Bayesian approach to interpreting somatic cancer sequencing data: a case in point.

Abstract:

:Cancer lineage/tissue-of-origin assignment in cancers of unknown primary remains a challenge even when aided by massively parallel sequencing. The stakes are high for patients as many contemporary therapeutic strategies are disease-specific, and the biological differences can influence the patients' responses. Herein, we provide an example of how Bayesian analysis can be used to merge data from clinical history, histology, immunohistochemistry (IHC) and cancer DNA sequencing to assist in tissue-of-origin assignment. Iterative Bayesian analysis is performed through a set of simple calculations to calculate the OR between the differential diagnoses. We illustrate a clinical case, where the distinction between a primary lung versus metastatic bladder cancer was aided meaningfully by iterative Bayesian analyses, incorporating IHC and sequencing data.

journal_name

J Clin Pathol

authors

Yoon JY,Rosenbaum JN,Vergara N,Cohen RB,Wilson RB

doi

10.1136/jclinpath-2020-206895

subject

Has Abstract

pub_date

2020-08-27 00:00:00

eissn

0021-9746

issn

1472-4146

pii

jclinpath-2020-206895

pub_type

杂志文章
  • Rapid cytological diagnosis of basal cell carcinoma of the skin.

    abstract::Cytological diagnosis in a series of 153 skin lesions is presented. The diagnosis in each case has been compared with the clinical assessment and, where available, the biopsy result (85 lesions). Of 131 basal cell carcinomas, a cytological diagnosis was possible in 124 while biopsyl failed to identify two of the 73 le...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.32.4.361

    authors: Brown CL,Klaber MR,Robertson MG

    更新日期:1979-04-01 00:00:00

  • Rapid detection of hepatitis B virus DNA in liver tissue by in situ hybridisation and its combination with immunohistochemistry for simultaneous detection of HBV antigens.

    abstract::A rapid technique using a non-radioactive receptor molecule (digoxigenin) for intrahepatic hepatitis B virus (HBV) DNA detection using in situ hybridisation was developed. It can be adapted for use in combination with standard immunohistochemistry for simultaneous detection of both HBV DNA and HBV antigens. The total ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.44.11.905

    authors: Lau JY,Naoumov NV,Alexander GJ,Williams R

    更新日期:1991-11-01 00:00:00

  • The Splendore-Hoeppli phenomenon in hepatic botryomycosis.

    abstract::A 68 year old diabetic man developed septicaemia and multiple liver abscesses due to Streptococcus intermedius. Liver biopsy revealed streptococcal botryomycosis which showed the Splendore-Hoeppli phenomenon. Diabetes mellitus is an example of the immunosuppressed states that have been associated with botryomycosis. ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.51.5.399

    authors: Schlossberg D,Pandey M,Reddy R

    更新日期:1998-05-01 00:00:00

  • Expression and prognostic value of putative cancer stem cell markers CD117 and CD15 in choroidal and ciliary body melanoma.

    abstract:AIMS:The aim of the present study was to immunohistochemically investigate the expression and prognostic significance of putative cancer stem cell markers CD117 (c-kit), CD34, CD20 and CD15 in a cohort of patients with primary choroidal and ciliary body melanoma. METHODS:The immunohistochemical expression of these mar...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jclinpath-2015-203130

    authors: Lukenda A,Dotlic S,Vukojevic N,Saric B,Vranic S,Zarkovic K

    更新日期:2016-03-01 00:00:00

  • Intraduct papillary mucinous neoplasm of the pancreas: a tumour linked with IgG4-related disease?

    abstract:OBJECTIVES:Intraduct papillary mucinous neoplasm (IPMN) is a pancreatic tumour that is often associated with chronic pancreatitis (CP) in the surrounding pancreas. Type 1 autoimmune pancreatitis (AIP) is a fibro-inflammatory condition with characteristic histological features and prominent IgG4+ plasma cells and is par...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jclinpath-2013-201516

    authors: Bateman AC,Culver EL,Sommerlad M,Chetty R

    更新日期:2013-08-01 00:00:00

  • Expression of ATM, p53, and the MRE11-Rad50-NBS1 complex in myoepithelial cells from benign and malignant proliferations of the breast.

