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  1. Article ; Online: Laboratory Action Plan for Emerging SARS-CoV-2 Variants.

    Filkins, Laura / SoRelle, Jeffrey A / Schoggins, John / Park, Jason Y

    Clinical chemistry

    2021  Volume 67, Issue 5, Page(s) 720–723

    MeSH term(s) COVID-19/diagnosis ; COVID-19/genetics ; COVID-19 Serological Testing/standards ; Humans ; Laboratories/standards ; SARS-CoV-2/genetics
    Language English
    Publishing date 2021-01-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 80102-1
    ISSN 1530-8561 ; 0009-9147
    ISSN (online) 1530-8561
    ISSN 0009-9147
    DOI 10.1093/clinchem/hvab020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Endometrial Polyps-Are They Characterized by HMGA Rearrangements or Not? Reply to Bullerdiek et al.

    Koduru, Prasad / Sahoo, Subhransu S / Aguilar, Mitzi / Bishop, Justin A / SoRelle, Jeffrey A / Castrillon, Diego H

    Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc

    2023  Volume 36, Issue 2, Page(s) 100058

    MeSH term(s) Humans ; Polyps/genetics ; HMGA Proteins
    Chemical Substances HMGA Proteins
    Language English
    Publishing date 2023-01-11
    Publishing country United States
    Document type Letter
    ZDB-ID 645073-8
    ISSN 1530-0285 ; 0893-3952
    ISSN (online) 1530-0285
    ISSN 0893-3952
    DOI 10.1016/j.modpat.2022.100058
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Pancreatic Fibrosis Assessment Using Picosirius Red Staining in Chronic Pancreatitis Patients Undergoing Total Pancreatectomy with Islet Autotransplantation.

    Liu, Yang / Vasu, Srividya / Kumano, Kenjiro / SoRelle, Jeffrey A / Lawrence, Michael C / Naziruddin, Bashoo

    Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract

    2022  Volume 26, Issue 8, Page(s) 1766–1768

    MeSH term(s) Fibrosis ; Humans ; Islets of Langerhans Transplantation ; Pancreatectomy ; Pancreatic Diseases/surgery ; Pancreatitis, Chronic/surgery ; Staining and Labeling ; Transplantation, Autologous ; Treatment Outcome
    Language English
    Publishing date 2022-05-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2012365-6
    ISSN 1873-4626 ; 1934-3213 ; 1091-255X
    ISSN (online) 1873-4626 ; 1934-3213
    ISSN 1091-255X
    DOI 10.1007/s11605-022-05360-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Assembling and Validating Bioinformatic Pipelines for Next-Generation Sequencing Clinical Assays.

    SoRelle, Jeffrey A / Wachsmann, Megan / Cantarel, Brandi L

    Archives of pathology & laboratory medicine

    2020  Volume 144, Issue 9, Page(s) 1118–1130

    Abstract: Context.—: Clinical next-generation sequencing (NGS) is being rapidly adopted, but analysis and interpretation of large data sets prompt new challenges for a clinical laboratory setting. Clinical NGS results rely heavily on the bioinformatics pipeline ... ...

