Biomedical subjects

Dilip Gupta

Publications and source records attributed to Dilip Gupta.

11 recordsLinked to original sources

PubMed2006

Evaluation of Her-2/neu gene status in osteosarcoma by fluorescence in situ hybridization and multiplex and monoplex polymerase chain reactions.

CONTEXT: Previous reports suggest that the human epidermal growth factor 2 (HER-2/neu) receptor may be overexpressed in osteosarcoma. OBJECTIVE: To determine whether osteosarcomas have amplifications of the HER-2/neu gene. DESIGN: We studied a series of osteosarcomas by fluorescence in situ hybridization (FISH) and by 2 real-time polymerase chain reaction assays that measure the amount of HER-2/neu DNA relative to a control gene. The HER-2/ neu monoplex and multiplex assays were capable of identifying those cases of breast cancer that were known to overexpress HER-2/neu as assessed by FISH. We initially studied 21 cases of osteosarcoma by FISH analysis (using a technique that included a probe for chromosome 17), 11 of which had their HER-2/neu gene amplification status previously reported. RESULTS: None of these osteosarcoma cases showed HER-2/neu amplification by our FISH analysis and subsequent quantitative (multiplex) polymerase chain reaction. Apparent expression of HER-2/neu protein was observed in several of the cases but the immunoreactivity was localized to the cytoplasm and was not membranous in character. An additional 35 osteosarcoma specimens were subjected to monoplex polymerase chain reaction analysis, and amplifiable DNA was recovered from 19 specimens (54%). None of these samples had HER-2/neu amplification by monoplex PCR analysis and only one case had membranous immunoreactivity graded as 1+. CONCLUSION: Although a small subset of osteosarcomas had weak noncircumferential membranous immunoreactivity for HER-2/neu protein, no osteosarcomas demonstrated positive (2+ or 3+) immunoreactivity for HER-2/ neu protein and none showed HER-2/neu gene amplification by either FISH or polymerase chain reaction.

Bone Neoplasms↗

PubMed2005

Cardiac murmur prompting diagnosis of metastatic nonseminomatous germ cell testicular neoplasia in an 18-year-old patient.

Most retroperitoneal tumors such as renal cell carcinoma have been associated with tumor thrombus extending into the renal vein, inferior vena cava (IVC), and heart. The retroperitoneal metastatic potential of testicular tumors is well known. We report here the first instance of a cardiac murmur prompting diagnosis of metastatic testicular neoplasia in an 18-year-old patient. Chemotherapy was delayed and after successful surgical resection of the ventricular mass, the patient recovered uneventfully. This case underscores the need to pursue abnormal cardiac exams in newly diagnosed testicular cancer patients.

Adolescent↗

PubMed2005

Database construction for improving patient safety by examining pathology errors.

A critical component of improving patient safety is reducing medical errors. "Improving Patient Safety by Examining Pathology Errors" is a project designed to collect data about and analyze diagnostic errors voluntarily reported by 4 academic anatomic pathology laboratories and to develop and implement interventions to reduce errors and improve patient outcomes. The study database is Web-mediated and Oracle-based, and it houses de-identified error data detected by cytologic-histologic correlation and interdepartmental conference review. We describe the basic design of the database with a focus on challenges faced as a consequence of the absence of standardized and detailed laboratory workload and quality assurance data sets in widely used laboratory information systems and the lack of efficient and comprehensive electronic de-identification of unlinked institutional laboratory information systems and clinical data. Development of these electronic data abstraction capabilities is critical for efforts to improve patient safety through the examination of pathology diagnostic errors.

Databases, Factual↗

PubMed2004

Perforated acute appendicitis in a term neonate.

Acute appendicitis is rare in term neonates. In most of the reported cases, it is seen as a complication of necrotizing enterocolitis, Hirschsprung's disease, cystic fibrosis, meconium plug, inguinal hernia, umbilical hernia, Group B Streptococcal septicemia and chorioamnionitis. A surviving term male newborn with isolated acute appendicitis with perforation is reported. A high index of suspicion of acute appendicitis, early surgery and the importance of a thorough search for a perforation in cases of neonatal acute abdominal distention is stressed. Literature of this rare condition is reviewed briefly.

Acute Disease↗

PubMed2004

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

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.

Confidentiality↗

PubMed2004

Implementation and evaluation of a negation tagger in a pipeline-based system for information extract from pathology reports.

