Evaluation of a deidentification (De-Id) software engine to share pathology reports and clinical documents for research.

Abstract:

:We evaluated a comprehensive deidentification engine at the University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA, that uses a complex set of rules, dictionaries, pattern-matching algorithms, and the Unified Medical Language System to identify and replace identifying text in clinical reports while preserving medical information for sharing in research. In our initial data set of 967 surgical pathology reports, the software did not suppress outside (103), UPMC (47), and non-UPMC (56) accession numbers; dates (7); names (9) or initials (25) of case pathologists; or hospital or laboratory names (46). In 150 reports, some clinical information was suppressed inadvertently (overmarking). The engine retained eponymic patient names, eg, Barrett and Gleason. In the second evaluation (1,000 reports), the software did not suppress outside (90) or UPMC (6) accession numbers or names (4) or initials (2) of case pathologists. In the third evaluation, the software removed names of patients, hospitals (297/300), pathologists (297/300), transcriptionists, residents and physicians, dates of procedures, and accession numbers (298/300). By the end of the evaluation, the system was reliably and specifically removing safe-harbor identifiers and producing highly readable deidentified text without removing important clinical information. Collaboration between pathology domain experts and system developers and continuous quality assurance are needed to optimize ongoing deidentification processes.

journal_name

Am J Clin Pathol

authors

Gupta D,Saul M,Gilbertson J

doi

10.1309/E6K3-3GBP-E5C2-7FYU

subject

Has Abstract

pub_date

2004-02-01 00:00:00

pages

176-86

issue

2

eissn

0002-9173

issn

1943-7722

journal_volume

121

pub_type

杂志文章
  • Primary osteomyelitis due to an anaerobic microorganism.

    abstract::Primary osteomyelitis in a teen-aged boy that mimicked Ewing's tumor radiologically showed small Gram-negative rods on the original smear. The organism isolated was an obligately anaerobic bacterium, finally identified as Clostridium sphenoides. This finding underlines the need for microbiologic analysis of orthopedic...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/64.3.385

    authors: Isenberg HD,Lavine LS,Painter BG,Rubins WH,Berkman JI

    更新日期:1975-09-01 00:00:00

  • Application of a rapid assay for detection of antibodies to human immunodeficiency virus in urine.

    abstract::The use of rapid, simple tests to detect antibodies to human immunodeficiency virus (HIV) in urine could be valuable for several testing situations, such as in private offices, for epidemiologic surveys, and in developing countries. The authors evaluated the performance of the SUDS HIV type 1 test to detect antibody t...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/101.2.157

    authors: Constantine NT,Zhang X,Li L,Bansal J,Hyams KC,Smialek JE

    更新日期:1994-02-01 00:00:00

  • Linking Statistics With Testing Policy to Manage COVID-19 in the Community.

    abstract:OBJECTIVES:To determine the public health surveillance severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing volume needed, both for acute infection and seroprevalence. METHODS:Required testing volumes were developed using standard statistical methods based on test analytical performance, disease preval...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/aqaa099

    authors: Hilborne LH,Wagner Z,Cabreros I,Brook RH

    更新日期:2020-07-07 00:00:00

  • Immunophenotyping of non-Hodgkin's lymphomas in paraffin-embedded tissue sections. A comparison with genotypic analysis.

    abstract::Several monoclonal antibodies (MoAbs) are now available for immunophenotyping non-Hodgkin's lymphomas (NHLs) in paraffin-embedded tissue sections. To determine the reliability of these reagents in predicting the genotype, 44 cases of NHL were studied with the alkaline phosphatase-anti-alkaline phosphatase technique wi...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/95.4.517

    authors: Elghetany MT,Kurec AS,Schuehler K,Forbes BA,Duggan DB,Davey FR

    更新日期:1991-04-01 00:00:00

  • Can We Identify Nephrogenic Adenoma in Urine Cytology Specimens? A Study Evaluating Previously Described Cytomorphologic Features in Correlation With PAX8 Immunohistochemical Staining Results.