    abstract:AIMS:To analyse the expression of proteins involved in DNA double strand break detection and repair in the luminal and myoepithelial compartments of benign breast lesions and malignant breast tumours with myoepithelial differentiation. METHODS:Expression of the ataxia telangiectasia (ATM) and p53 proteins was immunohi...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.2004.017434

    authors: Angèle S,Jones C,Reis Filho JS,Fulford LG,Treilleux I,Lakhani SR,Hall J

    更新日期:2004-11-01 00:00:00

  • A histochemical comparison of the O-acylated sialic acids of the epithelial mucins in ulcerative colitis, Crohn's disease, and normal controls.

    abstract::Two histochemical techniques, the PAT/KOH/PAS and the PBT/KOH/PAS, were used to investigate the side chain O-acyl substitution patterns of the sialic acids of the colonic epithelial mucins in cases of ulcerative colitis and Crohn's disease. In both diseases there was, as compared to normal, a reduction in the proporti...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.32.12.1272

    authors: Culling CF,Reid PE,Dunn WL

    更新日期:1979-12-01 00:00:00

  • Examination of operation specimens from patients with spinal tuberculosis for tubercle bacilli.

    abstract::Operation specimens from 52 Hong Kong patients considered to have tuberculosis of the spine were sent at -78 degrees C to London where they were cultured on two Löwenstein-Jensen medium slopes, a slope of 7H11 medium made selective with antibiotics and in two bottles of selective liquid Kirchner medium. Cultures of M ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.36.6.662

    authors: Allen BW,Mitchison DA,Darbyshire J,Chew WW,Gabriel M

    更新日期:1983-06-01 00:00:00

  • Inflammatory bowel disease biopsies: updated British Society of Gastroenterology reporting guidelines.

    abstract::Accurate histopathological assessment of biopsies is important for the diagnosis, subclassification, and management of chronic idiopathic inflammatory bowel disease (IBD). British Society of Gastroenterology (BSG) guidelines for the initial histopathological diagnosis of IBD were published in 1997. Changes since then ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章,实务指引

    doi:10.1136/jclinpath-2013-201885

    authors: Feakins RM,British Society of Gastroenterology.

    更新日期:2013-12-01 00:00:00

  • Ready, steady, go! What do histopathology trainees think they need from training to enable them to develop autonomy in surgical pathology reporting?

    abstract:AIMS:This is a qualitative study of the perceived learning needs of trainees for graded responsibility in histopathological training in the UK. METHODS:A focus group with trainees and interviews with consultants was carried out. Participants were asked 'What do you perceive are the learning needs of histopathology tra...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jclinpath-2015-203090

    authors: Finall A,Allery L

    更新日期:2016-01-01 00:00:00

  • Antibody to coliform antigens in urine samples from patients with symptoms of urinary tract infection.

    abstract::An enzyme linked immunoadsorbent assay (ELISA) was used to detect IgG, IgM, and IgA antibody in urine to a crude antigenic mixture prepared from six arbitrarily chosen strains of common coliform urinary pathogens. In a group of patients with symptoms of urinary tract infection 24 of 80 (30%) urine samples were positiv...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.40.7.787

    authors: McKenzie H,Young DN

    更新日期:1987-07-01 00:00:00

  • Malakoplakia of the adrenal gland.

    abstract::The clinical and pathological features of a case of malakoplakia of the adrenal gland occurring in a woman with Escherichia coli infection are described. This lesion mimicked a neoplasm, the true diagnosis only being revealed by histological examination. The light and electron microscopic features are described and it...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.34.6.606

    authors: Benjamin E,Fox H

    更新日期:1981-06-01 00:00:00

  • An in vitro study of the effects of t-PA and tranexamic acid on whole blood coagulation and fibrinolysis.

    abstract:AIMS:Acute traumatic coagulopathy is characterised by fibrinolysis and low fibrinogen. It is unclear how much fibrinogenolysis contributes to reduce fibrinogen levels. The study aim was to: investigate in vitro the effects of tissue-plasminogen activator (t-PA) and tranexamic acid (TXA) on coagulation and fibrinolysis....

