Abstract:
AIMS:PCR amplicon-based next-generation sequencing (NGS) panels are increasingly used for clinical diagnostic assays. Amplification bias is a well-known limitation of PCR amplicon-based approaches. We sought to characterise lower-performance amplicons in an off-the-shelf NGS panel (TruSight Myeloid Sequencing Panel) for myeloid neoplasms and attempted to patch the low read depth for one of the affected genes, CEBPA. METHODS:We performed targeted NGS of 158 acute myeloid leukaemia samples and analysed the amplicon read depths across 568 amplicons to identify lower-performance amplicons. We also correlated the amplicon read depths with the template GC content. Finally, we attempted to patch the low read depth for CEBPA using a parallel library preparation (Nextera XT) workflow. RESULTS:We identified 16 lower-performance amplicons affecting nine genes, including CEBPA. There was a slight negative correlation between the amplicon read depths and template GC content. Addition of the separate CEBPA library generated a minimum read depth per base across the CEBPA gene ranging from 268x to 758x across eight samples. CONCLUSIONS:The identification of lower-performance amplicons will be informative to laboratories intending to use this panel. We have also demonstrated proof-of-concept that different libraries (TruSight Myeloid and Nextera XT) can be combined and sequenced on the same flow cell to generate additional reads for CEBPA.
journal_name
J Clin Patholjournal_title
Journal of clinical pathologyauthors
Yan B,Hu Y,Ng C,Ban KH,Tan TW,Huan PT,Lee PL,Chiu L,Seah E,Ng CH,Koay ES,Chng WJdoi
10.1136/jclinpath-2015-203580subject
Has Abstractpub_date
2016-09-01 00:00:00pages
801-4issue
9eissn
0021-9746issn
1472-4146pii
jclinpath-2015-203580journal_volume
69pub_type
杂志文章abstract::The plasma concentrations of biotin were measured for up to 49 days after injury in nine children with burns and scalds which involved from 12% to 50% of the surface area of the body. Biotin levels below the minimum of the control range were observed in eight of the nine injured children at some stage during the episo...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.29.1.58
更新日期:1976-01-01 00:00:00
abstract:AIMS:To compare the sensitivity and specificity of new rabbit monoclonal antibody SP3 with those of mouse monoclonal and rabbit polyclonal antibodies using HER2 amplification defined by chromogenic in situ hybridisation (CISH) as the gold standard. METHODS:Serial sections from tissue microarrays (TMAs) containing 84 b...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.2007.053892
更新日期:2008-08-01 00:00:00
abstract:AIMS:To determine the clinical performance of three cerebrospinal fluid (CSF) IgG synthesis formulae using data obtained from two quantitation methods. METHODS:Receiver operator characteristic (ROC) analysis and decision index plots were used to compare a rate nephelometric (RN) and a rocket immunoelectrophoretic (RIE...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.49.1.24
更新日期:1996-01-01 00:00:00
abstract:BACKGROUND:Epstein's syndrome is defined as a subtype of Alport's syndrome, and is distinguished from the other subtypes by accompanying macrothrombocytopenia. Mutations in collagen IV genes are known to be involved in the pathogenesis of typical Alport's syndrome. However, the presence of an underlying genetic defect ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.50.11.919
更新日期:1997-11-01 00:00:00
abstract:OBJECTIVES:As the best characterised cancer/testis antigen family members, melanoma-associated antigens (MAGE) have been reported to be expressed in various malignant tumours. However, the expression pattern of MAGE-A family in lung adenocarcinoma (LAC) specimens and their prognostic and therapeutic significance for pa...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jclinpath-2016-203718
更新日期:2017-06-01 00:00:00
abstract::A comparison is made of tests for thyroglobulin antibody, using gel diffusion, electroprecipitin, bentonite flocculation, tanned red cell agglutination, and latex slide agglutination techniques on sera from cases of Hashimoto's disease and other thyroid disorders. Any increase in gamma globulin was also noted from the...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.15.2.153
更新日期:1962-03-01 00:00:00
abstract::The finding of raised growth hormone concentrations in patients with secondary malignancy in the liver is reported. These concentrations were significantly higher than those found in patients with primary malignancy only or in those with non-hepatic secondaries. A wide range of malignancies was investigated and the hi...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.36.8.935
更新日期:1983-08-01 00:00:00
abstract:AIMS:To investigate proliferative activity in leukaemic and lymphomatous bone marrow infiltrates and to assess the feasibility of transport of specimens among institutions. METHODS:Proliferative activity in bone marrow trephine cryosections from 99 patients with non-Hodgkin's lymphoma (NHL), 23 patients with acute mye...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.47.3.209
更新日期:1994-03-01 00:00:00
abstract::Although Neisseria species other than N gonorrhoeae and N meningitidis normally comprise part of the commensal bacterial flora of the oropharynx, they may occasionally act as opportunistic pathogens. Infections in which these organisms have been implicated include cases of endocarditis, meningitis, septicaemia, otitis...