We have developed a pipeline-based system for automated annotation of Surgical Pathology Reports with UMLS terms that builds on GATE--an open-source architecture for language engineering. The system includes a module for detecting and annotating negated concepts, which implements the NegEx algorithm--an algorithm originally described for use in discharge summaries and radiology reports. We describe the implementation of the system, and early evaluation of the Negation Tagger. Our results are encouraging. In the key Final Diagnosis section, with almost no modification of the algorithm or phrase lists, the system performs with precision of 0.84 and recall of 0.80 against a gold-standard corpus of negation annotations, created by modified Delphi technique by a panel of pathologists. Further work will focus on refining the Negation Tagger and UMLS Tagger and adding additional processing resources for annotating free-text pathology reports.

Algorithms↗

PubMed2003

A knowledge-based approach to information extraction from surgical pathology reports.

We describe the development of a prototype system for knowledge-based information extraction from surgical pathology reports. The current system includes abstract problem solving methods and a frame-based knowledge representation of body parts, procedures, diseases, and findings for prostate and breast cases. The system currently extracts the organ, procedure, and diagnoses, and sets an agenda of goals for further processing. A potential advantage of this approach is the ability to increase specificity of information extraction.

Artificial Intelligence↗

PubMed2002

Immunohistochemical comparison of gastrointestinal stromal tumor and solitary fibrous tumor.

CONTEXT: The differential diagnosis of gastrointestinal stromal tumors (GIST) and solitary fibrous tumors (SFT) may be a diagnostic challenging because of overlapping clinicopathologic features. Many studies have shown consistent immunoreactivity for CD117 (c-Kit) in GIST. However, only a few studies have evaluated CD117 expression in SFT, and these studies have used an antibody from Santa Cruz Biotechnology. In non-GIST lesions, reactivity with this antibody has been shown to differ from that with a CD117 antibody from Dako Corporation. The immunoreactivity of SFT with the Dako CD117 antibody has not been reported. Conversely, CD99 is a marker for SFT, and its expression in GIST has not been evaluated. OBJECTIVE: To study the immunohistochemical profiles of GIST and SFT to evaluate their diagnostic overlap. DESIGN: We studied the immunoreactivity of 27 unequivocal GIST and 19 unequivocal extra-abdominal SFT for CD117, CD34, CD99, alpha-smooth muscle actin, vimentin, CD31, S100 protein, and muscle-specific actin. All antibodies, including CD117, were from Dako Corporation. RESULTS: We found positive immunoreactivity for CD117 in 100% of GIST and none of SFT; for CD34 in 89% of GIST, and 100% of SFT; for CD99 in 89% of GIST and 100% of SFT; for alpha-smooth muscle actin in 48% of GIST and 31% of SFT; for vimentin in 89% of GIST and 90% of SFT; and for muscle-specific actin in 22% of GIST and none of SFT. None of the GIST or SFT showed immunoreactivity for CD31 and S100 protein. CONCLUSIONS: The major difference between GIST and SFT was strong CD117 immunoexpression in all GIST and an absence of this expression in all SFT. With the exception of muscle-specific actin, the prevalence of immunoreactivity for the markers studied did not differ substantially between these 2 tumors. We conclude that GIST and SFT show distinctly divergent immunoprofiles with respect to CD117 and muscle-specific actin.

Adult↗

PubMed2002

Spectrum of congenital surgical malformations in newborns.

A prospective study to detect the frequency and distribution of congenital surgical malformations in a rural hospital setting in Maharashtra was carried out. A total of 3000 consecutive births over a 9-month period was included and the frequency of congenital malformations was 21.1 per 1000 births. Stillbirths were associated with a higher incidence of malformations (14.5%) as compared to live births (1.8%). The commonest systems affected were the gastro-intestinal tract and the genito-urinary tract (20.4% each) followed by the central nervous system (17.3%). Among the various possible risk factors studied, a higher incidence of congenital malformations was associated with increasing maternal age (> 35 years), higher gravida mothers (> G4), parental consanguineous marriages, previous history of abortions, maternal hypertension, etc.

Congenital Abnormalities↗

PubMed2000

Assessment of Tissue Estrogen and Progesterone Receptor Levels: A Survey of Current Practice, Techniques, and Quantitation Methods.

