Peter Tarczy-Hornoch

University of Washington Seattle | UW · Department of Biomedical Informatics and Medical Education

Background Pharmacogenomics (PGx) was one of the first genomics applications to hold promise in precision medicine. The cost-effectiveness of PGx has been estimated for many disease states, with the strongest evidence supporting the use of PGx-guided testing to inform prescribing for cardiovascular diseases. Most studies do not consider the present...

We constructed a cost-effectiveness model to assess the clinical and economic value of a CDS alert program that provides pharmacogenomic (PGx) testing results, compared to no alert program in acute coronary syndrome (ACS) and atrial fibrillation (AF), from a health system perspective. We defaulted that 20% of 500,000 health-system members between t...

Background For several major chronic diseases including asthma, chronic obstructive pulmonary disease, chronic kidney disease, and diabetes, a state-of-the-art method to avert poor outcomes is to use predictive models to identify future high-cost patients for preemptive care management interventions. Frequently, an American patient obtains care fro...

BACKGROUND For several major chronic diseases including asthma, chronic obstructive pulmonary disease, chronic kidney disease, and diabetes, a state-of-the-art method to avert poor outcomes is to use predictive models to identify future high-cost patients for preemptive care management interventions. Frequently, an American patient obtains care fro...

Objective: Academic medical centers and health systems are increasingly challenged with supporting appropriate secondary use of clinical data. Enterprise data warehouses have emerged as central resources for these data, but often require an informatician to extract meaningful information, limiting direct access by end users. To overcome this chall...

Background Clinical exome sequencing (CES) provides the advantage of assessing genetic variation across the human exome compared to a traditional stepwise diagnostic approach or multi-gene panels. Comparative effectiveness research methods offer an approach to better understand the patient-centered and economic outcomes of CES. Purpose To evaluate...

Background: In the United States, health care is fragmented in numerous distinct health care systems including private, public, and federal organizations like private physician groups and academic medical centers. Many patients have their complete medical data scattered across these several health care systems, with no particular system having com...

BACKGROUND In the United States, health care is fragmented in numerous distinct health care systems including private, public, and federal organizations like private physician groups and academic medical centers. Many patients have their complete medical data scattered across these several health care systems, with no particular system having compl...

The purpose of this study was to develop a brief instrument, the Feelings About genomiC Testing Results (FACToR), to measure the psychosocial impact of returning genomic findings to patients in research and clinical practice. To create the FACToR, we modified and augmented the Multidimensional Impact of Cancer Risk Assessment (MICRA) questionnaire...

Background The availability of high fidelity electronic health record (EHR) data is a hallmark of the learning health care system. Washington State’s Surgical Care Outcomes and Assessment Program (SCOAP) is a network of hospitals participating in quality improvement (QI) registries wherein data are manually abstracted from EHRs. To create the Compa...

Pharmacogenomics holds promise as a critical component of precision medicine. Yet, the use of pharmacogenomics in routine clinical care is minimal, partly due to the lack of efficient and effective use of existing evidence. This paper describes the design, development, implementation and evaluation of a knowledge-based system that fulfills three cr...

The use of pharmacogenomics (PGx) in clinical practice still faces challenges to fully adopt genetic information in targeting drug therapy. To incorporate genetics into clinical practice, many support the use of Pharmacogenomics Clinical Decision Support Systems (PGx-CDS) for medication prescriptions. This support was fueled by new guidelines to in...

The extent to which pharmacogenomic-guided medication use has been adopted in various health systems is unclear. To assess the uptake of pharmacogenomic-guided medication use, we determined its frequency across our health system, which does not have a structured testing program. Using a multi-site clinical data repository, we identified adult patie...

Objectives: To understand opinions and perceptions on the state of information resources specifically targeted to genomics, and approaches to delivery in clinical practice. Methods: We conducted a survey of genomic content use and its clinical delivery from representatives across eight institutions in the electronic Medical Records and Genomics...

Clinical decision support (CDS) within the electronic health record represents a promising mechanism to provide important genomic findings within clinical workflows. To better understand the current and possible future costs of genomic CDS, we leveraged our local CDS experience to assemble a simple model with inputs such as initial cost and numbers...