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jclinpath-2016-203854

    authors: Godier A,Parmar K,Manandhar K,Hunt BJ

    更新日期:2017-02-01 00:00:00

  • Vitamin D deficiency and low osteocalcin concentrations in anorexia nervosa.

    abstract::The calcium, vitamin D, and osteocalcin concentrations were investigated in 17 patients with anorexia nervosa. Serum 25-hydroxyvitamin D (25 OHD) concentrations below normal were observed in 15 (88%); only two patients has serum 1,25 dihydroxycholecalciferol (1,25(OH)2D) concentrations below normal. Serum parathyroid ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.41.2.195

    authors: Fonseca VA,D'Souza V,Houlder S,Thomas M,Wakeling A,Dandona P

    更新日期:1988-02-01 00:00:00

  • Effect of radiotherapy on oral mucosa assessed by quantitative exfoliative cytology.

    abstract::The effect of radiotherapy on normal buccal mucosa was investigated using the quantitative techniques of cytomorphology (measurement of nuclear and cytoplasmic area) and DNA cytophotometry. These techniques were applied to smears obtained before, during, and after irradiation. Nuclear area and cytoplasmic area increas...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.42.9.940

    authors: Ogden GR,Cowpe JG,Green MW

    更新日期:1989-09-01 00:00:00

  • Can the rapid semiquantitative estimation of serum C reactive protein be adapted for the management of bacterial infection?

    abstract::Serum C reactive protein concentrations measured by a laboratory based assay were compared with the semiquantitative results obtained with a visual agglutination method (Well-cotest, CRP kit). Using this agglutination kit, diluting serum 1/10 and 1/20 gave C reactive protein results which could be of more clinical val...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.38.4.464

    authors: Richards NP,Elliott TS,Powell RJ,O'Callaghan C,Franklin P

    更新日期:1985-04-01 00:00:00

  • Lysosomal enzyme cytochemistry of blood neutrophils.

    abstract::Patients with bacterial infection may show altered membrane permeability of the primary azurophilic lysosomes of blood neutrophils. A new enzyme cytochemical technique, sensitive to increased membrane permeability caused by contact of neutrophils with acetone, saponin, low pH, Streptolysin O, bacteria, and nylon wool,...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.31.7.648

    authors: Wozniak JT,Orchard TL,Mackie PH,Mistry DK,Stuart J

    更新日期:1978-07-01 00:00:00

  • Effect of margins of excision on recurrence after local excision of ductal carcinoma in situ of the breast.

    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

    authors: Douglas-Jones AG,Logan J,Morgan JM,Johnson R,Williams R

    更新日期:2002-08-01 00:00:00

  • Update on eighth edition American Joint Committee on Cancer classification for cutaneous melanoma and overview of potential pitfalls in histological examination of staging parameters.

    abstract::Cutaneous melanoma causes most of the skin cancer deaths in the USA. Melanoma is the fifth most common cancer among men and the sixth most common cancer among women. The incidence of melanoma has risen sharply over the past three decades. In this review, which is informed by our extensive experience at a large cancer ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章,评审

    doi:10.1136/jclinpath-2018-205417

    authors: Trinidad CM,Torres-Cabala CA,Curry JL,Prieto VG,Aung PP

    更新日期:2019-04-01 00:00:00

  • A novel BRCA2 mutation in an Indonesian family found with a new, rapid, and sensitive mutation detection method based on pooled denaturing gradient gel electrophoresis and targeted sequencing.

    abstract:BACKGROUND:Breast cancer is increasing in Indonesia and other developing countries. Germline mutations in the BRCA1/2 genes are most strongly associated with a high risk for breast cancer development. There have been no reports on BRCA1/2 gene mutations in the Indonesian population. Genetic research yielding insight in...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.2004.020388

    authors: Purnomosari D,Paramita DK,Aryandono T,Pals G,van Diest PJ

    更新日期:2005-05-01 00:00:00

  • Intradural bronchogenic cysts.

    abstract::The pathological findings of an intradural and extramedullary cyst in the mid cervical spinal canal are described in a 55 year old woman who presented with a short history of pain and paraesthesia of the right arm. Intradural well defined solitary cystic lesions in the spinal canal are uncommon, their pathogenesis is ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.45.11.1032

    authors: Wilkinson N,Reid H,Hughes D

    更新日期:1992-11-01 00:00:00

  • Nuclear pseudoinclusions in melanocytic naevi and melanomas.

    abstract::Melanocytes in melanocytic naevi and melanomas can display great variation. The presence of nuclear pseudoinclusions (NPI) is said to be useful in the histological and cytological differential diagnosis of malignant melanoma. The prevalence and characteristics of NPI in a series of 493 naevi and 50 melanomas are descr...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.48.7.676

    authors: Rose DS

    更新日期:1995-07-01 00:00:00

  • Comparison of three methods for culture confirmation of Neisseria gonorrhoeae strains currently circulating in the UK.

