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Pathology informatics

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https://www.readbyqxmd.com/read/29748851/a-platform-for-innovation-and-standards-evaluation-a-case-study-from-the-openmrs-open-source-radiology-information-system
#1
Judy W Gichoya, Marc Kohli, Larry Ivange, Teri S Schmidt, Saptarshi Purkayastha
Open-source development can provide a platform for innovation by seeking feedback from community members as well as providing tools and infrastructure to test new standards. Vendors of proprietary systems may delay adoption of new standards until there are sufficient incentives such as legal mandates or financial incentives to encourage/mandate adoption. Moreover, open-source systems in healthcare have been widely adopted in low- and middle-income countries and can be used to bridge gaps that exist in global health radiology...
May 10, 2018: Journal of Digital Imaging: the Official Journal of the Society for Computer Applications in Radiology
https://www.readbyqxmd.com/read/29721362/career-paths-of-pathology-informatics-fellowship-alumni
#2
Joseph W Rudolf, Christopher A Garcia, Matthew G Hanna, Christopher L Williams, Ulysses G Balis, Liron Pantanowitz, J Mark Tuthill, John R Gilbertson
Background: The alumni of today's Pathology Informatics and Clinical Informatics fellowships fill diverse roles in academia, large health systems, and industry. The evolving training tracks and curriculum of Pathology Informatics fellowships have been well documented. However, less attention has been given to the posttraining experiences of graduates from informatics training programs. Here, we examine the career paths of subspecialty fellowship-trained pathology informaticians. Methods: Alumni from four Pathology Informatics fellowship training programs were contacted for their voluntary participation in the study...
2018: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/29698836/system-for-informatics-in-the-molecular-pathology-laboratory-simpl-an-open-source-end-to-end-solution-for-next-generation-sequencing-clinical-data-management
#3
Wenjun Kang, Sabah Kadri, Rutika Puranik, Michelle N Wurst, Sushant A Patil, Ibro Mujacic, Sonia Benhamed, Nifang Niu, Chao Jie Zhen, Bekim Ameti, Bradley C Long, Filipo Galbo, David Montes, Crystal Iracheta, Venessa L Gamboa, Daisy Lopez, Michael Yourshaw, Carolyn A Lawrence, Dara L Aisner, Carrie Fitzpatrick, Megan E McNerney, Y Lynn Wang, Jorge Andrade, Samuel L Volchenboum, Larissa V Furtado, Lauren L Ritterhouse, Jeremy P Segal
Next-generation sequencing (NGS) diagnostic assays are increasingly becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems (LIS) and/or Laboratory Information Management Systems (LIMS) are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost prohibitive...
April 23, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29621832/identifying-associations-between-somatic-mutations-and-clinicopathologic-findings-in-lung-cancer-pathology-reports
#4
Nishant Kumar, Laura J Tafe, John H Higgins, Jason D Peterson, Francise Blumental de Abreu, Sophie J Deharvengt, Gregory J Tsongalis, Christopher I Amos, Saeed Hassanpour
OBJECTIVE: We aim to build an informatics methodology capable of identifying statistically significant associations between the clinical findings of non-small cell lung cancer (NSCLC) recorded in patient pathology reports and the various clinically actionable genetic mutations identified from next-generation sequencing (NGS) of patient tumor samples. METHODS: We built an information extraction and analysis pipeline to identify the associations between clinical findings in the pathology reports of patients and corresponding genetic mutations...
February 2018: Methods of Information in Medicine
https://www.readbyqxmd.com/read/29544642/characterization-of-the-ovarian-tumor-peptidome
#5
Tao Liu, Karin D Rodland, Richard D Smith
Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of the tumor peptidome has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the tumors peptidome information in cancer research have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing...
2018: Vitamins and Hormones
https://www.readbyqxmd.com/read/29475039/genes-and-micrornas-associated-with-mouse-cleft-palate-a-systematic-review-and-bioinformatics-analysis
#6
Akiko Suzuki, Nada Abdallah, Mona Gajera, Goo Jun, Peilin Jia, Zhongming Zhao, Junichi Iwata
Cleft palate (CP) is the most prevalent craniofacial deformity, with ethnic and geographic variation in prevalence in humans. Mice have been used as an animal model to study the cause(s) of CP by several approaches, including genetic and chemical-induced approaches. Mouse genetic approaches revealed that significant amounts of genes are involved in the CP pathology. The aim of this study was to identify common features of CP-associated genes and to explore the roles of microRNAs (miRNAs) as important post-transcriptional regulators that may be involved in the regulation of CP genes...