The assessment of steroid hormone receptors in resected breast carcinoma tissue is currently the standard of practice. The traditional method for assessment of receptor status is the ligand binding assay. More recently, immunohistochemistry (IHC) has become a popular method for such testing. Despite the widespread use of IHC and the availability of many antibodies, standardization of quantitative IHC for assessment of estrogen and progesterone receptors has not been achieved. While the College of American Pathologists (CAP) offers a Quality Assurance (QA) program for IHC quantitation of estrogen receptor (ER) and progesterone receptor (PgR), no universal standard is currently recognized in assessment of ER and PgR by IHC. We surveyed 300 laboratories within the United States for their current practices regarding the assessment of ER and PgR status in breast cancer tissue specimens. Eighty usable responses were received. Forty-nine (61%) laboratories performed the assay in-house, while the remainder sent the material out for assay. All responding laboratories performing their steroid receptor analysis in-house used the IHC technique. Forty-three (80%) laboratories answering the question on material accepted for analysis performed the assay only on paraffin-embedded material, three (6%) used either paraffin block or frozen material, and two (4%) used only frozen material. Eighty-eight percent of laboratories performing steroid receptor analysis in-house used a manual quantitation technique. Four (8%) used computer-assisted image analysis, and a single laboratory used laser scanning cytometry. Eight different antibodies were used among the 44 laboratories documenting the antibody supplier, and for any given commercially prepared antibody a wide variety of dilutions were used, with the exception of the standard solution used with the Ventana antibody. Of the laboratories using manual estimation techniques, 61% simply estimated the percentage of positive cells, 29% evaluated both the intensity of staining and percentage of nuclei staining, 6% used formal H-score analysis, 2% evaluated only intensity of nuclear staining, and 2% mainly counted the percentage of nuclei staining for ER but used a formal H score in the assessment of PgR. Cutoff points for the separation of positive and negative results varied widely, with some laboratories assessing any demonstrable positivity as a positive result, while others required as many as 19% of the nuclei to stain before a specimen was declared positive. Standardization techniques differed considerably among laboratories. Eighty-six percent used the CAP program for QA. While all laboratories utilized some form of intralaboratory control for assessment of ER and PgR, the nature of that control varied from laboratory to laboratory. Our survey indicates that a majority of laboratories perform their steroid hormone receptor analysis in-house using IHC. There is considerable variability in the antibodies utilized, the dilutions applied, and the quantitation method and level of expression used to dichotomize specimens into positive and negative groups. Finally, no universal control for interlaboratory standardization appears to exist.

Journal Article↗

PubMedDate not supplied

Utility of four-quadrant random sections in mastectomy specimens.

Standard practice in surgical pathology dictates that random sections from the four quadrants of the breast be taken in mastectomy specimens. These sections are obtained in addition to sampling of any grossly visible lesions within the breast specimen. While tradition dictates the submission of these sections, we are unaware of any study supporting their efficacy. We have investigated the utility and significance of these random sections in a series of 78 mastectomy specimens. This retrospective study identified mastectomy specimens from pathology files of Magee Woman's Hospital, the University of Pittsburgh, and the University of Utah School of Medicine between 1997 and 2000. Clinical data (palpable versus nonpalpable), radiographic features (mammographic diagnosis, presence of mass density and/or calcification), and pathologic features (size, histopathologic type, etc.) were studied. The histologic sections of the cases were reviewed and the random sections were specifically studied for pathologic findings. Diagnosis and clinically significant features obtained from examining these random sections, but not demonstrable in grossly selected sections, were tabulated. A total of 78 mastectomy specimens were analyzed. Diagnoses rendered were infiltrating ductal carcinoma (23), infiltrating ductal carcinoma with ductal carcinoma in situ (DCIS) (16), DCIS (25), infiltrating lobular carcinoma (4), biopsy cavity with no residual malignancy (4), infiltrating lobular carcinoma with lobular carcinoma in situ (3), invasive ductal and lobular carcinoma (1), adenoid cystic carcinoma (1), and atypical ductal hyperplasia (1). The number of random sections ranged from 2 to 17 (mean 9). Random sections provided additional information in 21 of 78 mastectomies (27%). The multifocal/multicentric nature of the lesion was diagnosed in 20 cases: DCIS (6), lobular carcinoma in situ and invasive (2), invasive ductal carcinoma (6), invasive and in situ ductal carcinoma (5), invasive lobular carcinoma (1), invasive ductal and lobular carcinoma (1). Additional findings include lymphovascular invasion (2 cases), atypical ductal hyperplasia (1), DCIS at the operative margin (1), DCIS within less than 1 mm of an operative margin (1), and atypical lobular hyperplasia (1). In the remaining 57 cases, random sections did not provide any additional information. Histologic examination of random sections from breast quadrants yielded important information about the presence of multifocality, multicentricity, vascular invasion, and margin involvement by carcinoma in only a minority of cases, many of which had a lobular morphology.

Biopsy↗