Abstract:
OBJECTIVE:To compare the whole genomes sequencing (WGS) results in the 100K Genomes project with the results of routine molecular diagnostics in precision medicine. MATERIALS AND METHODS:We analysed 374 cancers including a high tumour mutational burden (TMB-high) subgroup, defined as >10 non-synonymous single nucleotide variations per megabase. Colon cancers were evaluated for microsatellite instability (MSI), mismatch repair (MMR) genes and NRAS, KRAS and BRAF mutations using routine molecular diagnostics. Fluorescence in-situ hybridisation/immunohistochemistry was used to evaluate the Her2Neu status in breast cancers. RESULTS:There was high correlation between WGS and routine diagnostic testing results irrespective of TMB status in colon cancers. Her2Neu status was discordant in 3 out of the 5 TMB-high breast cancers (p=0.049). The presence of ductal carcinoma in-situ correlated significantly with discordance (p=0.04). There were 3 (5%) discordant colorectal cases, all in the KRAS gene, 2 of which were from the non-invasive adenomatous component (p=0.0058). Of the 374 cases we identified 24 tumours with a TMB >10; comprising (colorectal carcinomas (CRCs) n=16, breast carcinomas n=5, bladder urothelial cell cancers n=3). Of the 16 TMB-high colorectal adenocarcinomas, 13 had MSI-high status. The same 13 had defective MMR protein expression. TMB-high colorectal cancers had 100% concordant results between WGS and NGS testing for KRAS, BRAF and NRAS (16/16). CONCLUSION:The microsatellite and mutational status of colorectal cancers evaluated by WGS seem to correlate well with the routine diagnostic testing if it is ensured that the invasive component is sequenced. Evaluation of WGS results need to be carefully correlated with histomorphology, as tumour heterogeneity/contamination with pre-malignant components needs to be taken into account.
journal_name
J Clin Patholjournal_title
Journal of clinical pathologyauthors
Echejoh G,Liu Y,Chung-Faye G,Charlton J,Moorhead J,Clark B,Davidson P,Sarker D,Ross P,Ooft MLdoi
10.1136/jclinpath-2020-206998subject
Has Abstractpub_date
2020-10-29 00:00:00eissn
0021-9746issn
1472-4146pii
jclinpath-2020-206998pub_type
杂志文章abstract::A patient with hyperparathyroidism due to a parathyroid adenoma was found to have metastatic medullary carcinoma in lymph nodes close to the thyroid gland. The finding of normal calcitonin and parathormone concentrations after removal of the adenoma suggested that the parathyroid lesion was not the result of the hypoc...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.24.9.851
更新日期:1971-12-01 00:00:00
abstract::A spectrophotometric assay of proteolytic enzyme activity is described in which the optical density obtained by a given enzyme preparation is related (2 alpha less than 0.01) to the serological activity of that preparation in a two stage technique. The assay appears to be of use for the standardisation of enzyme prepa...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.37.3.329
更新日期:1984-03-01 00:00:00
abstract:AIMS:To validate the Singapore nomogram for outcome prediction in breast phyllodes tumours in a large cohort of Singaporean patients, as previous validation studies were conducted on small numbers of patients. We also investigate the association of fibroadenomas and phyllodes tumours within a subset of our cohort. MET...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jclinpath-2017-204568
更新日期:2018-02-01 00:00:00
abstract::Several diseases of the small intestine, including gluten-sensitivity, present with malabsorption and a "flat" mucosa. Determination of the mitotic index of epithelial lymphocytes provides a simple, objective method of assessing, and thus of predicting, whether a flat mucosa is due to gluten-sensitivity (index greater...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.36.2.149
更新日期:1983-02-01 00:00:00
abstract::The applicability of a hapten-antihapten sandwich technique incorporating a monoclonal antihapten bridge antibody to localisation of tissue antigen is described. The results show that the method is both versatile and selective and has the potential of being even more sensitive than currently used immunoperoxidase meth...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.34.9.1000
更新日期:1981-09-01 00:00:00
abstract:AIMS:In everyday practice, epidermal growth factor receptor (EGFR) testing is centralised in referral laboratories that receive paucicellular cytological specimens. Ideally, EGFR testing should be carried out in the centre where the patient is diagnosed such that the most cellular slide can be selected from in-house co...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jclinpath-2016-203989
更新日期:2017-04-01 00:00:00