April 2018: Mechanisms of Development
https://www.readbyqxmd.com/read/29441462/up-regulation-of-mir-340-5p-promotes-progression-of-thyroid-cancer-by-inhibiting-bmp4
#7
P Zhao, W Ma, Z Hu, Y Zhang, S Zhang, Y Wang
PURPOSE: The incidence of thyroid cancer is increasing and the proliferation of thyroid cancer cells is incompletely understood. microRNAs may play key roles in thyroid cancer progression. METHODS: We analyzed miR-340-5p in thyroid cancer tissue and normal tissue, and using informatics to predict its target. Cell lines and a mouse model were used to study the role of miR-340-5p in cancer proliferation. RESULTS: Overexpression of miR-340-5p was found in thyroid cancer specimens...
February 13, 2018: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/29344894/systems-biology-approaches-in-cancer-pathology
#8
Aaron DeWard, Rebecca J Critchley-Thorne
The complex network of the tissue system, in both pre-neoplastic tissues and tumors, demonstrates the need for a systems biology approach to cancer pathology, in which quantification of key tissue system processes is combined with informatics tools to produce actionable scores to aid clinical decision-making. A systems biology approach to cancer pathology enables integration of key system features that are relevant to diagnoses, patient outcomes, and responses to therapies. Key tissue system features relevant to cancer pathology include molecular and morphologic abnormalities in epithelia, cellular changes in the stroma such as immune infiltrates, and relationships between components of the system, such as interactions and spatial relationships between epithelial and stromal components, and also between specific immune cell subsets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29285339/medium-chain-acyl-coa-dehydrogenase-deficiency-in-a-premature-infant
#9
Steven F Dobrowolski, Lina Ghaloul-Gonzalez, Jerry Vockley
Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is identified by newborn screening (NBS). The natural history of MCADD includes metabolic decompensation with hypoglycemia, hyperammonemia, seizures, coma, and death. NBS enables expectant management thus severe symptoms are rare in managed patients. We report premature birth of an MCADD affected infant and resultant management challenges. Nutritional support advanced from parenteral nutrition at 24 hours to enteral feeds. A NBS sample was collected day 2, positive results for MCADD was reported day six, and diagnostic tests were performed day seven...
November 21, 2017: Pediatric Reports
https://www.readbyqxmd.com/read/29226007/houston-methodist-variant-viewer-an-application-to-support-clinical-laboratory-interpretation-of-next-generation-sequencing-data-for-cancer
#10
Paul A Christensen, Yunyun Ni, Feifei Bao, Heather L Hendrickson, Michael Greenwood, Jessica S Thomas, S Wesley Long, Randall J Olsen
Introduction: Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/29185142/initial-and-long-term-impact-of-a-multi-disciplinary-task-force-in-the-diagnosis-and-management-of-heparin-induced-thrombocytopenia
#11
Ming Y Lim, Joyce Foster, Angela Rourk, Charles S Greenberg
Many medical centers are faced with a major challenge in making an accurate diagnosis of heparin-induced thrombocytopenia (HIT) and ensuring appropriate changes in management strategy in line with guideline recommendations. We report the initial and long-term impact and challenges of institution-wide changes in the diagnosis and management of HIT in the inpatient setting at an academic medical center. We established a HIT Task Force, consisting of a multidisciplinary team of non-malignant hematologists, nursing, pharmacist, pathology, blood bank and clinical lab informatics...
January 2018: Journal of Thrombosis and Thrombolysis
https://www.readbyqxmd.com/read/29165940/-use-of-clinical-practice-guidelines-in-medicine-what-s-new
#12
Oriane Aebischer, Mathilde Rochat, Marie Méan
Clinicians are confronted to an abundance of clinical practice guidelines (CPG). It has been proven for several pathologies that the use of guidelines improves quality of care by reducing mortality, the number of hospitalisations and the length of stay. Despite these proven benefits, adherence to CPGs remains low, mainly due to lack of awareness and familiarity with the guidelines, as well as lack of applicability and flexibility for elderly and comorbid patients. Since adherence to CPGs are influenced by their accessibility and format, informatics will certainly play an important role in the development and implementation of CPGs in the future...
November 22, 2017: Revue Médicale Suisse
https://www.readbyqxmd.com/read/29154853/standards-and-guidelines-for-validating-next-generation-sequencing-bioinformatics-pipelines-a-joint-recommendation-of-the-association-for-molecular-pathology-and-the-college-of-american-pathologists
#13
REVIEW
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding, Chen Wang, Alexis B Carter
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care...