    Abstract Context.—: Clinical next-generation sequencing (NGS) is being rapidly adopted, but analysis and interpretation of large data sets prompt new challenges for a clinical laboratory setting. Clinical NGS results rely heavily on the bioinformatics pipeline for identifying genetic variation in complex samples. The choice of bioinformatics algorithms, genome assembly, and genetic annotation databases are important for determining genetic alterations associated with disease. The analysis methods are often tuned to the assay to maximize accuracy. Once a pipeline has been developed, it must be validated to determine accuracy and reproducibility for samples similar to real-world cases. In silico proficiency testing or institutional data exchange will ensure consistency among clinical laboratories.
    Objective.—: To provide molecular pathologists a step-by-step guide to bioinformatics analysis and validation design in order to navigate the regulatory and validation standards of implementing a bioinformatic pipeline as a part of a new clinical NGS assay.
    Data sources.—: This guide uses published studies on genomic analysis, bioinformatics methods, and methods comparison studies to inform the reader on what resources, including open source software tools and databases, are available for genetic variant detection and interpretation.
    Conclusions.—: This review covers 4 key concepts: (1) bioinformatic analysis design for detecting genetic variation, (2) the resources for assessing genetic effects, (3) analysis validation assessment experiments and data sets, including a diverse set of samples to mimic real-world challenges that assess accuracy and reproducibility, and (4) if concordance between clinical laboratories will be improved by proficiency testing designed to test bioinformatic pipelines.
    MeSH term(s) Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Pathology, Molecular/methods ; Software
    Language English
    Publishing date 2020-02-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 194119-7
    ISSN 1543-2165 ; 0363-0153 ; 0096-8528 ; 0003-9985
    ISSN (online) 1543-2165
    ISSN 0363-0153 ; 0096-8528 ; 0003-9985
    DOI 10.5858/arpa.2019-0476-RA
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Primary renal sarcoma with SS18::POU5F1 gene fusion.

    Argani, Pedram / Matoso, Andres / Gross, John M / Zhang, Yanming / SoRelle, Jeffrey A / Gagan, Jeffrey / Antonescu, Cristina R / Palsgrove, Doreen

    Genes, chromosomes & cancer

    2022  Volume 61, Issue 9, Page(s) 572–577

    Abstract: We report the first case of a primary renal undifferentiated sarcoma harboring an SS18::POU5F1 gene fusion. The patient was a 38 year-old male diagnosed with a 5 cm renal tumor which invaded the adrenal gland and extended into the renal vein. ... ...

    Abstract We report the first case of a primary renal undifferentiated sarcoma harboring an SS18::POU5F1 gene fusion. The patient was a 38 year-old male diagnosed with a 5 cm renal tumor which invaded the adrenal gland and extended into the renal vein. Microscopically, the neoplasm had a predominantly undifferentiated round cell morphology, with areas of rhabdoid and spindle cell growth. Similar to the previously reported cases with this fusion, by immunohistochemistry the neoplasm expressed S100 protein and epithelial markers (diffuse EMA, focal cytokeratin), suggesting the possibility of a myoepithelial phenotype. This report documents another example of a fusion-positive undifferentiated soft tissue sarcoma occurring as a primary renal neoplasm, adding to the already broad list of such entities. It highlights the crucial role of molecular analysis in establishing a specific diagnosis given the overlapping morphology and immunophenotypes such entities may exhibit.
    MeSH term(s) Biomarkers, Tumor/genetics ; Gene Fusion ; Humans ; Kidney Neoplasms/pathology ; Male ; Octamer Transcription Factor-3/genetics ; Oncogene Proteins, Fusion/genetics ; Proto-Oncogene Proteins/genetics ; Sarcoma/diagnosis ; Sarcoma/genetics ; Sarcoma/pathology ; Sarcoma, Synovial/genetics ; Soft Tissue Neoplasms/genetics
    Chemical Substances Biomarkers, Tumor ; Octamer Transcription Factor-3 ; Oncogene Proteins, Fusion ; POU5F1 protein, human ; Proto-Oncogene Proteins
    Language English
    Publishing date 2022-05-19
    Publishing country United States
    Document type Case Reports ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1018988-9
    ISSN 1098-2264 ; 1045-2257
    ISSN (online) 1098-2264
    ISSN 1045-2257
    DOI 10.1002/gcc.23053
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Study protocol: maintaining preventive care during public health emergencies through effective coordination.

    Hysong, Sylvia J / Giardina, Traber Davis / Freytag, Jennifer / SoRelle, Richard / Murphy, Daniel R / Cully, Jeffrey A / Sada, Yvonne H / Amspoker, Amber B

    Implementation science communications

    2023  Volume 4, Issue 1, Page(s) 150

    Abstract: Background: Screening lies at the heart of preventive care. However, COVID-19 dramatically disrupted routine screening efforts, resulting in excess mortality not directly attributable to COVID-19. Screening rates during COVID varied markedly by facility ...