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Huma...

The American Medical Informatics Association convened the 2014 Health Policy Invitational Meeting to develop recommendations for updates to current policies and to establish an informatics research agenda for personalizing medicine. In particular, the meeting focused on discussing informatics challenges related to personalizing care through the int...

The increasing reliance on electronic health data has created new opportunities for the secondary use of clinical data to impact practice. We analyzed the secondary uses of clinical data at the University of Washington (UW) to better understand the types of users and uses as well as the benefits and limitations of these electronic data. At the UW,...

Clinicians' ability to use and interpret genetic information depends upon how those data are displayed in electronic health records (EHRs). There is a critical need to develop systems to effectively display genetic information in EHRs and augment clinical decision support (CDS). The National Institutes of Health (NIH)-sponsored Clinical Sequencing...

To facilitate personalized drug dosing (PDD), this pilot study explored the communication effectiveness and clinical impact of using a prototype clinical decision support (CDS) system embedded in an electronic health record (EHR) to deliver pharmacogenomic (PGx) information to physicians. We employed a conceptual framework and measurement model to...

Purpose: Electronic health records (EHRs) and their associated decision support tools are potentially important means of disseminating a patient's pharmacogenomic profile to his or her health-care providers. We sought to create a proof-of-concept decision support alert system generated from pharmacogenomic incidental findings from exome sequencing...

Introduction: A key attribute of a learning health care system is the ability to collect and analyze routinely collected clinical data in order to quickly generate new clinical evidence, and to monitor the quality of the care provided. To achieve this vision, clinical data must be easy to extract and stored in computer readable formats. We conduct...

This paper describes a text processing system designed to automate the manual data abstraction process in a quality improvement (QI) program. The Surgical Care and Outcomes Assessment Program (SCOAP) is a clinician-led, statewide performance benchmarking QI platform for surgical and interventional procedures. The data elements abstracted as part of...

Recent successes in the use of gene sequencing for patient care highlight the potential of genomic medicine. For genomics to become a part of usual care, pertinent elements of a patient's genomic test must be communicated to the most appropriate care providers. Electronic medical records may serve as a useful tool for storing and disseminating geno...

The Electronic Medical Records and Genomics (eMERGE) Network is a national consortium that is developing methods and best practices for using the electronic health record (EHR) for genomic medicine and research. We conducted a multi-site survey of information resources to support integration of pharmacogenomics into clinical care. This work aimed t...

Background Despite evidence that electronic medical records (EMR) information technology innovations can enhance the quality of trauma center care, few investigations have systematically assessed United States (US) trauma center EMR capacity, particularly for screening of mental health comorbidities. Study Design Trauma programs at all US Level I...

Whole exome and whole genome sequencing are applications of next generation sequencing transforming clinical care, but there is little evidence whether these tests improve patient outcomes or if they are cost effective compared to current standard of care. These gaps in knowledge can be addressed by comparative effectiveness and patient-centered ou...

Delivering more appropriate, safer, and highly effective health care is the goal of a learning health care system. The Agency for Healthcare Research and Quality (AHRQ) funded enhanced registry projects: (1) to create and analyze valid data for comparative effectiveness research (CER); and (2) to enhance the ability to monitor and advance clinical...

The acquisition of high quality, richly an-notated human biospecimens for translational and clinical research represents a challenge for investigators. NWBioTrust(https://www.nwbiotrust.org), a collaboration between University of Washington (UW), Seattle Cancer Care Alliance(SCCA) and Fred Hutchinson Cancer Research Center, was formed to address th...

Background: Pharmacogenomics (PGx) is positioned to have a widespread impact on the practice of medicine, yet physician acceptance is low. The presentation of context-specific PGx information, in the form of clinical decision support (CDS) alerts embedded in a computerized provider order entry (CPOE) system, can aid uptake. Usability evaluations c...

Background Learning health care systems apply the experiences of prior patients to inform care and help to guide decision making for current patients. These systems should help to deliver more effective, efficient, and appropriate care. Most examples of learning systems derive from integrated care delivery systems and examples of such systems in th...

