User-centered design of multi-gene sequencing panel reports for clinicians

Determinants of targeted cancer therapy use in community oncology practice: a qualitative study using the Theoretical Domains Framework and Rummler-Brache process mapping

BACKGROUND

Precision medicine holds enormous potential to improve outcomes for cancer patients, offering improved rates of cancer control and quality of life. Not all patients who could benefit from targeted cancer therapy receive it, and some who may not benefit do receive targeted therapy. We sought to comprehensively identify determinants of targeted therapy use among community oncology programs, where most cancer patients receive their care.

METHODS

Guided by the Theoretical Domains Framework, we conducted semi-structured interviews with 24 community cancer care providers and mapped targeted therapy delivery across 11 cancer care delivery teams using a Rummler-Brache diagram. Transcripts were coded to the framework using template analysis, and inductive coding was used to identify key behaviors. Coding was revised until a consensus was reached.

RESULTS

Intention to deliver precision medicine was high across all participants interviewed, who also reported untenable knowledge demands. We identified distinctly different teams, processes, and determinants for (1) genomic test ordering and (2) delivery of targeted therapies. A key determinant of molecular testing was role alignment. The dominant expectation for oncologists to order and interpret genomic tests is at odds with their role as treatment decision-makers' and pathologists' typical role to stage tumors. Programs in which pathologists considered genomic test ordering as part of their staging responsibilities reported high and timely testing rates. Determinants of treatment delivery were contingent on resources and ability to offset delivery costs, which low- volume programs could not do. Rural programs faced additional treatment delivery challenges.

CONCLUSIONS

We identified novel determinants of targeted therapy delivery that potentially could be addressed through role re-alignment. Standardized, pathology-initiated genomic testing may prove fruitful in ensuring patients eligible for targeted therapy are identified, even if the care they need cannot be delivered at small and rural sites which may have distinct challenges in treatment delivery. Incorporating behavior specification and Rummler-Brache process mapping with determinant analysis may extend its usefulness beyond the identification of the need for contextual adaptation.

Investigating the presentation of uncertainty in an icon array: A randomized trial

BACKGROUND

Clinicians are often advised to use pictographs to communicate risk, but whether they offer benefits when communicating risk imprecision (e.g., 65%-79%) is unknown.

PURPOSE

To test whether any of three approaches to visualizing imprecision would more effectively communicate breast and ovarian cancer risk for BRCA1 pathogenic variant carriers.

METHODS

1,300 UK residents were presented with a genetic report with information about BRCA1-related risks, with random assignment to one of four formats: no visualization (text alone), or a pictograph using shaded icons, a gradient, or arrows marking range endpoints. We also tested pictographs in two layouts. Analysis of variance (ANOVA) and regression was employed.

RESULTS

There was no effect of format. Participants shown pictographs vs. text alone had better uptake of breast cancer risk messages (p < .05, η ² = 0.003). Pictographs facilitated memory for the specific amount of risk (p < 0.001, η ² = 0.019), as did the tabular layout. Individuals not having completed upper secondary education may benefit most.

CONCLUSIONS

We found weak evidence in favor of using simple pictographs with ranges to communicate BRCA risk (versus text alone), and of the tabular layout.

INNOVATION

Testing different ways of communicating imprecision within pictographs is a novel and promising line of research.

Making BRCA1 genetic test reports easier to understand through user-centered design: A randomized trial

PURPOSE

Our objective was to apply a user-centered design process to identify phrases, graphics, and ways of communicating numerical risks that could be used to help patients understand their cancer risk and next steps on receiving BRCA1 genetic test results (positive, negative, and variants of uncertain significance).

METHODS

The first phase of the study, a user-centered design process, consisted of 4 rounds of interviews (N = 42, including 13 health care professionals and 16 patients having undergone BRCA testing). The second was a randomized, between-participants experimental study of 456 United Kingdom residents that compared the resulting reports to reports used in a United Kingdom national genomic laboratory hub. Outcomes were subjective and objective comprehension, communication efficacy, actionability, and perceived risk.

RESULTS

Subjective comprehension, communication efficacy, and actionability were all higher for the user-centered reports, with no difference in perceived risk. Comprehension of participants viewing user-centered reports was significantly better on 2 items, directionally (but not significantly) better on 6 items, and directionally (but not significantly) worse on 2 items.