abstract::Four assays for the detection of alphafetoprotein (AFP) in the diagnosis of primary hepatocellular carcinoma (HCC) were evaluated. The frequency of AFP detection was compared in 89 HCC patients and in 71 patients with chronic active hepatitis/cirrhosis. Of the four assays, immunodiffusion, counterimmunoelectrophoresis...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.33.8.792
更新日期:1980-08-01 00:00:00
abstract:BACKGROUND:Primary biliary cirrhosis (PBC) is an autoimmune liver disease characterised by the presence of various laboratory abnormalities but the precise role of laboratory staff in initiating clinical referral and subsequent biopsy is not clear. OBJECTIVE:To examine the impact of laboratory abnormalities in the inv...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.2005.028936
更新日期:2006-04-01 00:00:00
abstract::The need for separate swab transport methods for aerobes and anaerobes may result in inadequate transport of specimens for anaerobic bacteriology. Most microbiology laboratories in Australia rely on Stuart's transport medium to protect anaerobic bacteria. This paper presents a new, simple transport medium (Transport D...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.35.5.555
更新日期:1982-05-01 00:00:00
abstract::The role of active hepatitis B virus (HBV) infection in chronic HBsAg positive hepatitis with and without hepatitis delta virus (HDV) superinfection was analysed in percutaneous liver biopsy specimens from 50 patients. Each specimen was divided into two--one part for histological evaluation and for the detection of HB...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.42.7.689
更新日期:1989-07-01 00:00:00
abstract:AIMS:To investigate the association of cagA positivity and non-opsonic neutrophil activation capacity in wild-type Helicobacter pylori strains with peptic ulcer disease or chronic gastritis only. METHODS:Helicobacter pylori were isolated from antral biopsies of 53 consecutive patients with chronic antral gastritis, of...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.53.4.318
更新日期:2000-04-01 00:00:00
abstract:AIMS:To assess A103 (melan-A) immunoreactivity in a range of ovarian sex cord stromal tumours and to evaluate it for the differential diagnosis of other neoplasms. METHODS:Paraffin embedded tissue sections from 45 sex cord stromal tumours and 44 potential histological mimics were examined immunohistochemically using t...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.53.3.206
更新日期:2000-03-01 00:00:00
abstract::An ultrastructural cytochemical study of lysosomal acid phosphatase was performed on leukemic cells in a case of chronic lymphocytic leukaemia of T cell origin (T-CLL). The cells showed inclusion bodies known as parallel tubular arrays, which often lay within acid phosphatase-positive, membrane-bound spaces. This sugg...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.35.2.167
更新日期:1982-02-01 00:00:00
abstract::Antithrombin activities in 30 severely malnourished children and 40 normal children were estimated in clotting tests by thrombin neutralisation as anti-Xa and by a heparin antithrombin assay; and by immunodiffusion as alpha 2-globulin and alpha 1-antitrypsin. The patients' mean alpha 2-globulin was severely depressed,...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.32.10.1025
更新日期:1979-10-01 00:00:00
abstract:AIM:The rapid and fully automated Idylla EGFR Mutation Assay has been specifically designed to process formalin-fixed, paraffin-embedded sections without requiring preliminary DNA extraction. This study evaluates whether this approach can also process archival smears from patients with non-small cell lung cancer (NSCLC...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jclinpath-2019-205863
更新日期:2019-09-01 00:00:00
abstract::The development of sensitive reagents and detection systems, together with the introduction of heat-induced antigen retrieval, has rapidly entrenched immunohistology as an indispensable adjunct to routine histological examination, contributing to diagnosis, prognosis and treatment. New antibodies continue to be produc...
journal_title:Journal of clinical pathology
pub_type: 杂志文章,评审
doi:10.1136/jcp.2005.031179
更新日期:2006-11-01 00:00:00
abstract::A simple, standardised procedure was used for processing data from External Quality Assessment Schemes and for producing performance charts. A graphic presentation of cumulative performance is generated for each test, using an integrated software package to display results in a standardised format. This permits interp...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.44.1.17
更新日期:1991-01-01 00:00:00
abstract::Two groups of women with non-specific genital infection were treated for two weeks with tetracycline 250 mg six-hourly and minocycline 100 mg twice daily respectively. Cultures for yeasts were performed before treatment and at the end of the first and second weeks. Before treatment yeasts, mostly Candida albicans, wer...
