The price of whole-genome sequencing may be decreasing, but who will be sequenced?

The current stage of Italy in the implementation of genomics into the National Healthcare System: an application of the B1MG maturity level model

Introduction

Genomics holds significant promise for prevention and clinical care yet integrating it into the national healthcare system (NHS) requires considerable system-wide changes. This study assessed the current stage of Italy in the use of genomics, to map critical areas for improvement and contribute to a strategic plan.

Methods

A total of 18 experts rated individually the level of maturity of the Italian NHS on a scale from 1 (lowest) to 5 (highest) using the B1MG Maturity Level Model tool. This instrument is an European matrix of 49 indicators grouped into eight domains: governance, economic aspects, ethics and legislation, public awareness, workforce skills, clinical organization, clinical guidelines, and data infrastructure. Consensus procedures were performed within each domain to finally agree on one maturity level per indicator.

Results

Despite a few national initiatives, Italy shows a local level of implementation in most indicators. Genomic medicine is considered a priority, but still lacks an updated strategy and investment plans. A higher maturity is reached for ethical and legal aspects, but there is a strong need to invest in workforce training, citizen engagement and literacy, and large-scale adoption of tools and novel technologies. Infrastructures and guidelines to improve data storage, management, analysis, interpretation, and sharing are not yet widespread available.

Discussion

Italy is at the beginning of its journey towards a sustainable implementation of genomics. An updated national strategy with coordinated actions and investment plans is needed to make progress in key areas, including personnel education, public engagement, technical infrastructure, and clinical organization.

EARLY CONSIDERATIONS OF GENETICS IN APHASIA REHABILITATION: A NARRATIVE REVIEW

Background

Early investigations linking language and genetics were focused on the evolution of human communication in populations with developmental speech and language disorders. Recently, studies suggest that genes may also modulate recovery from post-stroke aphasia.

Aims

Our goal is to review current literature related to the influence of genetics on post-stroke recovery, and the implications for aphasia rehabilitation. We describe candidate genes implicated by empirical findings and address additional clinical considerations.

Main Contribution

We describe existing evidence and mechanisms supporting future investigations into how genetic factors may modulate aphasia recovery and propose that two candidate genes, brain derived neurotrophic factor (BDNF) and apolipoprotein E (APOE), may be important considerations for future research assessing response to aphasia treatment. Evidence suggests that BDNF is important for learning, memory, and neuroplasticity. APOE influences cognitive functioning and memory in older individuals and has also been implicated in neural repair. Moreover, recent data suggest an interaction between specific alleles of the BDNF and APOE genes in influencing episodic memory.

Conclusions

Genetic influences on recovery from aphasia have been largely unexplored in the literature despite evidence that genetic factors influence behaviour and recovery from brain injury. As researchers continue to explore prognostic factors that may influence response to aphasia treatment, it is time for genetic factors to be considered as a source of variability. As the field moves in the direction of personalized medicine, eventually allied health professionals may utilize genetic profiles to inform treatment decisions and education for patients and care partners.

The patients view on genetics and functional imaging for precision medicine: a willingness-to-pay analysis

Purpose: Willingness-to-pay (WTP) analyses can support allocation processes considering the patients preferences in personalized medicine. However, genetic testing especially might imply ethical concerns that have to be considered. Methods: A WTP questionnaire was designed to compare preferences for imaging and genetic testing in cancer patients and to evaluate potential ethical concerns. Results: Comparing the options of imaging and genetics showed comparable WTP values. Ethical concerns about genetic testing seemed to be minor. Treatment success was the top priority irrespective of the diagnostic modality. In general, the majority of patients considered personalized medicine to be beneficial. Conclusion: Most patients valued personalized approaches and rated the benefits of precision medicine of overriding importance irrespective of modality or ethical concerns.

ShareDNA: a smartphone app to facilitate family communication of genetic results

BACKGROUND

Genetic testing allows patients and clinicians to understand the risk of hereditary diseases. By testing early, individuals can make informed medical decisions about management which may minimize the risk of developing certain diseases. Importantly, genetic test results may also be applicable to patients' biological relatives; thus, these results could also lead to minimizing their risk of disease. However, sharing genetic test results between patients and their relatives is scarce. The most frequently reported problems are that patients cannot clearly explain this information and relatives misinterpret the results. Smartphone apps in the healthcare field are a possible solution as they allow patients to accurately share sensitive information to others, while providing educational material to support understanding the information. However, these apps may not provide security to protect patients' identifiable information. We developed ShareDNA, a smartphone app that (1) allows patients to securely share their genetic test results with others, (2) provides information on how to interpret these results, and (3) minimizes the amount of patient information needed to use the service.