    abstract:AIMS:To establish the current sensitivity of two commercial kits for culture confirmation of Neisseria gonorrhoeae strains circulating in the UK. METHODS:A total of 544 strains were studied (199 gonococci from male patients attending hospitals in the county of Avon, 204 unselected N gonorrhoeae isolates from male pati...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.48.10.919

    authors: Turner A,Gough KR,Jephcott AE

    更新日期:1995-10-01 00:00:00

  • A COMPARISON OF PLATELET AGGREGATION PRODUCED BY SEVEN COMPOUNDS AND A COMPARISON OF THEIR INHIBITORS.

    abstract::The aggregating effects of adenosine diphosphate, thrombin, 5-hydroxytryptamine, tryptamine, adrenaline and noradrenaline, and tri-ethyl tin have been carefully compared. The first three compounds in some circumstances produce remarkably similar effects although there are important differences. The kinetics of aggrega...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.17.3.275

    authors: O'BRIEN JR

    更新日期:1964-05-01 00:00:00

  • Reactogenicity and immunogenicity of a surface-antigen-adsorbed influenza virus vaccine in children.

    abstract::An influenza virus vaccine containing the purified surface haemagglutinin and neuraminidase antigens of A/Victoria/75 and B/Hong Kong/73 viruses adsorbed to an aluminium hydroxide gel was assessed for reactogenicity and immunogenicity in children aged 4 to 11 years, since there is no influenza virus vaccine available ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.32.6.534

    authors: Eastwood LM,Jennings R,Milner RD,Potter CW

    更新日期:1979-06-01 00:00:00

  • Principal neuropathological and general necropsy findings in 24 renal transplant patients.

    abstract::The principal neuropathological and general pathological findings in a group of 24 patients with renal transplants who died in a nine-year period at the Western Infirmary, Glasgow, are described. Opportunistic infections--bacterial, protozoal, and fungal--were the commonest causes of death. Other causes included cardi...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.35.1.31

    authors: Morton R,Graham DI,Briggs JD,Hamilton DN

    更新日期:1982-01-01 00:00:00

  • Expression of c-myc oncogene in coeliac disease.

    abstract::A monoclonal antibody, produced by peptide immunisation was used to detect the distribution of p62c/myc by immunohistology in normal and coeliac small intestinal mucosa. The effect of gluten in four treated coeliac patients was investigated by taking serial jejunal biopsy specimens for six hours after a 10 g oral glut...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.40.3.307

    authors: Ciclitira PJ,Stewart J,Evan G,Wight DG,Sikora K

    更新日期:1987-03-01 00:00:00

  • Diagnosis of genital infection caused by human papillomavirus using in situ hybridisation: the importance of the size of the biopsy specimen.

    abstract:AIM:To determine the size of a cervical biopsy specimen with human papillomavirus (HPV) infection required to enable in situ hybridisation to be carried out with a guarantee of a reliable result. METHODS:In situ hybridisation was carried out in 142 cervical uterine biopsy specimens classified histologically as low gra...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.48.1.57

    authors: Gómez F,Corcuera MT,Muñoz E,Roldan M,Alonso MJ,Abad M,Paz JI,López-Bravo A

    更新日期:1995-01-01 00:00:00

  • THE THYMUS IN HEPATIC CIRRHOSIS.

    abstract::A post-mortem examination, in the case of a 34-year-old man dying suddenly from head injuries sustained in a road accident, showed early cirrhosis of the liver and associated splenomegaly 17 years after an attack of infective hepatitis. The histology of the thymus showed abnormal changes in the medulla, consisting of ...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.16.5.445

    authors: CORRIDAN M

    更新日期:1963-09-01 00:00:00

  • Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction.

    abstract::Several DNA extraction techniques were quantitatively and qualitatively compared using both fresh and paraffin wax embedded tissue and their suitability investigated for providing DNA and RNA for the polymerase chain reaction (PCR). A one hour incubation with proteinase K was the most efficient DNA extraction procedur...

    journal_title:Journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1136/jcp.43.6.499

    authors: Jackson DP,Lewis FA,Taylor GR,Boylston AW,Quirke P

    更新日期:1990-06-01 00:00:00