Abstract：
BACKGROUND:Microsatellite instability (MSI) is a useful phenotype in cancer diagnosis and prognosis. Nevertheless, methods to detect MSI status from next generation DNA sequencing (NGS) data are underdeveloped. METHODS:We developed an approach to detect the MSI phenotype using NGS (mSINGS). The method was used to evaluate mononucleotide microsatellite loci that were incidentally sequenced after targeted gene enrichment and could be applied to gene or exome capture panels designed for other purposes. For each microsatellite locus, the number of differently sized repeats in experimental samples were quantified and compared to a population of normal controls. Loci were considered unstable if the experimental number of repeats was statistically greater than in the control population. MSI status was determined by the fraction of unstable microsatellite loci. RESULTS:We examined data from 324 samples generated using targeted gene capture assays of 3 different sizes, ranging from a 0.85-Mb to a 44-Mb exome design and incorporating from 15 to 2957 microsatellite markers. When we compared mSING results to MSI-PCR as a gold standard for 108 cases, we found the approach to be both diagnostically sensitive (range of 96.4% to 100% across 3 panels) and specific (range of 97.2% to 100%) for determining MSI status. The fraction of unstable microsatellite markers calculated from sequencing data correlated with the number of unstable loci detected by conventional MSI-PCR testing. CONCLUSIONS:NGS data can enable highly accurate detection of MSI, even from limited capture designs. This novel approach offers several advantages over existing PCR-based methods.
journal_name
Clin Chemjournal_title
Clinical chemistryauthors
Salipante SJ,Scroggins SM,Hampel HL,Turner EH,Pritchard CCdoi
10.1373/clinchem.2014.223677subject
Has Abstractpub_date
2014-09-01 00:00:00pages
1192-9issue
9eissn
0009-9147issn
1530-8561pii
clinchem.2014.223677journal_volume
60pub_type
杂志文章abstract：:Laboratories of the Lipid Research Clinics Program (LRC) maintained the accuracy of their measurements of total cholesterol by using seven pooled serum calibrators supplied by the Centers for Disease Control (CDC). Over the 11-year life of the LRC, each calibrator was prepared in succession and a target value was assi...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1986-04-01 00:00:00
abstract：:Liquid scintillation counting of 3H-labeled whole-blood samples is severely impaired owing to quenching by blood pigments. In this study, dry oxidation and chemical solubilization followed by decolorization were the two general methods used to eliminate color quenching. Three blood volumes were examined: 0.25, 0.50, a...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1981-04-01 00:00:00
abstract：:Energy-dispersive x-ray spectroscopy and inductively coupled plasma emission spectrometry were evaluated as methods for routine multielement analysis of biological material. Standard samples included Standard Reference Materials (National Bureau of Standards), compounded mixtures, and supplements that provided a wide ...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1976-12-01 00:00:00
abstract：BACKGROUND:The current diagnosis and monitoring of bladder cancer are heavily reliant on cystoscopy, an invasive and costly procedure. Previous efforts in urine-based detection of bladder cancer focused on targeted approaches that are predicated on the tumor expressing specific aberrations. We aimed to noninvasively de...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2018.301341
更新日期：2019-07-01 00:00:00
abstract：BACKGROUND:Multiplexed amplicon melting is a closed-tube method for genotyping that does not require probes, real-time analysis, asymmetric PCR, or allele-specific PCR; however, correct differentiation of homozygous mutant and wild-type samples by melting temperature (T(m)) analysis requires high-resolution melting ana...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2007.097121
更新日期：2008-01-01 00:00:00
abstract：:We compared a chemiluminescent assay and a colorimetric endpoint assay for measuring an alkaline phosphatase (EC 3.1.3.1) label in an enzyme immunoassay of thyrotropin (TSH). The substrate in the chemiluminescent assay is a derivative of adamantyl 1,2-dioxetane phosphate. On dephosphorylation, catalyzed by alkaline ph...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1989-07-01 00:00:00