    Abstract Background: Screening lies at the heart of preventive care. However, COVID-19 dramatically disrupted routine screening efforts, resulting in excess mortality not directly attributable to COVID-19. Screening rates during COVID varied markedly by facility and clinical condition, suggesting susceptibilities in screening and referral process workflow. To better understand these susceptibilities and identify new practices to mitigate interrupted care, we propose a qualitative study comparing facilities that exhibited high, low, and highly variable performance (respectively) in screening rates before and during the pandemic. We will be guided by Weaver et al.'s multi-team systems (MTS) model of coordination, using cancer and mental health screening rates as exemplars.
    Method: Qualitative analysis of interviews and focus groups with primary care personnel, leadership, and patients at 10 VA medical centers. We will select sites based on rurality, COVID-19 caseload at the beginning of the pandemic, and performance on five outpatient clinical performance indicators of cancer and mental health screening. Sites will be categorized into one of five screening performance groups: high performers, low performers, improvers, plummeters, and highly variable. We will create process maps for each performance measure to create a workflow baseline and then interview primary care leadership to update the map at each site. We will clinician conduct focus groups to elicit themes regarding clinician coordination patterns (e.g., handoffs), strategies, and barriers/facilitators to screening during COVID. We will also conduct patient interviews to examine their screening experience during this period, for context. All interviews and focus groups will be audio-recorded, transcribed, and enhanced by field notes. We will analyze clinician transcripts and field notes using iterative, rapid analysis. Patient interviews will be analyzed using inductive/deductive content analysis.
    Discussion: Our study represents a unique opportunity to inform the multi-team systems literature by identifying specific forms of information exchange, collective problem solving, and decision-making associated with higher and improved clinical performance. Specifically, our study aims to detect the specific points in the screening and referral process most susceptible to disruption and coordination processes that, if changed, will yield the highest value. Findings apply to future pandemics or any event with the potential to disrupt care.
    Language English
    Publishing date 2023-11-27
    Publishing country England
    Document type Journal Article
    ISSN 2662-2211
    ISSN (online) 2662-2211
    DOI 10.1186/s43058-023-00507-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: β-catenin, Pax2, and Pten Panel Identifies Precancers Among Histologically Subdiagnostic Endometrial Lesions.

    Aguilar, Mitzi / Chen, Hao / Sahoo, Subhransu S / Zheng, Wenxin / Grubman, Jessica / SoRelle, Jeffrey A / Lucas, Elena / Castrillon, Diego H

    The American journal of surgical pathology

    2023  Volume 47, Issue 5, Page(s) 618–629

    Abstract: Despite refinements in histologic criteria for the diagnosis of endometrioid precancers, many challenging cases are encountered in daily practice, creating diagnostic uncertainty and suboptimal patient management. Recently, an immunohistochemical 3- ... ...

    Abstract Despite refinements in histologic criteria for the diagnosis of endometrioid precancers, many challenging cases are encountered in daily practice, creating diagnostic uncertainty and suboptimal patient management. Recently, an immunohistochemical 3-marker panel consisting of β-catenin, Pax2, and Pten was identified as a useful diagnostic adjunct. However, previous studies focused either on cancers or diagnostically unambiguous precancers, leaving questions about the applicability and utility of the panel in endometria with architectural features near or below the threshold of accepted histologic criteria for endometrioid precancers. Here, in a retrospective study of 90 patients, we evaluated the performance of the 3-marker panel. Notably, the panel detected a subset of disordered proliferative endometria (8/44, 18%), nonatypical hyperplasias (19/40, 48%), and cases with ambiguous features (3/6, 50%) with aberrancy for ≥1 markers. Marker-aberrant cases were more likely to progress to endometrioid precancer or cancer ( P =0.0002). Patterns of marker aberrancy in the index and progressor cases from individual patients provided evidence for origin in a common precursor, and next-generation sequencing of the progressor cases rationalized marker aberrancy for β-catenin and Pten. The results unequivocally demonstrate that some lesions that do not approach current histologic thresholds are bona fide neoplastic precursors with clinically-relevant driver events that can be detected by the 3-marker panel. The findings provide further validation for the diagnostic utility of the panel in clinical practice and its application in difficult or ambiguous cases.
    MeSH term(s) Female ; Humans ; Endometrial Neoplasms/diagnosis ; Endometrial Neoplasms/pathology ; beta Catenin ; Retrospective Studies ; Biomarkers, Tumor ; PTEN Phosphohydrolase ; Endometrium/pathology ; Carcinoma, Endometrioid/diagnosis ; Carcinoma, Endometrioid/pathology ; PAX2 Transcription Factor
    Chemical Substances beta Catenin ; Biomarkers, Tumor ; PTEN Phosphohydrolase (EC 3.1.3.67) ; PTEN protein, human (EC 3.1.3.67) ; PAX2 protein, human ; PAX2 Transcription Factor
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 752964-8
    ISSN 1532-0979 ; 0147-5185
    ISSN (online) 1532-0979
    ISSN 0147-5185
    DOI 10.1097/PAS.0000000000002034
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Increasing severity of COVID-19 in pregnancy with Delta (B.1.617.2) variant surge.