RESULTS

We recruited thirteen participants to test the usability of our app and provide feedback. We found overall that participants were comfortable with using this app and could easily learn each app function when filling out our questionnaire. Additionally, based on vocalized impressions of the usefulness of the app, participants indicated that the user-interface could be more intuitive and that we needed to add more text within the app to explain why ShareDNA is a secure service.

CONCLUSIONS

ShareDNA is a free smartphone app that allows patients to share their genetic test results with others, including their biological relatives. Sharing these results along with educational material will enable relatives to share accurate information and discuss their possible risk for disease with their clinical providers. As a result, appropriate testing in relatives could be improved.

Economic burden of congenital athymia in the United States for patients receiving supportive care during the first 3 years of life

AIMS

Congenital athymia is an ultra-rare pediatric condition characterized by the lack of thymus in utero and the naïve T cells critical for infection defense and immune regulation. Patients with congenital athymia receive supportive care to minimize and treat infections, autoimmune phenomena, and autologous graft-versus-host disease (aGVHD) manifestations, but historically, die within the first 3 years of life with supportive care only. We estimated the healthcare resource utilization and economic burden of supportive care over patients' first 3 years of life in the United States.

METHODS

A medical chart audit by the treating physician was used to collect patient data from birth to age 3 on clinical manifestations associated with congenital athymia (clinical manifestations due to underlying syndromic conditions excluded). Using costs and charges from publicly available sources, the total economic burden of direct medical costs and charges for the first 3 years of life (considered "lifetime" for patients receiving supportive care) and differences in economic burden between patients with higher and lower inpatient hospitalization durations were estimated.

RESULTS

All patients (n = 10) experienced frequent infections and aGVHD manifestations; 40% experienced ≥1 episode of sepsis, and 20% had recurrent sepsis episodes annually. The estimated mean 3-year economic burden per patient was US$5,534,121 (2020 US dollars). The annual mean inpatient hospitalization duration was 150.6 days. Inpatient room charges accounted for 79% of the economic burden, reflecting the high costs of specialized care settings required to prevent infection, including isolation. Patients with high inpatient utilization (n = 5; annual mean inpatient hospitalization duration, 289.6 days) had an estimated 3-year economic burden of US$9,926,229.

LIMITATIONS

The total economic burden may not be adequately represented due to underestimation of some direct costs or overestimation of others.

CONCLUSIONS

Current treatment of patients with congenital athymia (supportive care) presents a high economic burden to the healthcare system.

Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections

Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different infection severities (P < 0.05). Mild and severe stages of infections were dominated by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of 132 metabolic pathways were identified of which ribosome and thiamin being among the most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, primarily involved in the multidrug efflux pumps/exporters, were identified. Furthermore, iron acquisition systems (synthesize and regulation of siderophores) and pathways involved in the synthesis and regulation of cell-surface components associated with adhesion, colonization, and movement of bacterial cells were the most common virulence factors. These virulence factors may help bacteria compete for scares resources and survive the host wound proteases. Characterization of transcriptionally active bacterial communities can help to provide an understanding of the role of key pathogens in the development of DFIs. Such information can be clinically useful allowing replacement of DFIs empirical therapy with targeted treatment.

Bridging the Gaps in Personalized Medicine Value Assessment: A Review of the Need for Outcome Metrics across Stakeholders and Scientific Disciplines

Despite monumental advances in genomics, relatively few health care provider organizations in the United States offer personalized or precision medicine as part of the routine clinical workflow. The gaps between research and applied genomic medicine may be a result of a cultural gap across various stakeholders representing scientists, clinicians, patients, policy makers, and third party payers. Scientists are trained to assess the health care value of genomics by either quantifying population-scale effects, or through the narrow lens of clinical trials where the standard of care is compared with the predictive power of a single or handful of genetic variants. While these metrics are an essential first step in assessing and documenting the clinical utility of genomics, they are rarely followed up with other assessments of health care value that are critical to stakeholders who use different measures to define value. The limited value assessment in both the research and implementation science of precision medicine is likely due to necessary logistical constraints of these teams; engaging bioethicists, health care economists, and individual patient belief systems is incredibly daunting for geneticists and informaticians conducting research. In this narrative review, we concisely describe several definitions of value through various stakeholder viewpoints. We highlight the existing gaps that prevent clinical translation of scientific findings generally as well as more specifically using two present-day, extreme scenarios: (1) genetically guided warfarin dosing representing a handful of genetic markers and more than 10 years of basic and translational research, and (2) next-generation sequencing representing genome-dense data lacking substantial evidence for implementation. These contemporary scenarios highlight the need for various stakeholders to broadly adopt frameworks designed to define and collect multiple value measures across different disciplines to ultimately impact more universal acceptance of and reimbursement for genomic medicine.