) risk, which is not explained by male/female differences in lipid and lipoprotein concentrations, narrows with age. We examined whether this differential CHD risk might, in part, be attributable to the sizes of lipoprotein particles or concentrations of lip...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:10.1373/clinchem.2004.032763
更新日期:2004-07-01 00:00:00
abstract::Intra- and interindividual components of biological variation have been determined for total thyroxin (TT4), free thyroxin (FT4), total triiodothyronine (TT3), free triiodothyronine (FT3), and thyrotropin (TSH). Calculated analytical goals (CV, %) for the precision required for optimal patient care are: TT4 less than ...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1986-06-01 00:00:00
abstract::Using "high performance" liquid chromatography, we studied non-protein-bound fractions and total concentrations of 18 solutes accumulating in sera from a group of 12 patients who were undergoing chronic ambulatory peritoneal dialysis (CAPD) and in predialysis sera from a group of 15 hemodialysis (HD) patients. We moni...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1988-01-01 00:00:00
abstract::We measured advanced glycosylation end products in the mesenteric artery of 37 patients (ages 29-82 years), 34 of whom were nondiabetic. Samples of arterial tissue were obtained during bowel resectioning. Advanced glycosylation end products were measured as collagen-linked fluorescence (excitation wavelength 370 nm, e...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1992-04-01 00:00:00
abstract:BACKGROUND:Yersinia pestis, the causative agent of the zoonotic infection plague, is a major concern as a potential bioweapon. Current real-time PCR assays used for Y. pestis detection are based on plasmid targets, some of which may generate false-positive results. METHODS:Using the yp48 gene of Y. pestis, we designed...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:10.1373/clinchem.2005.051839
更新日期:2005-10-01 00:00:00
abstract::We describe an automated assay of glycohemoglobin performed with the Abbott Vision analyzer. The assay is based on batch affinity-extraction with 3-aminophenylboronic acid-derivatized agarose beads. Reagents are packaged in a disposable test pack. Whole-blood specimens are hemolyzed with saponin within a glass capilla...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1992-12-01 00:00:00
abstract:BACKGROUND:First introduced into clinical microbiology laboratories in Europe, MALDI-TOF MS is being rapidly embraced by laboratories around the globe. Although it has multiple applications, its widespread adoption in clinical microbiology relates to its use as an inexpensive, easy, fast, and accurate method for identi...
journal_title:Clinical chemistry
pub_type: 杂志文章,评审
doi:10.1373/clinchem.2014.221770
更新日期:2015-01-01 00:00:00
abstract::Serum specimens from patients on primidone therapy were assayed by two currently available procedures: a commercially available enzyme immunoassay (EMIT) and a published gas-chromatographic procedure. Both procedures were done with commercially available materials and equipment. Results by the two procedures agreed we...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1976-06-01 00:00:00
abstract::Proteinuria, long recognized as a sign of renal disease, is a common laboratory abnormality in children and adults. Proteinuria may be transient or persistent; when persistent, the cause must be determined. Proteinuria may be primarily glomerular or tubular in origin. Glomerular proteinuria is usually an important con...
journal_title:Clinical chemistry
pub_type: 杂志文章,评审
doi:
更新日期:1989-05-01 00:00:00
abstract:BACKGROUND:The emergence of a novel pandemic human strain of influenza A (H1N1/09) has clearly demonstrated the need for flexible tools enabling the rapid development of new diagnostic methods. METHODS:We designed a set of reverse-transcription quantitative real-time PCR (RT-qPCR) assays based on the Universal ProbeLi...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:10.1373/clinchem.2009.136192
更新日期:2009-12-01 00:00:00
abstract::We recently proposed a quantitative PCR procedure for the absolute measurement of c-erbB-2 oncogene amplification, based on the simultaneous polymerase chain reaction (PCR) amplification of the target gene and of a competitor DNA molecule acting as internal standard. To increase the number of assayable oncogenes and t...
journal_title:Clinical chemistry
pub_type: 杂志文章
doi:
更新日期:1995-06-01 00:00:00