January 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29136101/identification-of-topological-features-in-renal-tumor-microenvironment-associated-with-patient-survival
#14
Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani, Qianjin Feng, Kun Huang
Motivation: As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However, traditional qualitative and/or semi-quantitative parameters obtained by pathologist's visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem...
March 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29092947/an-image-analysis-resource-for-cancer-research-piip-pathology-image-informatics-platform-for-visualization-analysis-and-management
#15
Anne L Martel, Dan Hosseinzadeh, Caglar Senaras, Yu Zhou, Azadeh Yazdanpanah, Rushin Shojaii, Emily S Patterson, Anant Madabhushi, Metin N Gurcan
Pathology Image Informatics Platform (PIIP) is an NCI/NIH sponsored project intended for managing, annotating, sharing, and quantitatively analyzing digital pathology imaging data. It expands on an existing, freely available pathology image viewer, Sedeen. The goal of this project is to develop and embed some commonly used image analysis applications into the Sedeen viewer to create a freely available resource for the digital pathology and cancer research communities. Thus far, new plugins have been developed and incorporated into the platform for out of focus detection, region of interest transformation, and IHC slide analysis...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29054270/the-peptidome-comes-of-age-mass-spectrometry-based-characterization-of-the-circulating-cancer-peptidome
#16
David W Greening, Eugene A Kapp, Richard J Simpson
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases...
2017: Enzymes
https://www.readbyqxmd.com/read/28939981/-annual-report-2017-of-the-working-group-on-informatics-digital-pathology-and-biobanks
#17
G Kayser, G Haroske
No abstract text is available yet for this article.
September 22, 2017: Der Pathologe
https://www.readbyqxmd.com/read/28913416/using-focused-laboratory-management-and-quality-improvement-projects-to-enhance-resident-training-and-foster-scholarship
#18
Matthew D Krasowski, Bradley A Ford, J Stacey Klutts, Chris S Jensen, Angela S Briggs, Robert A Robinson, Leslie A Bruch, Nitin J Karandikar
Training in patient safety, quality, and management is widely recognized as an important element of graduate medical education. These concepts have been intertwined in pathology graduate medical education for many years, although training programs face challenges in creating explicit learning opportunities in these fields. Tangibly involving pathology residents in management and quality improvement projects has the potential to teach and reinforce key concepts and further fulfill Accreditation Council for Graduate Medical Education goals for pursuing projects related to patient safety and quality improvement...
January 2017: Academic Pathology
https://www.readbyqxmd.com/read/28828200/pathedex-uncovering-high-explanatory-visual-diagnostics-heuristics-using-digital-pathology-and-multiscale-gaze-data
#19
Dmitriy Shin, Mikhail Kovalenko, Ilker Ersoy, Yu Li, Donald Doll, Chi-Ren Shyu, Richard Hammer
BACKGROUND: Visual heuristics of pathology diagnosis is a largely unexplored area where reported studies only provided a qualitative insight into the subject. Uncovering and quantifying pathology visual and nonvisual diagnostic patterns have great potential to improve clinical outcomes and avoid diagnostic pitfalls. METHODS: Here, we present PathEdEx, an informatics computational framework that incorporates whole-slide digital pathology imaging with multiscale gaze-tracking technology to create web-based interactive pathology educational atlases and to datamine visual and nonvisual diagnostic heuristics...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/28828198/teaching-digital-pathology-the-international-school-of-digital-pathology-and-proposed-syllabus
#20
Vincenzo Della Mea, Antonino Carbone, Carla Di Loreto, Gloria Bueno, Paolo De Paoli, Marcial García-Rojo, David de Mena, Annunziata Gloghini, Mohammad Ilyas, Arvydas Laurinavicius, Allan Rasmusson, Massimo Milione, Riccardo Dolcetti, Marco Pagani, Andrea Stoppini, Sandro Sulfaro, Michelangelo Bartolo, Emanuela Mazzon, H Peter Soyer, Liron Pantanowitz
Digital pathology is an interdisciplinary field where competency in pathology, laboratory techniques, informatics, computer science, information systems, engineering, and even biology converge. This implies that teaching students about digital pathology requires coverage, expertise, and hands-on experience in all these disciplines. With this in mind, a syllabus was developed for a digital pathology summer school aimed at professionals in the aforementioned fields, as well as trainees and doctoral students. The aim of this communication is to share the context, rationale, and syllabus for this school of digital pathology...
2017: Journal of Pathology Informatics
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