To effectively articulate the results of exome and genome sequencing we refined the structure and content of molecular test reports. To communicate results of a randomized control trial aimed at the evaluation of exome sequencing for clinical medicine, we developed a structured narrative report. With feedback from genetics and non-genetics professi...

The field of clinical research informatics includes creation of clinical data repositories (CDRs) used to conduct quality improvement (QI) activities and comparative effectiveness research (CER). Ideally, CDR data are accurately and directly abstracted from disparate electronic health records (EHRs), across diverse health-systems. Investigators fro...

The Biotrust resource provides a web-accessible method to coordinate discovery and request of annotated biospecimens for research. The system is built on an open-source web-application framework, and has a modular approach to defining education on process, study registration and feasibility review, patient identification and cohort forwarding, cons...

Purpose: Genome-scale clinical sequencing is being adopted more broadly in medical practice. The National Institutes of Health developed the Clinical Sequencing Exploratory Research (CSER) program to guide implementation and dissemination of best practices for the integration of sequencing into clinical care. This study describes and compares the...

Clinical decision support embedded into clinical information systems, such as electronic health records, is recognized as necessary to facilitate the appropriate use of genomic information. There are many lessons learned from more than five decades of experience in CDS implementation that can guide us during the genomic era. We provide an overview...

To describe the inaugural comparative effectiveness research (CER) cohort study of Washington State's Comparative Effectiveness Research Translation Network (CERTAIN), which compares invasive with noninvasive treatments for peripheral artery disease, and to focus on the patient centeredness of this cohort study by describing it within the context o...

Personalized medicine can be defined broadly as a model of healthcare that is predictive, personalized, preventive and participatory. Two US President's Council of Advisors on Science and Technology reports illustrate challenges in personalized medicine (in a 2008 report) and in use of health information technology (in a 2010 report). Translational...

The Biotrust resource provides a web-accessible method to coordinate discovery and request of annotated biospecimens for research. The system is built on an open-source web-application framework, and has a modular approach to defining education on process, study registration and feasibility review, patient identification and cohort forwarding, cons...

A national investment in clinical and translational research has resulted in an analysis of the gaps that prevent the rapid translation of discoveries into therapies. By identifying the challenges facing clinical and translational researchers, best practices for streamlining resources and the development of novel informatics tools will aim to close...

In this paper, the authors present the results of a qualitative case-study seeking to characterize data discovery needs and barriers of principal investigators and research support staff in clinical translational science. Several implications for designing and implementing translational research systems have emerged through the authors’ analysis. T...

Background Methods of weakening and attenuating pathogens’ abilities to infect and propagate in a host, thus allowing the natural immune system to more easily decimate invaders, have gained attention as alternatives to broad-spectrum targeting approaches. The following work describes a technique to identifying proteins involved in virulence by rely...

txt – Specific virulence class labels. This tab-delimited file contains two columns. The first column is the unique sequence identifier matched to some protein sequence in the specific virulence FASTA file, and the second column indicates the specific virulence label, per Table 2. Non-virulent proteins are assigned class ‘12’ in this file.

faa — Specific virulence protein sequences. This FASTA file contains the 3700 protein sequences used for training and testing the specific virulence classifiers. Note that the FASTA sequence headers contain only the unique identifiers; labels are located in a separate file.

pdf — Statistical significance outcomes of method and source comparisons. A PDF containing tabular results of statistical significance testing from six five-fold cross-validations of integrated data against each other and baselines. Data from these tables was used to construct the comparison networks in Figure 3.

Findings from pharmacogenomics (PGx) studies have the potential to be applied to individualize drug therapy to improve efficacy and reduce adverse drug events. Researchers have identified factors influencing uptake of genomics in medicine, but little is known about the specific technical barriers to incorporating PGx into existing clinical framewor...

Comparative effectiveness research (CER) has the potential to transform the current health care delivery system by identifying the most effective medical and surgical treatments, diagnostic tests, disease prevention methods, and ways to deliver care for specific clinical conditions. To be successful, such research requires the identification, captu...