CONCLUSION

Our results imply that user-centered design is a promising approach for developing materials about complex genetic risks. We suggest wordings that are likely to lead to improved comprehension when communicating BRCA-associated risks.

Recommendations for designing genetic test reports to be understood by patients and non-specialists

Patients and non-specialist healthcare professionals are increasingly expected to understand and interpret the results of genetic or genomic testing. These results are currently reported using a variety of templates, containing different amounts, levels, and layouts of information. We set out to establish a set of recommendations for communicating genetic test results to non-expert readers. We employed a qualitative-descriptive study design with user-centred design principles, including a mixture of in-person semi-structured interviews and online questionnaires with patients, healthcare professionals and the general public. The resulting recommendations and example template include providing at-a-glance comprehension of what the test results mean for the patient; suggested next steps; and details of further information and support. Separation and inclusion of technical methodological details enhances non-specialists' understanding, while retaining important information for specialists and the patients' records. The recommendations address the high-level needs of patients and their non-specialist clinicians when receiving genetic test results. These recommendations provide a solid foundation for the major content and structure of reports, and we recommend further engagement with patients and clinicians to tailor reports to specific types of test and results.

FHIR Lab Reports: using SMART on FHIR and CDS Hooks to increase the clinical utility of pharmacogenomic laboratory test results

Laboratory tests are a common aspect of clinical care and are the primary source of clinical genomic data. However, most laboratories use PDF documents to store and exchange the results of these tests. This locks the data into a static format and leaves the results only human-readable. The ordering clinician uses the results, but after that the information is unlikely to be used again. Future use would require a clinician to know that the test was performed, know where to find the PDF report, and take the time to open it and determine relevance to that future scenario. New computational standards such as SMART on FHIR and CDS Hooks present opportunities to better utilize these results, both physically upon receipt and asynchronously in future clinical encounters for that patient. Full app available at https://github.com/mwatkin8/FHIR-Lab-Reports-App. Demo available at http://hematite.genetics.utah.edu/FHIR-Lab-Reports/.

Implementing the VMC Specification to Reduce Ambiguity in Genomic Variant Representation

Current methods used for representing biological sequence variants allow flexibility, which has created redundancy within variant archives and discordance among variant representation tools. While research methodologies have been able to adapt to this ambiguity, strict clinical standards make it difficult to use this data in what would otherwise be useful clinical interventions. We implemented a specification developed by the GA4GH Variant Modeling Collaboration (VMC), which details a new approach to unambiguous representation of variants at the allelic level, as a haplotype, or as a genotype. Our implementation, called the VMC Test Suite (http://vcfclin.org), offers web tools to generate and insert VMC identifiers into a VCF file and to generate a VMC bundle JSON representation of a VCF file or HGVS expression. A command line tool with similar functionality is also introduced. These tools facilitate use of this standard-an important step toward reliable querying of variants and their associated annotations.

AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting

BACKGROUND

Next-Generation Sequencing (NGS) enables large-scale and cost-effective sequencing of genetic samples in order to detect genetic variants. After successful use in research-oriented projects, NGS is now entering clinical practice. Consequently, variant analysis is increasingly important to facilitate a better understanding of disease entities and prognoses. Furthermore, variant calling allows to adapt and optimize specific treatments of individual patients, and thus is an integral part of personalized medicine.However, the analysis of NGS data typically requires a number of complex bioinformatics processing steps. A flexible and reliable software that combines the variant analysis process with a simple, user-friendly interface is therefore highly desirable, but still lacking.

RESULTS

With AMLVaran (AML Variant Analyzer), we present a web-based software, that covers the complete variant analysis workflow of targeted NGS samples. The software provides a generic pipeline that allows free choice of variant calling tools and a flexible language (SSDL) for filtering variant lists. AMLVaran's interactive website presents comprehensive annotation data and includes curated information on relevant hotspot regions and driver mutations. A concise clinical report with rule-based diagnostic recommendations is generated.An AMLVaran configuration with eight variant calling tools and a complex scoring scheme, based on the somatic variant calling pipeline appreci8, was used to analyze three datasets from AML and MDS studies with 402 samples in total. Maximum sensitivity and positive predictive values were 1.0 and 0.96, respectively. The tool's usability was found to be satisfactory by medical professionals.