    abstract:OBJECTIVES:The aim of this study is to determine if the diagnosis of nephrogenic adenoma (NA) can be made on cytologic criteria alone and if pair box gene transcription factor 8 (PAX8) is useful in the diagnosis of NA in daily cytology practice. METHODS:Cytologic features of NA previously described in a literature wer...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/aqw006

    authors: McCroskey Z,Pambuccian SE,Wojcik EM,Barkan GA

    更新日期:2016-03-01 00:00:00

  • Giant forms of Blastomyces dermatitidis in the pulmonary lesions of blastomycosis. Potential confusion with Coccidioides immitis.

    abstract::Typical yeast-phase cells of Blastomyces dermatitidis have a characteristic appearance in tissue sections. Fungal morphologic variation occurs infrequently in the lesions of blastomycosis, yet it can complicate the differential diagnosis, particularly if fresh tissue is not available for microbiologic culture. The aut...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/93.4.575

    authors: Watts JC,Chandler FW,Mihalov ML,Kammeyer PL,Armin AR

    更新日期:1990-04-01 00:00:00

  • The autopsy. Simple thoughts about the public needs and how to address them.

    abstract::Dialogue regarding the autopsy has been sustained largely by medical students and professionals, and by families of deceased patients. Exclusion of the general public may represent a significant reason for the inexorable decline of autopsy rates and politicoeconomic support. Sensitivity to public concerns regarding th...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章,评审

    doi:

    authors: McManus BM,Wood SM

    更新日期:1996-10-01 00:00:00

  • Adamantinoma of the pretibial soft tissue. Clinicopathologic features, differential diagnosis, and possible relationship to intraosseous disease.

    abstract::The authors illustrate two neoplasms arising in the pretibial soft tissue that are histologically identical to adamantinoma of the long bones. The tumors developed in a 24-year-old woman and a 31-year-old man. Both were treated by local excision. Histologically, one tumor had a tubular pattern and one was composed of ...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/83.1.108

    authors: Mills SE,Rosai J

    更新日期:1985-01-01 00:00:00

  • The use of fine needle aspiration cytology for the distinction of pancreatic mucinous neoplasia.

    abstract::Cytology frequently has some role in preoperatively distinguishing pancreatic mucus-producing neoplasia (intraductal papillary mucinous neoplasms [IPMNs] and mucinous cystic neoplasms [MCNs]) from other pancreatic cysts. We evaluated all cytologic specimens at our institutions from resected pancreatic cystic lesions f...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/Y16QCXE3YGMXX19Q

    authors: Stelow EB,Shami VM,Abbott TE,Kahaleh M,Adams RB,Bauer TW,Debol SM,Abraham JM,Mallery S,Policarpio-Nicolas ML

    更新日期:2008-01-01 00:00:00

  • Cytologic/histologic correlation for quality control in cervicovaginal cytology. Experience with 1,582 paired cases.

    abstract::For quality-control purposes, federal regulations require cytology laboratories to compare Papanicolaou smear and cervical biopsy reports, if available, and determine the cause of any discrepancies. The authors reviewed 56,497 cervicovaginal smears, of which 1,582 (2.8%) had a subsequent cervical biopsy or endocervica...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/103.1.32

    authors: Joste NE,Crum CP,Cibas ES

    更新日期:1995-01-01 00:00:00

  • Serum bicarbonate declines with sample size in vacutainer tubes.

    abstract::Serum bicarbonate testing has been reported to be inaccurate in several clinical studies. This prompted a search for systemic errors in bicarbonate testing devices, which has been inconclusive. The effect on serum bicarbonate level measurement of partially filling plain red-top (clot) vacutainer tubes was studied in h...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/97.2.213

    authors: Herr RD,Swanson T

    更新日期:1992-02-01 00:00:00

  • Sysmex SE-9000 hematology analyzer: performance evaluation on leukocyte differential counts using an NCCLS H20-A protocol. National Committee for Clinical Laboratory Standards.

