Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations

Assessing genomics confidence and learning needs in Australian nurses and midwives: an educational program evaluation

Introduction: The mainstreaming of genomics across healthcare specialties necessitates that all nurses and midwives have a high literacy in genomics. Methods: We aimed to design, develop, implement and evaluate a genomics education workshop for nurses and midwives using action research principles. Results: Registered nurses and midwives completed an online survey regarding genomics confidence and learning needs (n = 274). The results of this survey were used to develop the genomics education workshop. The workshop was run three times (n = 105) with evaluation data being collected both before and after each workshop. Significant improvements in confidence across all learning domains was found following the workshops (p < 0.001). A desire for more education across all learning domains except for genetics knowledge was also identified (p < 0.001). Discussion: Genomics education workshops were found to increase the confidence of nurses and midwives across a range of specialties. Nurses and midwives also expressed a desire for further education in genomics.

Pairing a bioinformatics-focused course-based undergraduate research experience with specifications grading in an introductory biology classroom

Introducing bioinformatics-focused concepts and skills in a biology classroom is difficult, especially in introductory biology classrooms. Course-based Undergraduate Research Experiences (CUREs) facilitate this process, introducing genomics and bioinformatics through authentic research experiences, but the many learning objectives needed in scientific research and communication, foundational biology concepts, and bioinformatics-focused concepts and skills can make the process challenging. Here, the pairing of specifications grading with a bioinformatics-focused CURE developed by the Genomics Education Partnership is described. The study examines how the course structure with specifications grading facilitated scaffolding of writing assignments, group work, and metacognitive activities; and describes the synergies between CUREs and specifications grading. CUREs require mastery of related concepts and skills for working through the research process, utilize common research practices of revision and iteration, and encourage a growth mindset to learning-all of which are heavily incentivized in assessment practices focused on specifications grading.

It is time to authenticate the Microbiome Sciences with accredited educational programs and departments

The Microbiome Sciences are at a crucial maturation stage. Scientists and educators should now view the Microbiome Sciences as a flourishing and autonomous discipline, creating degree programs and departments that are conducive to cohesive growth.

A data science practicum to introduce undergraduate students to bioinformatics for research

An explosion of data available in the life sciences has shifted the discipline toward genomics and quantitative data science research. Institutions of higher learning have been addressing this shift by modifying undergraduate curriculums resulting in an increasing number of bioinformatics courses and research opportunities for undergraduates. The goal of this study was to explore how a newly designed introductory bioinformatics seminar could leverage the combination of in-class instruction and independent research to build the practical skill sets of undergraduate students beginning their careers in the life sciences. Participants were surveyed to assess learning perceptions toward the dual curriculum. Most students had a neutral or positive interest in these topics before the seminar and reported increased interest after the seminar. Students had increases in confidence level in their bioinformatic proficiency and understanding of ethical principles for data/genomic science. By combining undergraduate research with directed bioinformatics skills, classroom seminars facilitated a connection between student's life sciences knowledge and emerging research tools in computational biology.

Genetic/genomic literacy, attitudes and receptivity of nursing students and practising nurses: A cross-sectional online survey

BACKGROUND

The growing demand for personalised nursing care in the genomic era requires nursing students and practising nurses to be better prepared to apply the knowledge of genetics/genomics to nursing practice. Several studies have shown that, despite having positive attitudes/receptivity towards integrating genetics/genomics into nursing practice, nursing students and professionals report a low level of genetic/genomic literacy. However, little is known about the status in Hong Kong.

OBJECTIVES

We assessed and compared the genetic/genomic literacy and attitudes/receptivity towards integrating genetics/genomics into nursing practice among nursing students and practising nurses in Hong Kong. We also explored the relationships between the students' background characteristics, attitudes/receptivity towards integrating genetics/genomics into nursing practice and genetic/genomic literacy.

DESIGN

A cross-sectional online survey conducted between March 2020 and January 2022.

SETTINGS

A government-funded university in Hong Kong.

PARTICIPANTS

We recruited a convenience sample of 234 nursing students, 145 were final-year undergraduate students (median age = 22 years, 84.1 % female) and 89 were practising registered nurses (postgraduate students studying part-time programme, median age = 28 years, 77.5 % female).

METHODS

The survey collected the participants' background information, attitudes/receptivity towards integrating genetics/genomics into nursing practice and levels of genetic/genomic literacy.

RESULTS

Overall, the participants reported positive attitudes/receptivity towards practice integration but had low levels of genetic/genomic literacy. Practising nurses were more likely to have lower genetic/genomic literacy, but more positive attitudes/receptivity towards practice integration, than undergraduate students. Multiple regression analysis suggested that the level of study (postgraduate/undergraduate programme) and perceptions of the disadvantages of 'needing to re-tool professionally' were significant independent factors associated with the level of genetic/genomic literacy.

CONCLUSIONS

Findings from this study call for the strategic integration of genetics/genomics education into all levels of nursing education in Hong Kong and across the globe. In particular, sustained efforts should be made to ensure that practising nurses receive further education in genetics/genomics.