The AMIA biomedical informatics (BMI) core competencies have been designed to support and guide graduate education in BMI, the core scientific discipline underlying the breadth of the field's research, practice, and education. The core definition of BMI adopted by AMIA specifies that BMI is 'the interdisciplinary field that studies and pursues the...

The future of neonatal informatics will be driven by the availability of increasingly vast amounts of clinical and genetic data. The field of translational bioinformatics is concerned with linking and learning from these data and applying new findings to clinical care to transform the data into proactive, predictive, preventive, and participatory h...

Pharmacogenomics evaluations of variability in drug metabolic processes may be useful for making individual drug response predictions. We present an approach to deriving 'phenotype scores' based on existing pharmacogenomics knowledge and a patient's genomics data. Pharmacogenomics plays an important role in the bioactivation of tamoxifen, a prodrug...

The University of Washington Institute of Translational Health Sciences is engaged in a project, LC Data QUEST, building data sharing capacity in primary care practices serving rural and tribal populations in the Washington, Wyoming, Alaska, Montana, Idaho region to build research infrastructure. We report on the iterative process of developing the...

In this paper, the authors present the results of a qualitative case-study seeking to characterize data discovery needs and barriers of principal investigators and research support staff in clinical translational science. Several implications for designing and implementing translational research systems have emerged through the authors' analysis. T...

We evaluated the functional support currently existing University of Washington clinical systems provide to execute approximate pharmacogenomic decision support rules. In addition, we evaluated proposed clinical decision support system user interface features with use scenarios to provide contextual information. Based on results from these evaluati...

Objective: The Cross-Institutional Clinical Translational Research project explored a federated query tool and looked at how this tool can facilitate clinical trial cohort discovery by managing access to aggregate patient data located within unaffiliated academic medical centers. Methods: The project adapted software from the Informatics for Int...

Nearly a decade since the completion of the first draft of the human genome, the biomedical community is positioned to usher in a new era of scientific inquiry that links fundamental biological insights with clinical knowledge. Accordingly, holistic approaches are needed to develop and assess hypotheses that incorporate genotypic, phenotypic, and e...

Though there have been many advances in providing access to linked and integrated biomedical data across repositories, developing methods which allow users to specify ambiguous and exploratory queries over disparate sources remains a challenge to extracting well-curated or diversely-supported biological information. In the following work, we discus...

The United States (US) Health Information Technology for Economic and Clinical Health Act of 2009 has spurred adoption of electronic health records. The corresponding meaningful use criteria proposed by the Centers for Medicare and Medicaid Services mandates use of computerized provider order entry (CPOE) systems. Yet, adoption in the US and other...

In pursuing personalized medicine, pharmacogenomic (PGx) knowledge may help guide prescribing drugs based on a person's genotype. Here we evaluate the feasibility of incorporating PGx knowledge, combined with clinical data, to support clinical decision-making by: 1) analyzing clinically relevant knowledge contained in PGx knowledge resources; 2) ev...

The breadth and depth of the Summit continues to grow with twenty-five 90-minute scientific sessions. Original research was presented in forty-nine papers and abstract presentations covering all six tracks and spanning from methods to applications. Ten late breaking sessions covered work in press or published since the 2009 Summit including for exa...

Health data sharing with and among practices is a method for engaging rural and underserved populations, often with strong histories of marginalization, in health research. The Institute of Translational Health Sciences, funded by a National Institutes of Health Clinical and Translational Science Award, is engaged in the LC Data QUEST project to bu...

This paper describes one organization's interpretation of the Patient-Centered Medical Home concept and the healthcare delivery system that has emerged from their participatory redesign initiative. Group Health, a large integrated healthcare system based in Seattle, Washington, USA initiated a Patient-Centered Medical Home care delivery system tran...

Genome wide association studies (GWAS) are an important approach to understanding the genetic mechanisms behind human diseases. Single nucleotide polymorphisms (SNPs) are the predominant markers used in genome wide association studies, and the ability to predict which SNPs are likely to be functional is important for both a priori and a posteriori...

Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to understanding human genetic variation. A key element in assessing role of a given SNP is determining if the variation is likely to result in chang...

Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to therapy. These scientific discoveries need to be translated into practical applications to optimize patient care. Translating research into p...

Levels of curation across biological databases are widely recognized as being highly variable, depending on provenance and type. In spite of ambiguous quality, searches against biological sources, such as those for sequence homology, remain a frontline strategy for biomedical scientists studying molecular data. In the following, we investigate the...

Genome wide association studies can potentially identify the genetic causes behind the majority of human diseases. With the advent of more advanced genotyping techniques, there is now an explosion of data gathered on single nucleotide polymorphisms (SNPs). The need exists for an integrated system that can provide up-to-date functional annotation in...

Mediator-based data integration systems resolve exploratory queries by joining data elements across sources. In the presence of uncertainties, such multiple expansions can quickly lead to spurious connections and incorrect results. The BioRank project investigates formalisms for modeling uncertainty during scientific data integration and for rankin...

In the following work, we test a generalized approach to integrating, transforming and learning data from disparate data sources for the classification of bacterial proteins involved in pathogenesis. We rely on the implicit inter-linkages between biological databases to draw relevant records, and leverage statistical learning methods to infer class...

Proteins of unknown function are a barrier to our understanding of molecular biology. Assigning function to these "uncharacterized" proteins is imperative, but challenging. The usual approach is similarity searches using annotation databases, which are useful for predicting function. However, since the performance of these databases on uncharacteri...

Due to its complex nature, modern biomedical research has become increasingly interdisciplinary and collaborative in nature. Although a necessity, interdisciplinary biomedical collaboration is difficult. There is, however, a growing body of literature on the study and fostering of collaboration in fields such as computer supported cooperative work...

Knowledge about people and organizational issues pertinent to implementation and maintenance of clinical systems has grown steadily over the past fifteen years. Less is known about implementation of systems used for clinical and biomedical research. In conjunction with current National Institutes of Health Roadmap efforts that promote translational...

In the following work, we test a generalized approach to integrating, transforming and learning data from disparate data sources for the classification of bacterial proteins involved in pathogenesis. We rely on the implicit inter-linkages between biological databases to draw relevant records, and leverage statistical learning methods to infer class...

CTSAs have brought about a push to find better EDC systems, which facilitate translational research. Based on the data management needs of a specific clinical/translational research lab, concept mapping was used to create a framework to evaluate EDCs. After refinement based on a spiral model, including consultations with the UW CTSA and a survey of...

Clinical trials are important for the advancement of medical research. Despite of the benefits clinical trial enrollment is low. We study the feasibility of using NLP to assist with automatic eligibility screening by extracting medical diagnoses from the inclusion and exclusion criteria of cancer clinical trial announcements posted on the internet....

To explore how the implementation of a comprehensive new bioinformatics analysis system would affect workflow, collaboration and information management in a small genetic research lab. This was a longitudinal qualitative study of seven individuals involved in genomic and proteomic research. The study data were gathered using the illuminative/respon...

There is a significant need for data integration capabilities in the scientific domain, which has manifested itself as products in the commercial world as well as academia. However, in our experiences in dealing with biological data it has become apparent to us that existing data integration products do not handle uncertainties in the data very wel...

A. Identify the current state of data management needs of academic biomedical researchers. B. Explore their anticipated data management and analysis needs. C. Identify barriers to addressing those needs. A multimodal needs analysis was conducted using a combination of an online survey and in-depth one-on-one semi-structured interviews. Subjects wer...

Genomic medicine aims to revolutionize health care by applying our growing understanding of the molecular basis of disease. Research in this arena is data intensive, which means data sets are large and highly heterogeneous. To create knowledge from data, researchers must integrate these large and diverse data sets. This presents daunting informatic...

Genomic medicine aims to revolutionize health care by applying our growing understanding of the molecular basis of disease. Research in this arena is data intensive, which means data sets are large and highly heterogeneous. To create knowledge from data, ...