    abstract::We evaluated the performance (ie, imprecision, inaccuracy, and analytic sensitivity) of the Sysmex SE-9000 commercial hematology analyzer (TOA Medical Electronics, Kobe, Japan) on differential leukocyte counts according to the National Committee for Clinical Laboratory Standards H20-A protocol. The results obtained we...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/108.6.674

    authors: Buttarello M,Bulian P,Temporin V,Rizzotti P

    更新日期:1997-12-01 00:00:00

  • Recombinant factor VIIa in the treatment of bleeding.

    abstract::Recombinant factor VIIa (rFVIIa) has become available for treating people with hemophilia with inhibitors who experience bleeding or require surgery. It has become apparent that rFVIIa is useful in controlling bleeding in a variety of clinical situations. This review attempts to collate and summarize the nonhemophilia...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章,评审

    doi:10.1309/D0G0-C96V-05CJ-5B4J

    authors: Midathada MV,Mehta P,Waner M,Fink LM

    更新日期:2004-01-01 00:00:00

  • Immunohistochemical staining for terminal deoxynucleotidyl transferase (TDT). An enhanced method in routinely processed formalin-fixed tissue sections.

    abstract::This report describes an improved technique for sensitive and specific localization of terminal deoxynucleotidyl transferase (TdT) in routinely processed paraffin-embedded, formalin-fixed tissue sections using DNAse pretreatment and the avidin-biotin complex (ABC) technique. This method is useful in identifying lympho...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/89.5.649

    authors: Said JW,Shintaku IP,Pinkus GS

    更新日期:1988-05-01 00:00:00

  • Telangiectatic oncocytoma: a previously undescribed variant of renal oncocytoma.

    abstract:OBJECTIVES:To identify, describe, and investigate the clinical, radiologic, and pathologic features of 8 cases of telangiectatic oncocytoma. METHODS:Fifty-three consecutive renal oncocytomas were reviewed for the telangiectatic pathologic features that were subsequently correlated with the demographic, clinical, and r...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/AJCP9HDXYB2WYYJX

    authors: Xiao GQ,Ko HB,Unger P

    更新日期:2013-07-01 00:00:00

  • Cytochemistry of acid hydrolases in chronic B- and T-cell leukemias.

    abstract::Four acid hydrolases, acid phosphatase (AP), alpha-naphthyl acetate esterase (ANAE), beta-glucuronidase, and N-acetyl-beta-glucosaminidase, were determined cytochemically in peripheral blood lymphocytes from 50 patients with B and T chronic lymphocytic and prolymphocytic leukemias (CLL, PLL) and related disorders. Str...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/78.4.437

    authors: Crockard A,Chalmers D,Matutes E,Catovsky D

    更新日期:1982-10-01 00:00:00

  • Giant lymph node hyperplasia of the hyaline vascular type with plasmacytoid T-cells and presentation in infancy.

    abstract::Giant lymph node hyperplasia is uncommon in children and is exceptionally rare in infancy. The authors report a case of giant lymph node hyperplasia that presented as a right supraclavicular mass in an asymptomatic two-month-old female infant. Clinically, the mass was thought to be either a lipoma or a cystic hygroma,...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/91.3.344

    authors: Hunt SJ,Anderson WD

    更新日期:1989-03-01 00:00:00

  • The effect of fibrin polymerization inhibitors on quantitative measurements of plasma fibrinogen.

    abstract::A number of reports have highlighted discrepancies between the DuPont aca and fibrometer-based methods for quantitating plasma fibrinogen levels. Although many authors have suggested that the presence of fibrin(ogen) degradation products are in some way responsible for the discrepancies, no direct test of this hypothe...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/88.4.490

    authors: Hoffman M,Greenberg CS

    更新日期:1987-10-01 00:00:00

  • Novel t(1;8)(p31.3;q21.3) NFIA-RUNX1T1 Translocation in an Infant Erythroblastic Sarcoma.

