Abstract：
BACKGROUND:Next generation sequencing (NGS)-based assays continue to redefine the field of genetic testing. Owing to the complexity of the data, bioinformatics has become a necessary component in any laboratory implementing a clinical NGS test. CONTENT:The computational components of an NGS-based work flow can be conceptualized as primary, secondary, and tertiary analytics. Each of these components addresses a necessary step in the transformation of raw data into clinically actionable knowledge. Understanding the basic concepts of these analysis steps is important in assessing and addressing the informatics needs of a molecular diagnostics laboratory. Equally critical is a familiarity with the regulatory requirements addressing the bioinformatics analyses. These and other topics are covered in this review article. SUMMARY:Bioinformatics has become an important component in clinical laboratories generating, analyzing, maintaining, and interpreting data from molecular genetics testing. Given the rapid adoption of NGS-based clinical testing, service providers must develop informatics work flows that adhere to the rigor of clinical laboratory standards, yet are flexible to changes as the chemistry and software for analyzing sequencing data mature.
journal_name
Clin Chemjournal_title
Clinical chemistryauthors
Oliver GR,Hart SN,Klee EWdoi
10.1373/clinchem.2014.224360subject
Has Abstractpub_date
2015-01-01 00:00:00pages
124-35issue
1eissn
0009-9147issn
1530-8561pii
clinchem.2014.224360journal_volume
61pub_type
杂志文章,评审abstract：BACKGROUND:Extracellular matrix alterations are important elements in the arterial changes seen in diabetes, being associated with increased vascular stiffness and the development of cardiovascular diseases. However, no biomarkers for diabetes-related arterial changes have been defined. METHODS:Mammary artery specimen...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2011.162966
更新日期：2011-11-01 00:00:00
abstract：:Bush and Reed reported (Clin Chem 1987;33:821-3) that the reaction of albumin with bromcresol purple but not with bromcresol green underestimated the concentration of albumin in synthetically obtained bilirubin-albumin (Bd) by 29%. Their unproven assumption was that chemically synthesized Bd behaved in a manner indist...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1991-07-01 00:00:00
abstract：:Two-hour postprandial specimens have a -14% proportional bias for lipoprotein(a) [Lp(a)], a -0.035 g/L systematic bias for apolipoprotein (apo) A-I, and a -9% proportional bias for apo B, compared with values in 12-h fasting specimens. Although a physiological hemodilution appears to account for a portion of these bia...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1992-03-01 00:00:00
abstract：:We have modified the 63Ni radiochemical method of Ho (Anal Biochem 1970;36:105) for determination of free fatty acids (FFA) in plasma. Extracting 1 or 0.1 mL of plasma with Dole's mixture (J Biol Chem 1960;235:2595) and washing the "heptane" layer with two volumes of isopropanol/water/dilute (0.5 mol/L) H2SO4 (25/25/1...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1987-01-01 00:00:00
abstract：:Two-dimensional protein maps of biopsies from normal mucosa, tubular adenomas (polyps), and colonic carcinomas in humans have been studied in order to obtain information on the possible precancerous role of intestinal polyps. The maps are complex and several hundred protein spots are seen after staining with Coomassie...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1982-04-01 00:00:00
abstract：:Two major components of rRNA (18S and 28S rRNA) were separated by electrophoresis in injection-molded acrylic chips with a microchannel 100 microm in width, 40 microm in depth, and with 1 cm of separation distance. Microchannels were filled with 4 g/L hydroxypropylmethylcellulose as sieving polymer and 5 mg/L ethidium...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1998-11-01 00:00:00
abstract：:In this enzyme-linked immunoassay for human thyrotropin (TSH) in unextracted serum we use 96-well immunoenzymometric assay plates, first coated with polyclonal antibody to TSH, then incubated with the serum samples and reacted with mouse monoclonal antibody to human TSH. After incubation with alkaline phosphatase-labe...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1985-07-01 00:00:00
abstract：BACKGROUND:The optimal situation in external quality assessment (EQA) is to use commutable materials. No previous study has examined the commutability of a whole-blood material for point-of-care (POC) testing. The aim of this study was to determine the commutability of the Norwegian Quality Improvement of Laboratory Ex...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2018.300202