journal_title:Journal of clinical pathology
pub_type: 杂志文章,评审
doi:10.1136/jcp.36.2.213
更新日期:1983-02-01 00:00:00
abstract::A method for the differential determination of plasma antithrombins, antithrombin III and alpha2 macroglobulin, is described. The method is based on the selective inactivation of plasma alpha2 macroglobulin by treatment with 0-1 M methylamine for 10 minutes at 37 degrees C and on the observation that antithrombin III ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.29.1.63
更新日期:1976-01-01 00:00:00
abstract:AIMS:To establish whether abnormalities in the course of the vertebral artery occur and whether they are relevant to arterial injury associated with head and neck movements. METHODS:Twenty vertebral arteries were carefully dissected at necropsy and abnormalities in course were noted, along with any other bony or carti...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.48.7.637
更新日期:1995-07-01 00:00:00
abstract:AIMS:To assess the association between Helicobacter pylori-associated gastritis and HLA-DR antigen (class II antigen) expression. METHODS:Fifty endoscopic gastric biopsy specimens were studied for the presence of H pylori, degree and type of inflammation, and for HLA-DR antigen expression in the epithelium. The cases ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.45.1.30
更新日期:1992-01-01 00:00:00
abstract:AIMS:To establish a mechanism to examine the components of turnaround time in a representative cross-section of laboratory users; and to identify potential areas for improvement. METHODS:Information was collected manually from result reports received by eight laboratory users: three wards in the main hospital, four GP...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.47.7.585
更新日期:1994-07-01 00:00:00
abstract::The sellar region is the site of a large number of pathological entities arising from the pituitary and adjacent anatomical structures, including brain, blood vessels, nerves and meninges. The surgical pathology of this area requires the accurate identification of neoplastic lesions, including pituitary adenoma and ca...
journal_title:Journal of clinical pathology
pub_type: 杂志文章,评审
doi:10.1136/jcp.2005.031187
更新日期:2006-12-01 00:00:00
abstract::VARIOUS LABORATORIES HAVE REPORTED DIFFERING SUCCESS RATES IN THEIR ABILITY TO DETECT INTRATHECAL SYNTHESIS OF ANTIBODY WHEN COMPARING THE INDEX OF [FORMULA: see text] with electrophoretic analysis. We selected 44 patients in the borderline area of minimal and/or equivocal abnormality by IgG index. Electrophoretic ana...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.36.3.312
更新日期:1983-03-01 00:00:00
abstract::Of 30 children with bleeding disorders exposed to an index tuberculosis case, six developed primary pulmonary tuberculosis and two others became positive skin reactors. There was a significant correlation between the amount of replacement treatment received and the development of evidence of tuberculous infection. Onl...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.38.10.1163
更新日期:1985-10-01 00:00:00
abstract::A histochemical method is described of differentiating between normal and neoplastic cells in plasma using the activity of various enzymes characteristic of plasma cells. It was found that in both types of cell increased or diminished activity of cytoenzymes is a useful means of distinguishing between normal and abnor...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.18.3.345
更新日期:1965-05-01 00:00:00
abstract::A variety of blood culture media were compared to determine the optimal method for the isolation of Mycobacterium avium-intracellulare (MAI) from the blood of patients with AIDS. Simulated laboratory blood cultures and clinical blood cultures were tested. Glucose broth, Bactec aerobic medium, Kirschner's medium, and B...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.41.6.687
更新日期:1988-06-01 00:00:00
abstract:BACKGROUND:Some uterine endometrioid adenocarcinomas exhibit a distinctive morphological phenotype characterised by the formation of microcystic, elongated and fragmented (MELF) glands. Immunohistochemical studies have suggested that MELF-type changes represent an epithelial-mesenchymal transition which has been associ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.2009.069500
更新日期:2010-07-01 00:00:00