Scientists working on genomics projects are often faced with the difficult task of sifting through large amounts of biological information dispersed across various online data sources that are relevant to their area or organism of research. Gene annotation, the process of identifying the functional role of a possible gene, in particular has become...

Setting: The University of Washington Health Sciences Libraries and Information Center BioCommons serves the bioinformatics needs of researchers at the university and in the vibrant for-profit and not-for-profit biomedical research sector in the Washington area and region. Program components: The BioCommons comprises services addressing internal...

Supplementary data in the form of an Excel spreadsheet (696 K) detailing the data supporting Method 1 and Method 2 is available online from BMC Bioinformatics.

Providing for long-term and consistent public access to scientific data is a growing concern in biomedical research. One aspect of this problem can be demonstrated by evaluating the persistence of supplementary data associated with published biomedical papers. We manually evaluated 655 supplementary data links extracted from PubMed abstracts publis...

Medical geneticists, genetics counselors and nurses in genetics who staff medical genetics clinics rely upon internet-accessible and stand-alone databases for access to the medical literature, for disease recognition, for current information on genetic test availability and use, for patient-support materials, and for locating other genetics profess...

BioMediator is a data integration system that provides a common interface to multiple Internet-accessible databases containing information about genetics and molecular biology. Ontologies play several important roles in the BioMediator system: First, ontologies of genetics and molecular biology can serve as data sources. In this role concepts from...

The BioMediator system developed at the University of Washington (UW) provides a theoretical and practical foundation for data integration across diverse biomedical research domains and various data types. In this paper we demonstrate the generalizability of its architecture through its application to the UW Human Brain Project (HBP) for understand...

Biological research today involves aggregating and analyzing large amounts of data from disparate sources. Tools such as the University of Washington's BioMediator system integrate heterogeneous data. Analytic packages such as the R environment have a rich set of tools to analyze biomedical research data. Our pilot project bridged data integration...

Gene annotation requires integration of data from multiple sources in order to functionally classify genes. We are using BioMediator, a general purpose data-integration solution, to develop a gene annotation system to automate the process of collecting data from disparate genomic databases. Integration of annotation data from multiple sources into...

As biomedical research and healthcare continue to progress in the genomic/post genomic era a number of important challenges and opportunities exist in the broad area of biomedical informatics. In the context of this chapter we define bioinformatics as the field that focuses on information, data, and knowledge in the context of biological and biomed...

This paper describes a strategy for the development of ontologies in the life sciences, tools to support the creation and use of those ontologies, and a framework whereby these ontologies can support the development of commercial applications within the field. At the core of these efforts is the need for an organization that will provide a focus fo...

Many information systems have failed when deployed into complex health-care settings. We believe that one cause of these failures is the difficulty in systematically accounting for the collaborative and exception-filled nature of medical work. In this methodological review paper, we highlight research from the field of computer-supported cooperativ...

We recently found documentation discrepancies in 60% of resident daily-progress notes with respect to patient weight, medications, or vascular lines. To what extent information systems can decrease such discrepancies is unknown. To determine whether a point-of-care personal digital assistant (PDA)-based patient record and charting system could redu...

We present the BioMediator (www.biomediator.org) system and the process of executing queries on it. The system was designed as a tool for posing queries across semantically and syntactically heterogeneous data particularly in the biological arena. We use examples from researchers at the University of Washington, and the University of Missouri-Colum...

BioMediator is a data integration system tailored to the domain of molecular biology. Based on our collaborations with biologic researchers, we have identified several challenges in building a data integration system that addresses their needs. BioMediator provides a common interface to several Web-accessible data sources using a novel source knowl...

Medical errors are common and potentially dangerous. Little is known about the role of documentation errors. To determine the proportion of resident physician progress notes that contained discrepancies, and to identify predictors of such discrepancies. We conducted a retrospective cross-sectional chart review of resident physician progress notes o...

This paper presents the implementation of a model for expression array annotation (EAA) using the BioMediator biological data integration system along with BioConductor, an analytic tools platform. The model presented addresses the need for annotation sources identified during BioConductor inverted exclamation mark s development. Annotation provide...