CONCLUSION

Coverage analysis, reproducible variant filtering and software usability are important for clinical assessment of variants. AMLVaran performs reliable NGS variant analyses and generates reports fulfilling the requirements of a clinical setting. Due to its generic design, the software can easily be adapted for use with different targeted panels for other tumor entities, or even for whole-exome data. AMLVaran has been deployed to a public web server and is distributed with Docker scripts for local use.

Creating genetic reports that are understood by nonspecialists: a case study

PURPOSE

Guidelines recommend that genetic reports should be clear to nonspecialists, including patients. We investigated the feasibility of creating reports for cystic fibrosis carrier testing through a rapid user-centered design process that built on a previously developed generic template. We evaluated the new reports' communication efficacy and effects on comprehension against comparable reports used in current clinical practice.

METHODS

Thirty participants took part in three rounds of interviews. Usability problems were identified and rectified in each round. One hundred ninety-three participants took part in an evaluation of the resulting reports measuring subjective comprehension, risk probability comprehension, perceived communication efficacy, and other factors, as compared with standard reports.

RESULTS

Participants viewing the user-centered reports rated them as clearer, easier to understand, and more effective at communicating key information than standard reports. Both groups ended up with equivalent knowledge of risk probabilities, although we observed differences in how those probabilities were perceived.

CONCLUSION

Our findings demonstrate that by starting with a patient-friendly generic report template and modifying it for specific scenarios with a rapid user-centered design process, reports can be produced that are more effective at communicating key information. The resulting reports are now being implemented into clinical care.

Advances in Sharing Multi-sourced Health Data on Decision Support Science 2016-2017

INTRODUCTION

 Clinical decision support science is expanding to include integration from broader and more varied data sources, diverse platforms and delivery modalities, and is responding to emerging regulatory guidelines and increased interest from industry.

OBJECTIVE

 Evaluate key advances and challenges of accessing, sharing, and managing data from multiple sources for development and implementation of Clinical Decision Support (CDS) systems in 2016-2017.

METHODS

 Assessment of literature and scientific conference proceedings, current and pending policy development, and review of commercial applications nationally and internationally.

RESULTS

 CDS research is approaching multiple landmark points driven by commercialization interests, emerging regulatory policy, and increased public awareness. However, the availability of patient-related "Big Data" sources from genomics and mobile health, expanded privacy considerations, applications of service-based computational techniques and tools, the emergence of "app" ecosystems, and evolving patient-centric approaches reflect the distributed, complex, and uneven maturity of the CDS landscape. Nonetheless, the field of CDS is yet to mature. The lack of standards and CDS-specific policies from regulatory bodies that address the privacy and safety concerns of data and knowledge sharing to support CDS development may continue to slow down the broad CDS adoption within and across institutions.

CONCLUSION

 Partnerships with Electronic Health Record and commercial CDS vendors, policy makers, standards development agencies, clinicians, and patients are needed to see CDS deployed in the evolving learning health system.

Prototype of a Standards-Based EHR and Genetic Test Reporting Tool Coupled with HL7-Compliant Infobuttons

Integration of genetic information is becoming increasingly important in clinical practice. However, genetic information is often ambiguous and difficult to understand, and clinicians have reported low-self-efficacy in integrating genetics into their care routine. The Health Level Seven (HL7) Infobutton standard helps to integrate online knowledge resources within Electronic Health Records (EHRs) and is required for EHR certification in the US. We implemented a prototype of a standards-based genetic reporting application coupled with infobuttons leveraging the Infobutton and Fast Healthcare Interoperability Resources (FHIR) Standards. Infobutton capabilities were provided by Open Infobutton, an open source package compliant with the HL7 Infobutton Standard. The resulting prototype demonstrates how standards-based reporting of genetic results, coupled with curated knowledge resources, can provide dynamic access to clinical knowledge on demand at the point of care. The proposed functionality can be enabled within any EHR system that has been certified through the US Meaningful Use program.

Simplifying the use of pharmacogenomics in clinical practice: Building the genomic prescribing system

BACKGROUND

A barrier to the use of genomic information during prescribing is the limited number of software solutions that combine a user-friendly interface with complex medical data. We built and designed an online, secure, electronic custom interface termed the Genomic Prescribing System (GPS).