journal_title:Journal of clinical pathology
pub_type: 临床试验,杂志文章
doi:10.1136/jcp.28.5.403
更新日期:1975-05-01 00:00:00
abstract::Protein HC and protein HC-IgA complex were measured in 18 different types of fluid sample from healthy subjects and patients with different illnesses to determine if the concentrations of protein HC and protein HC-IgA complexes could be used to monitor certain diseases, when measured separately. The normal values for ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.41.11.1176
更新日期:1988-11-01 00:00:00
abstract:BACKGROUND:Clinical outcome in patients with diffuse large B cell lymphomas (DLBCL) is highly variable and poorly predictable. Microarray studies showed that patients with DLBCL with a germinal centre B cell-like (GCB) phenotype have a better prognosis than those with an activated B cell-like (ABC) phenotype. The BMI1 ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.2006.038752
更新日期:2007-02-01 00:00:00
abstract::A method for identifying Helicobacter pylori using a non-isotopic in situ hybridisation technique is described. A probe generated by polymerase chain reaction (PCR) with primers directed against parts of the Helicobacter pylori 16SrRNA sequence was used. Paraffin wax embedded gastric biopsy specimens from patients wit...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.47.9.862
更新日期:1994-09-01 00:00:00
abstract::A quantitative method of estimating heparin co-factor in terms of percentage activity is presented. The activity in sera from 75 normal subjects varied little from 100%. Low results were obtained in sera from 50 cases of varying types of malignancy. ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.16.2.115
更新日期:1963-03-01 00:00:00
abstract::Rocket-line immunoelectrophoresis (R-LIE) with antigen containing intermediate gel, and co-agglutination utilising protein A-containing staphylococci coated with specific antibodies, were adapted for serotyping the prototypes of group B meningococci. Both were found to have the same specificity as agar gel double diff...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.32.2.136
更新日期:1979-02-01 00:00:00
abstract::A case of chromoblastomycosis confined to the mucous membrane of one side of the nasal septum is reported. The organism was not cultivated, but its characteristics in histological preparations were typical of those of the organisms in sections of cutaneous lesions known to be caused by Phialophora pedrosoi and related...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.13.4.287
更新日期:1960-07-01 00:00:00
abstract::Review of published work and analysis of clinical data and pathology of four biopsy specimens from two patients with laryngeal contact granuloma showed that its peptic origin was derived from a gastro-oesophago-laryngeal reflux. It is proposed that the term "peptic granuloma" should be given to this phenomenon. This t...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.42.8.800
更新日期:1989-08-01 00:00:00
abstract:AIM:To examine tumour samples immunohistochemically for MUC1 (episialin), epidermal growth factor receptor (EGFR), and c-erbB-2, since the disruption of the cell-cell adhesion system by MUC1 and the c-erbB oncoprotein family is known to be important in the development of metastasis in human cancers. METHODS:93 tumour ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.51.9.667
更新日期:1998-09-01 00:00:00
abstract::Staphylococcus aureus isolated between 1967 and 1975 from the nose and skin lesions of patients in dermatology wards and from the burns of patients in a burns unit in Birmingham showed a high incidence of multiple antibiotic-resistant strains in both environments. Over 20% of the strains isolated from patients on admi...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.30.1.40
更新日期:1977-01-01 00:00:00
abstract:AIMS:To isolate RNA and DNA simultaneously from formalin fixed paraffin wax embedded tissue to assess the clonality of enteropathy associated T cell lymphomas and to analyse it in detail by a non-radioactive method of T cell receptor complementarity determining region 3 (CDR3) spectratyping. METHODS:DNA and RNA were i...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.50.10.811
更新日期:1997-10-01 00:00:00
abstract:AIMS:Common variable immunodeficiency (CVID) is the most common serious primary immunodeficiency. This paper describes the immunological consequences of human immunodeficiency virus (HIV) infection in a patient with familial CVID subsequently treated with highly active antiretroviral therapy (HAART). METHODS:Serial me...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.54.9.713
更新日期:2001-09-01 00:00:00
abstract::In a population of 432 apparently healthy men aged 50 years and over 19-2% had one or more erythrocytes per high-power field in the urine while 8-1% had more than 10. Erythrocyturia seemed to be strongly correlated with tobacco consumption. No significant association with occupation could be demonstrated but the data ...
journal_title:Journal of clinical pathology
pub_type: 杂志文章
doi:10.1136/jcp.30.4.341
更新日期:1977-04-01 00:00:00