abstract::Visceral botryomycosis is rare, and documented sites are lung, brain, kidney, liver and prostate. This report describes a rare autopsy case of disseminated visceral botryomycosis, with bulky, grape-like botryomycotic vegetations in the heart, and similar abscesses in the lungs and bone marrow. This is the first such r...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.2008.057588
更新日期:2008-08-01 00:00:00
abstract::A recently developed procedure, that has been shown to be suitable for detailed immunohistological analysis, has been used to prepare cryostat sections of bone marrow to investigate whether enzyme-histochemical techniques are also feasible on such material. A selected group of enzymes, some of which are inhibited or d...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.35.11.1220
更新日期:1982-11-01 00:00:00
abstract::The results of using a product of serum thyroxine and triiodothyronine binding coefficient, estimated by simple methods, to give a ;free thyroxine index' in normal women, in pregnant women, and in patients taking oral contraceptives is described. The method is believed to provide a reliable means of assessing thyroid ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.21.6.767
更新日期:1968-11-01 00:00:00
abstract::Platelet adhesiveness has been assessed on whole blood from a series of 34 diabetics and 50 control subjects using adenosine diphosphate (A.D.P.) and by adherence to glass microspherules (ballotini). Using both techniques it was possible to demonstrate a significant increase in platelet adhesiveness in the diabetic pa...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.20.6.845
更新日期:1967-11-01 00:00:00
abstract::Immunoreactive trypsin (IRT) content in blood spots from 17 cystic fibrosis (CF) children born between 1975-80 were assayed with reagents from two commercial radioimmunoassay kits. The manufacturers' procedures were modified to allow assay of blood spot IRT. Half of the CF samples had a significantly raised IRT conten...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.34.8.906
更新日期:1981-08-01 00:00:00
abstract::An ultramicro electrophoretic technique for the separation of serum lipoproteins is described using agarose gel on microscope slides.The interaction between the agarose gel and lipoproteins has been reduced and the separation between beta- and pre-beta-lipoproteins has been improved over existing methods. A semiquanti...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.24.1.83
更新日期:1971-02-01 00:00:00
abstract::The sensitivity of methods to detect antibodies to intrinsic factor was assessed. Five sera of known antibody content were tested in 31 laboratories and 30 sera from patients with pernicious anaemia were tested in one laboratory. Five non-commercial methods and two kits for type I antibodies and one non-commercial met...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.42.2.210
更新日期:1989-02-01 00:00:00
abstract::Only four cases of tracheopathia osteoplastica have been reported in Britain in the past 110 years. Ten further cases are now reported; in two the diagnosis was made at bronchoscopy. It is suggested that the reputed rarity of the condition in Britain is not the whole picture. ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.20.6.814
更新日期:1967-11-01 00:00:00
abstract::Haemoglobin (Hb) Bonn is a newly described benign Hb variant that causes falsely depressed oxygen saturation as measured by pulse oximetry. It was found to be associated with mild haemolysis. Since its first report in a German family, no further cases have been documented in the literature. We report the first Chinese...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.2010.078147
更新日期:2010-10-01 00:00:00
abstract:AIMS:To determine important factors influencing recurrence after local excision of duct carcinoma in situ (DCIS) of the breast. MATERIALS AND METHODS:The extent (size) in millimetres, classification (by cytonuclear grade (NHSBSP system), by extent of necrosis, and by the Van Nuys system), and excision margins of 115 c...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.55.8.581
更新日期:2002-08-01 00:00:00
abstract::Primary low grade marginal zone B cell lymphoma (MZL) of the breast and localised mammary amyloidosis are exceedingly rare entities. This report describes the case of a woman with long standing Sjögren's syndrome presenting with asymptomatic MZL of the breast showing plasmacytic differentiation, associated with local ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.56.1.74
更新日期:2003-01-01 00:00:00