    abstract:OBJECTIVES:Pure erythroid leukemia (PEL) is exceptionally rare in the pediatric setting. Four pediatric PEL cases with t(1;16)(p31;q24) NFIA-CBFA2T3 were reported previously. We present a case of an infant with PEL presenting with erythroblastic sarcoma and harboring a novel t(1;8)(p31.3;q21.3) NFIA-RUNX1T1 fusion dete...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/aqaa216

    authors: King RL,Siaghani PJ,Wong K,Edlefsen K,Shane L,Howard MT,Reichard KK,Mai M,Viswanatha DS,Greipp PT,Goble TA,Ruiz M,Hara H

    更新日期:2020-12-14 00:00:00

  • Comparison of touch imprints with aspirate smears for evaluating bone marrow specimens.

    abstract::We compared the differential counts of normal and abnormal bone marrow from touch imprints with those from aspirate smears to determine whether the touch imprint was reliable for independent routine use in the examination of bone marrow and the classification of hematologic abnormalities. Normocellular bone marrow spe...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/111.6.753

    authors: Aboul-Nasr R,Estey EH,Kantarjian HM,Freireich EJ,Andreeff M,Johnson BJ,Albitar M

    更新日期:1999-06-01 00:00:00

  • Performance characteristics of nested polymerase chain reaction vs real-time polymerase chain reaction methods for detecting Mycobacterium tuberculosis complex in paraffin-embedded human tissues.

    abstract:OBJECTIVES:Nucleic acid amplification tests on formalin-fixed, paraffin-embedded (FFPE) tissue specimens enable Mycobacterium tuberculosis complex (MTB) detection and rapid tuberculosis diagnosis in the absence of microbiologic culture tests. We aimed to evaluate the efficacy of different polymerase chain reaction (PCR...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/AJCP2QZRH4ZNPRDD

    authors: Seo AN,Park HJ,Lee HS,Park JO,Chang HE,Nam KH,Choe G,Park KU

    更新日期:2014-09-01 00:00:00

  • erbB-2 oncoprotein expression in breast carcinoma. Poor prognosis associated with high degree of cytoplasmic positivity using CB-11 antibody.

    abstract::The relationship between immunohistochemically measured membranous expression of erbB-2 oncoprotein and prognosis in breast cancer is controversial, and the relationship between cytoplasmic positivity and prognosis has been minimally investigated. The clinical course of 300 women with infiltrating breast carcinoma, wh...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/108.4.456

    authors: Keshgegian AA,Cnaan A

    更新日期:1997-10-01 00:00:00

  • Hemolytic disease of the newborn due to anti-C and anti-G masquerading as anti-D.

    abstract::After several transfusions with D-negative blood, an O Rh-negative women was apparently sensitized to the C and D antigens. In her prenatal workup, it became evident that she had in fact not been sensitized to D but to G, which initially appeared as anti-D plus anti-C. This sensitization pattern is an unusual occurren...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/84.6.769

    authors: Yesus YW,Akhter JE

    更新日期:1985-12-01 00:00:00

  • Characterization of tissue findings in bone marrow biopsy specimens with small monoclonal B-cell populations.

    abstract:OBJECTIVES:Bone marrows (BMs) with incidentally identified, small monotypic B-cell populations (MBPs) were evaluated. METHODS:BM aspirates with MBPs representing 5% or less of total events by flow cytometry, less than 5.0 × 10(9)/L B cells in blood, and no history of lymphoma or MBP with a different phenotype from pri...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/AJCPD5TOBDJU4GKO

    authors: Nelson BP,Abdul-Nabi A,Goolsby C,Winter J,Peterson L

    更新日期:2014-05-01 00:00:00

  • Comparison of anti-estrogen receptor antibodies SP1, 6F11, and 1D5 in breast cancer: lower 1D5 sensitivity but questionable clinical implications.