abstract：:A coated microtiter-well, enzyme-linked immunometric assay for quantifying immunoreactive trypsinogen in dried blood spots was modified to use time-resolved fluorescence of europium in place of end-point enzymatic color development as the quantification step. The streptavidin-horseradish peroxidase and color developme...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1993-02-01 00:00:00
abstract：:We describe a two-site time-resolved immunofluorometric assay for guinea pig vascular permeability factor (VPF) for quantifying VPF in different biological fluids. Antibody against the carboxy terminus (C-IgG) is immobilized on microtiter wells, and antibody against the amino terminus (N-IgG) is labeled with Eu(3+)-ch...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1992-01-01 00:00:00
abstract：:We describe a system for detection of leukemia cells involving complement-mediated cytotoxic reaction and an image processing system, consisting of a charge-coupled-device image sensor, an image memory board, a personal computer, and a phase-contrast microscope. Then added to a cell suspension, monoclonal antibody spe...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1987-04-01 00:00:00
abstract：:Published estimates of the imprecision characteristics of immunoassays are often based on quantities of data that seem to be inadequate. The increasing use of imprecision profiles has not necessarily improved the situation. We describe and illustrate a method of computing 95% confidence intervals for profiles estimate...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1990-07-01 00:00:00
abstract：:This improved assay of rheumatoid factors in serum, described here for use with the Baker "Encore" centrifugal analyzer, is efficient, with 250-sample throughput per hour; reproducible, with between-batch CV = 5% and within-batch CV = 2% (mid-assay range); and results correlate well (r = 0.9) with those by other metho...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1989-02-01 00:00:00
abstract：:We present evidence for the utility of an improved assay for the activity of lactate dehydrogenase (EC 1.1.1.27) isoenzymes 1 and 2 in serum, involving inhibition of the H-subunit of LD by pyruvate at pH 7.1. Results correlate well with the LD-1/total LD ratio as evaluated by immunological assay and, as an index to in...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1986-05-01 00:00:00
abstract：:We report the presence of complexes between aspartate aminotransferase (AST, EC 2.6.1.1) and immunoglobulin (Ig) in the serum of a patient suffering from lung cancer with metastasis to the liver. After fractionation of the serum by gel filtration, AST-Ig complexes (AST-IgA, AST-IgG) were demonstrated by counterimmunoe...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1983-02-01 00:00:00
abstract：:The optimal measurement method and clinical application of the therapeutic drug monitoring of cyclosporine remain uncertain. At a workshop held at Hawk's Cay, FL, from January 14 to January 17, 1990, 57 scientists presented their latest research findings, either in formal papers or as discussants. Lively debate and di...
journal_title：Clinical chemistry
pub_type： 共识发展会议,杂志文章,评审
doi：
更新日期：1990-08-01 00:00:00
abstract：:The difference in absorbance (delta A) between equimolar acid and alkaline solutions of methyl red, at a wavelength near the isosbestic point of the indicator, is reproducible. Furthermore, this delta A is sensitive to changes in the wavelength calibration of the instrument used to make the measurement. The delta A of...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1986-01-01 00:00:00
abstract：:We compared different sample-handling techniques for measurement of Na+ and K+ with ion-selective electrodes (ISE). Imprecision was less for venous blood (with a minimum of heparin) than for plasma, serum, or capillary blood. The results for K+ were higher for serum than for whole blood, and higher for whole blood tha...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1984-03-01 00:00:00
abstract：BACKGROUND:A genomic deletion of exon 3 (d3-GHR) of the growth hormone (GH) receptor (GHR) has been linked to the effectiveness of GH therapy in children with GH deficiency. Carriers of the d3-GHR genotype had higher GH-induced growth rates than children homozygous for the full-length (fl)-GHR. The aim of this study wa...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2007.085712
更新日期：2007-08-01 00:00:00
abstract：:Two families with benign hyperphosphatasemia of intestinal origin were studied and compared with six other cases reported in the literature. No evidence of clinical abnormalities or explanations for the unusual enzyme concentrations were found. Agarose gel electrophoresis of alkaline phosphatase (ALP, EC 3.1.3.1) isoe...