    Adhikari, Emily H / SoRelle, Jeffrey A / McIntire, Donald D / Spong, Catherine Y

    American journal of obstetrics and gynecology

    2021  Volume 226, Issue 1, Page(s) 149–151

    MeSH term(s) COVID-19/complications ; COVID-19 Vaccines/immunology ; Female ; Humans ; Pregnancy ; Pregnancy Complications, Infectious ; Prospective Studies ; SARS-CoV-2 ; Severity of Illness Index ; Vaccination
    Chemical Substances COVID-19 Vaccines
    Language English
    Publishing date 2021-09-14
    Publishing country United States
    Document type Letter ; Research Support, Non-U.S. Gov't
    ZDB-ID 80016-8
    ISSN 1097-6868 ; 0002-9378
    ISSN (online) 1097-6868
    ISSN 0002-9378
    DOI 10.1016/j.ajog.2021.09.008
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  9. Article ; Online: Mass Spectrometry for COVID-19.

    SoRelle, Jeffrey A / Patel, Khushbu / Filkins, Laura / Park, Jason Y

    Clinical chemistry

    2020  Volume 66, Issue 11, Page(s) 1367–1368

    MeSH term(s) Betacoronavirus/genetics ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques ; Contact Tracing ; Coronavirus Infections/diagnosis ; Humans ; Limit of Detection ; Nasal Mucosa/virology ; Pandemics ; Pneumonia, Viral/diagnosis ; Proof of Concept Study ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2 ; Smartphone ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Viral Load
    Keywords covid19
    Language English
    Publishing date 2020-09-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 80102-1
    ISSN 1530-8561 ; 0009-9147
    ISSN (online) 1530-8561
    ISSN 0009-9147
    DOI 10.1093/clinchem/hvaa222
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Different Interpretations of the Same Genetic Data.

    SoRelle, Jeffrey A / Gemmell, Amber P / Ross, Theodora S

    Annals of internal medicine

    2020  Volume 173, Issue 3, Page(s) 239–240

    MeSH term(s) Adult ; Checkpoint Kinase 2/genetics ; Female ; Genetic Counseling/methods ; Genetic Counseling/standards ; Genetic Predisposition to Disease/genetics ; Genetic Testing/standards ; Genetic Variation/genetics ; Humans ; Neoplasms/genetics ; Reproducibility of Results ; Risk Assessment/methods
    Chemical Substances Checkpoint Kinase 2 (EC 2.7.1.11) ; CHEK2 protein, human (EC 2.7.11.1)
    Language English
    Publishing date 2020-06-30
    Publishing country United States
    Document type Letter
    ZDB-ID 336-0
    ISSN 1539-3704 ; 0003-4819
    ISSN (online) 1539-3704
    ISSN 0003-4819
    DOI 10.7326/L20-0192
    Database MEDical Literature Analysis and Retrieval System OnLINE

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