    abstract::We compared the anti-estrogen receptors (ER) SP1, 6F11, and 1D5 antibodies in breast carcinoma cases with different ranges of positive cells to evaluate whether this could generate different therapies for patients. We selected 66 cases of breast cancer, each of which was immunostained with the 3 antibodies. 1D5 was le...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/AJCPLX0QJROV2IJG

    authors: Bogina G,Zamboni G,Sapino A,Bortesi L,Marconi M,Lunardi G,Coati F,Massocco A,Molinaro L,Pegoraro C,Venturini M

    更新日期:2012-11-01 00:00:00

  • Detection of hepatitis C virus RNA sequences in B-cell non-Hodgkin lymphoma.

    abstract::Serologic testing shows that hepatitis C virus (HCV) may have a role in the pathogenesis of B-cell non-Hodgkin lymphomas (B-cell NHLs). We tried to demonstrate HCV RNA sequences in paraffin-embedded tissue from B-cell NHLs by reverse-transcription double polymerase chain reaction (RT-PCR) and Southern blotting. We stu...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/REV9-FDTM-5NGC-HBWY

    authors: Karavattathayyil SJ,Kalkeri G,Liu HJ,Gaglio P,Garry RF,Krause JR,Dash S

    更新日期:2000-03-01 00:00:00

  • Restriction fragment length polymorphism and polymerase chain reaction: HLA-DQA1 and polymarker analysis of blood samples from transfusion recipients.

    abstract::The effect of blood transfusion on DNA profiles of an individual is a significant issue in the forensic context. In the present study, the effects of blood transfusion in 5 recipients were studied by performing restriction fragment length polymorphism and polymerase chain reaction HLA-DQA1 and Polymarker (LDLR, GYPA, ...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/KAWA-QHBU-6D1J-XY3G

    authors: Giroti RI,Biswas R,Mukherjee K

    更新日期:2002-09-01 00:00:00

  • Screening for dyslipidemia. Practice parameter.

    abstract::Screening for serum lipid disorders is recommended by numerous specialty societies to identify patients at risk for coronary heart disease (CHD). The best screening tests will identify patients at highest risk for CHD who would benefit from intervention. This report discusses an appropriate test panel to use as the in...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/103.4.380

    authors: Hostetter AL

    更新日期:1995-04-01 00:00:00

  • Common genomic aberrations in basaloid squamous cell carcinoma and carcinosarcoma of the esophagus detected by CGH and array CGH.

    abstract::Basaloid squamous cell carcinoma (BSCC) and carcinosarcoma of the esophagus are rare entities, making up fewer than 2% of esophageal malignancies. Comparative genomic hybridization (CGH) in 1 case of BSCC and 2 cases of carcinosarcoma and subsequent array CGH in 1 case each of BSCC and carcinosarcoma revealed common c...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1309/AJCPZ1O7UUUISPNR

    authors: Schaefer IM,Enders C,Polten A,Haller F,Frölich AM,Cameron S,Schüler P,Schweiger P,Gunawan B,Beham A,Füzesi L

    更新日期:2011-04-01 00:00:00

  • Light microscopic, S-100 immunostaining, and ultrastructural analysis of dermatopathic lymphadenopathy, with and without associated mycosis fungoides.

    abstract::Thirty-five patients with dermatopathic lymphadenopathy, 12 with (9 patients and 3 follow-up) and 23 without associated mycosis fungoides, and 7 controls with 26 lymph nodes were studied by light microscopic examination and immunostaining for S-100 protein. Fourteen of these cases were examined ultrastructurally. The ...

    journal_title:American journal of clinical pathology

    pub_type: 杂志文章

    doi:10.1093/ajcp/87.2.187

    authors: Herrera GA

    更新日期:1987-02-01 00:00:00