更新日期：2019-06-01 00:00:00
abstract：:For normal and above-normal concentrations of angiotensin-converting enzyme (ACE; EC 3.4.15.1) activity in plasma, results of a manual fluorometric method [with hippuryl-histidyl-leucine (HHL), 5 mmol/L, as substrate] correlated well with those of an automated spectrophotometric method [with 3-(2-furylacryloyl)-L-phen...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1991-08-01 00:00:00
abstract：:I present the general pattern relationship between (a) plasma fibrinogen and cholinesterase activity and (b) plasma fibrinogen and hemoglobin, in 250 and 310 hospitalized adults, respectively. Although responses of cholinesterase were often unrelated to fibrinogen, when its activity in plasma was depressed, above-norm...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1977-01-01 00:00:00
abstract：:Creatinine and specific gravity (relative density) measurements both allow differences in urine concentration to be taken into account in determining urine cotinine concentrations. In this study we demonstrate that the variance of urine cotinine measurements is reduced comparably when either creatinine or specific gra...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1994-04-01 00:00:00
abstract：BACKGROUND:Astilbin is a flavonoid isolated from the rhizome of Smilax glabra. In a previous study, we revealed its unique immunosuppressive activity, a selective inhibition against activated T lymphocytes. This characteristic of astilbin is beneficial for the treatment of human immune diseases. METHODS:We incubated a...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2006.077297
更新日期：2007-03-01 00:00:00
abstract：INTRODUCTION:Parathyroid hormone-related peptide (PTHrP) is involved in activating pathways, allowing tumor cells to form bone metastases. Measurement of PTHrP is used for the diagnosis and clinical management of patients suspected of hypercalcemia of malignancy. We developed an LC-MS/MS method for measuring PTHrP, est...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2015.244012
更新日期：2016-01-01 00:00:00
abstract：:The use of 4-chlorotestosterone acetate by farmers for cattle fattening was recently demonstrated although the use of this anabolic steroid is strictly forbidden in the European Union. We investigated the metabolism of 4-chlorotestosterone acetate in the bovine species after intramuscular and oral administration. Nine...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1998-05-01 00:00:00
abstract：:We describe specifications for high-purity 4-nitrophenol, which is suitable for spectrophotometric standardization. Such a reference material is needed in clinical enzymology to establish the proper molar absorptivity of 4-nitrophenol under final reaction conditions, particularly for measuring alkaline phosphatase act...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1980-05-01 00:00:00
abstract：BACKGROUND:The TDx Fetal Lung Maturity II (FLM II) assay uses amniotic fluid to assess lung maturity of the unborn infant. We investigated common preanalytical factors that influence FLM results, including centrifugation, sample storage, and contamination by whole blood. METHODS:We tested 18 specimens after centrifuga...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/49.6.935
更新日期：2003-06-01 00:00:00
abstract：BACKGROUND:Recent publications have explored the possibility of using fingerprints to confirm drug use, but none has yet dealt with environmental contamination from fingertips. Here we explored the possibility of establishing an environmental cutoff for drug testing from a single fingerprint. METHODS:Fingerprint sampl...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2017.281469
更新日期：2018-06-01 00:00:00
abstract：:A method has been developed for the determination of inorganic arsenic [As(III) and As(V)] and its organic metabolites (monomethylarsenic and dimethylarsenic) in urine by flow-injection hydride generation atomic absorption spectrometry. The nontoxic seafood-derived arsenobetaine and arsenocholine species were first se...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1993-08-01 00:00:00
abstract：:We directly compared the reliability of a single-isotope enzymatic derivative technique for measurement of plasma catecholamines with that of the well-established double-isotope method. A significant (p less than 0.001) correlation was observed between measurements (n = 52) in the two assays, both for norepinephrine (...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1978-04-01 00:00:00