journal_title：Clinical chemistry
pub_type： 杂志文章,评审
doi：
更新日期：1991-08-01 00:00:00
abstract：:We are developing a method for quantifying plasma lipoproteins by proton nuclear magnetic resonance (NMR) spectroscopy that offers advantages over existing clinical methods. We showed that the major lipoproteins have distinct NMR properties sufficient to permit their concentrations to be extracted from a computer line...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1992-09-01 00:00:00
abstract：:Ammonia concentrations in plasma may increase because of contamination and deterioration of blood components during specimen handling and storage. Using replicate specimens from healthy volunteers, we studied influences of specimen processing and storage procedures on ammonia measurements made with a self-contained re...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1984-06-01 00:00:00
abstract：:The immunoreactivity of anti-triiodothyronine (anti-T3) IgG, pretreated at acidic pH and adsorbed onto polystyrene beads, was significantly greater than that determined for native anti-T3 IgG immobilized at optimum pH 3.5. Acidic-pH-pretreated IgG, adsorbed at pH 7.0 onto ethanol-treated beads, had less immunoreactivi...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1990-03-01 00:00:00
abstract：:We assessed several methods of inorganic phosphate assay for their suitability in estimating phospholipids in digested extracts of amniotic fluids. The extraction and digestion procedures used for phospholipids from amniotic fluid were also examined critically. The effect of contamination by blood or obstetric cream h...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1975-09-01 00:00:00
abstract：:We report the production and comparative specificities of antisera raised to different immunogens containing codeine, morphine, and oxycodone. Antisera raised to bovine serum albumin (BSA) conjugates of codeine-6-hemisuccinate, ethylmorphine-6-hemisuccinate, or oxycodone-6-carboxymethyloxime had greatest recognition o...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1981-09-01 00:00:00
abstract：:This semi-automated colorimetric assay for the MB isoenzyme of creatine kinase (EC 2.7.3.2) is based on a monoclonal antibody ("Conan-MB") specific for this isoenzyme and is a modification of a previously published method (Vaidya et al., Clin Chem 1986;32:657-63). A 0.64-cm bead coated with 2 to 3 micrograms of antibo...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1988-03-01 00:00:00
abstract：:We determined approximately 15,000 laboratory values in 236 individuals between the ages of 60 and 90 y, 22 individuals between 90 and 99 y, and 69 individuals greater than or equal to 100 y, and compared these with values in young adults. We tested 47 different analytes in the 60-90-y group and 93 analytes in the gre...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1992-06-01 00:00:00
abstract：:Lactate dehydrogenase (LD) isoenzymes 1 and 2 in human serum were separated on a column of diethylaminoethyl-Sephadex. Samples layered on mini-columns were eluted with buffered sodium chloride (100, 150, and 200 mmol/liter). Lactate dehydrogenase activity in column effluents was measured by the Wacker method, and thei...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1978-03-01 00:00:00
abstract：:Since 1991, the Ontario Laboratory Proficiency Testing Program has assessed the analytical performance of creatine kinase (CK; EC 2.7.3.2) isoenzyme-2, using fresh human serum supplemented with purified human CK isoenzymes. In Ontario, the 142 laboratories licensed to analyze CK-2 use a variety of methods: electrophor...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1994-02-01 00:00:00
abstract：:Brain proteins extractable with distilled water or 9 mol/L urea were subjected to two-dimensional gel electrophoresis. They are examined in relation to the identification of actin, tubulin, neurofilament proteins, glial fibrillary acidic protein; proteins of human embryonic neocortex, synaptosomes, myelin, and plasma;...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1982-04-01 00:00:00
abstract：:We describe a multiprobe colorimeter that permits the reading of enzyme-linked immunosorbent assays (ELISA) in situ, by use of microhemagglutination plates. The use of dipping probes eliminates interference from meniscus effects and air-bubble entrapment. Detailed validation tests have been done and potential sources ...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1979-04-01 00:00:00
abstract：:Two patients with Paget's disease of bone were subjected to plasmapheresis. Alkaline phosphatase activities of serum declined sharply, but returned to preplasmapheresis values within eight to 10 days. The biological half-life of circulating skeletal alkaline phosphatase, as calculated from these experiments, is betwee...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1982-01-01 00:00:00