METHODS

Actionable pharmacogenomic (PGx) information was reviewed, collected, and stored in the back-end of GPS to enable creation of customized drug- and variant-specific clinical decision support (CDS) summaries. The database architecture utilized the star schema to store information. Patient raw genomic data underwent transformation via custom-designed algorithms to enable gene and phenotype-level associations. Multiple external data sets (PubMed, The Systematized Nomenclature of Medicine (SNOMED), National Drug File - Reference Terminology (ND-FRT), and a publically-available PGx knowledgebase) were integrated to facilitate the delivery of patient, drug, disease, and genomic information. Institutional security infrastructure was leveraged to securely store patient genomic and clinical data on a HIPAA-compliant server farm.

RESULTS

As of May 17, 2016, the GPS back-end housed 257 CDS encompassing 112 genetic variants, 42 genes, and 46 PGx-actionable drugs. The GPS user interface presented patient-specific CDS alongside a recognizable traffic light symbol (green/yellow/red), denoting PGx risk for each genomic result. The number of traffic lights per visit increased with the corresponding increase in the number of available PGx-annotated drugs over time. An integrated drug and disease search functionality, links to primary literature sources, and potential alternative PGx drugs were indicated. The system, which was initially used as stand-alone CDS software within our clinical environment, was then integrated with the institutional electronic medical record for enhanced usability. There have been nearly 2000 logins in 43months since inception, with usage exceeding 56 logins per month and system up-times of 99.99%. For all patient-provider visits encompassing >3years of implementation, unique alert click-through rates corresponded to genomic risk: red lights clicked 100%, yellow lights 79%, green lights 43%.

CONCLUSIONS

Successful deployment of GPS by combining complex data and recognizable iconography led to a tool that enabled point-of-care genomic delivery with high usability. Continued scalability and incorporation of additional clinical elements to be considered alongside PGx information could expand future impact.

A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine

Objectives: To highlight and provide insights into key developments in translational bioinformatics between 2014 and 2016. Methods: This review describes some of the most influential bioinformatics papers and resources that have been published between 2014 and 2016 as well as the national genome sequencing initiatives that utilize these resources to routinely embed genomic medicine into healthcare. Also discussed are some applications of the secondary use of patient data followed by a comprehensive view of the open challenges and emergent technologies. Results: Although data generation can be performed routinely, analyses and data integration methods still require active research and standardization to improve streamlining of clinical interpretation. The secondary use of patient data has resulted in the development of novel algorithms and has enabled a refined understanding of cellular and phenotypic mechanisms. New data storage and data sharing approaches are required to enable diverse biomedical communities to contribute to genomic discovery. Conclusion: The translation of genomics data into actionable knowledge for use in healthcare is transforming the clinical landscape in an unprecedented way. Exciting and innovative models that bridge the gap between clinical and academic research are set to open up the field of translational bioinformatics for rapid growth in a digital era.

Integrating Genomic Resources with Electronic Health Records using the HL7 Infobutton Standard

BACKGROUND

The Clinical Genome Resource (ClinGen) Electronic Health Record (EHR) Workgroup aims to integrate ClinGen resources with EHRs. A promising option to enable this integration is through the Health Level Seven (HL7) Infobutton Standard. EHR systems that are certified according to the US Meaningful Use program provide HL7-compliant infobutton capabilities, which can be leveraged to support clinical decision-making in genomics.

OBJECTIVES

To integrate genomic knowledge resources using the HL7 infobutton standard. Two tactics to achieve this objective were: (1) creating an HL7-compliant search interface for ClinGen, and (2) proposing guidance for genomic resources on achieving HL7 Infobutton standard accessibility and compliance.

METHODS

We built a search interface utilizing OpenInfobutton, an open source reference implementation of the HL7 Infobutton standard. ClinGen resources were assessed for readiness towards HL7 compliance. Finally, based upon our experiences we provide recommendations for publishers seeking to achieve HL7 compliance.

RESULTS

Eight genomic resources and two sub-resources were integrated with the ClinGen search engine via OpenInfobutton and the HL7 infobutton standard. Resources we assessed have varying levels of readiness towards HL7-compliance. Furthermore, we found that adoption of standard terminologies used by EHR systems is the main gap to achieve compliance.

CONCLUSION

Genomic resources can be integrated with EHR systems via the HL7 Infobutton standard using OpenInfobutton. Full compliance of genomic resources with the Infobutton standard would further enhance interoperability with EHR systems.