abstract：:We present a case of advanced ovarian carcinoma associated with high concentrations of serum and urine amylase. Biochemical analysis to elucidate the nature and origin of the hyperamylasemia identified seven amylase isoenzymes, of which five appeared to be distinct from normal salivary and pancreatic amylase. We discu...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1979-06-01 00:00:00
abstract：:The effect of serum-clot contact time on laboratory results was studied by dividing each blood specimen into four blood collection tubes. The control sera were separated from the clot within 30 min of the collection. The other tubes were incubated at 32 degrees C, and the sera were separated at 3, 6, and 24 h. The ser...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1998-06-01 00:00:00
abstract：:We describe a new and specific method for measurement of lecithin palmitic acid in amniotic fluid. Dipalmitoyl lecithin, the major alveolar surfactant, has previously been estimated by measuring the lecithin-sphingomyelin ratio, total lecithin, total phospholipid phosphorus, and (or) total palmitic acid. Our method is...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1977-01-01 00:00:00
abstract：:We compared the results obtained by a micromethod for the determination of plasma lipoprotein cholesterol, in which electrophoresis is used to separate the lipoprotein fractions (beta-, pre-beta-, and alpha-lipoproteins), with those determinations with ultracentrifugation (low-density, very-low-density, and high-densi...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1979-10-01 00:00:00
abstract：BACKGROUND:The lead mobilization test reflects the mobilizable and likely toxicologically active fraction of the lead body burden. We propose a safe and convenient protocol for this test, to assess concomitant copper and zinc excretion and to determine the size of the chelatable lead pool in nonoccupationally exposed a...
journal_title：Clinical chemistry
pub_type： 临床试验,杂志文章
doi：10.1373/clinchem.2005.051128
更新日期：2006-01-01 00:00:00
abstract：:We report the intermediate-term effects of three consecutive evenings of moderate ethanol ingestion (0.75 g/kg body weight each evening) on activity values for alkaline phosphatase, gamma-glutamyltransferase, creatine kinase, aspartate aminotransferase, alanine aminotransferase, and lactate dehydrogenase in sera of ni...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1977-05-01 00:00:00
abstract：BACKGROUND:Institutions face increasing charges related to molecular genetic testing for neurological diseases. The literature contains little information on the utilization and performance of these tests. METHODS:A retrospective utilization review was performed to determine the diagnostic yield of neurogenetic tests ...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2006.083360
更新日期：2007-06-01 00:00:00
abstract：:We measured cyclosporine in whole blood from normal volunteers administered single oral doses of the drug and from two renal-transplant patients on immunosuppressive maintenance therapy, by liquid chromatography (I) and by radioimmunoassay with use of nonspecific polyclonal (II), specific monoclonal (III), and nonspec...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1987-12-01 00:00:00
abstract：:We used a modification of the polymerase chain reaction (PCR), involving two pairs of oligonucleotide primers, to detect a mutation in the low-density lipoprotein (LDL) receptor gene, commonly occurring among patients with familial hypercholesterolemia (FH) in Finland. This mutation, called FH-Helsinki, involves a lar...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：
更新日期：1990-06-01 00:00:00
abstract：:Correlation between coronary heart disease and lipoprotein size and composition is well documented. Within the low-density lipoprotein (LDL) family the small LDL particles are associated with increased risk of coronary heart disease. These particles also have increased apolipoprotein (apo) B content. The appearance of...
journal_title：Clinical chemistry
pub_type： 杂志文章,评审
doi：
更新日期：1995-01-01 00:00:00
abstract：BACKGROUND:Immunoassays specific for 1-84 parathyroid hormone (PTH) reportedly reflect the bioactivity of PTH; however, PTH immunoassays can be susceptible to interference by cross-reacting PTH fragments. In addition, these assays currently lack standardization. A methodology using immunocapture purification with liqui...
journal_title：Clinical chemistry
pub_type： 杂志文章
doi：10.1373/clinchem.2009.134643
更新日期：2010-02-01 00:00:00