The implementation of large-scale genomic screening or diagnostic programmes: A rapid evidence review

Genomic healthcare programmes, both in a research and clinical context, have demonstrated a pivotal opportunity to prevent, diagnose, and treat rare diseases. However, implementation factors could increase overall costs and affect uptake. As well, uncertainties remain regarding effective training, guidelines and legislation. The purpose of this rapid evidence review was to draw together the available global evidence on the implementation of genomic testing programmes, particularly on population-based screening and diagnostic programmes implemented at the national level, to understand the range of factors influencing implementation. This review involved a search of terms related to genomics, implementation and health care. The search was limited to peer-reviewed articles published between 2017-2022 and found in five databases. The review included thirty articles drawing on sixteen countries. A wide range of factors was cited as critical to the successful implementation of genomics programmes. These included having policy frameworks, regulations, guidelines; clinical decision support tools; access to genetic counselling; and education and training for healthcare staff. The high costs of implementing and integrating genomics into healthcare were also often barriers to stakeholders. National genomics programmes are complex and require the generation of evidence and addressing implementation challenges. The findings from this review highlight that there is a strong emphasis on addressing genomic education and engagement among varied stakeholders, including the general public, policymakers, and governments. Articles also emphasised the development of appropriate policies and regulatory frameworks to govern genomic healthcare, with a focus on legislation that regulates the collection, storage, and sharing of personal genomic data.

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC's functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

Allergy, asthma, and proteomics: opportunities with immediate impact

Allergy is widely discussed by researchers due to its complex mechanism that leads to disorders and injuries, but the reason behind the allergic status remains unclear. Current treatments are insufficient to improve the patient's quality of life significantly. New technologies in scientific and technological development are emerging. For instance, the union between allergy and peptidomics and bioinformatics tools may help fill the gaps in this field, diagnosis, and treatment. In this review, we look at peptidomics and address some findings, such as target proteins or biomarkers that help better understand mechanisms that lead to inflammation, organ damage, and, consequently, poor quality of life or even death.

Development of Competency-based Online Genomic Medicine Training (COGENT)

The fields of genetics and genomics have greatly expanded across medicine through the development of new technologies that have revealed genetic contributions to a wide array of traits and diseases. Thus, the development of widely available educational resources for all healthcare providers is essential to ensure the timely and appropriate utilization of genetics and genomics patient care. In 2020, the National Human Genome Research Institute released a call for new proposals to develop accessible, sustainable online education for health providers. This paper describes the efforts of the six teams awarded to reach the goal of providing genetic and genomic training modules that are broadly available for busy clinicians.

Are We Prepared for Precision Public Health? An Examination of Genomics Content in Graduate Public Health Programs

OBJECTIVE

With the completion of the Human Genome Project and swift development of genomic technologies, public health practitioners can use these advancements to more precisely target disease interventions to populations at risk. To integrate these innovations into better health outcomes, public health professionals need to have at least a basic understanding of genomics within various disciplines of public health. This descriptive study focused on the current level of genomics content in accredited master of public health (MPH) programs in the United States.

METHODS

We conducted an internet search on all 171 Council on Education for Public Health (CEPH)-accredited MPH programs in the United States for genomics content in required and elective courses using the search terms "genetics," "genomics," and "molecular."

RESULTS

Of the 171 CEPH-accredited MPH programs examined, 52 (30.4%) schools and programs in 34 states offered some type of genomics education. Thirty-five (20.5%) schools and programs had a course in genetic epidemiology, 29 (16.9%) had a course in genetic biostatistics or bioinformatics, and 17 (9.9%) had a course in general public health genomics. The remaining 119 offered no course with a focus on genetics or genomics. In addition, some electives or specifically focused courses related to genomics were offered.

CONCLUSION

We found inadequate training in public health genomics for MPH students. To realize the promise of precision public health and to increase the understanding of genomics among the public health workforce, MPH programs need to find ways to integrate genomics education into their curricula.

Investigation of Biomedical Students' Attitudes toward Pharmacogenomics and Personalized Medicine: A Cross-Sectional Study

Background: The utilization of pharmacogenomics in everyday practice has shown several notable benefits. Keeping in mind the rising trend of applicability of pharmacogenomics and personalized medicine, we sought to compare the attitudes of future healthcare workers in different branches of the healthcare system. Methods: The present study was conducted as a questionnaire-based cross-sectional study in October of 2020. Students eligible to participate were all the students of the University of Split School of Medicine enrolled in the academic year 2020/2021. Results: The number of students that participated in the study was 503. Students were most interested in clinical examples of pharmacogenomics (31.4%) and the benefits of pharmacogenomics in clinical practice (36.4%). Furthermore, 72.6% of all students agreed that they should be able, in their future practice, to identify patients that could benefit from genetic testing. Conclusion: At the present time, the lack of education and appropriate clinical guidelines appear to be the major barriers to the clinical application of pharmacogenomics, especially in Croatia. Hence, in order to support health care professionals’ evidence-based therapeutic recommendations with patients’ pharmacogenomic data, universities should offer more pharmacogenomics education in their curricula.

A Formative Study of the Implementation of Whole Genome Sequencing in Northern Ireland

Background: The UK 100,000 Genomes Project was a transformational research project which facilitated whole genome sequencing (WGS) diagnostics for rare diseases. We evaluated experiences of introducing WGS in Northern Ireland, providing recommendations for future projects. Methods: This formative evaluation included (1) an appraisal of the logistics of implementing and delivering WGS, (2) a survey of participant self-reported views and experiences, (3) semi-structured interviews with healthcare staff as key informants who were involved in the delivery of WGS and (4) a workshop discussion about interprofessional collaboration with respect to molecular diagnostics. Results: We engaged with >400 participants, with detailed reflections obtained from 74 participants including patients, caregivers, key National Health Service (NHS) informants, and researchers (patient survey n = 42; semi-structured interviews n = 19; attendees of the discussion workshop n = 13). Overarching themes included the need to improve rare disease awareness, education, and support services, as well as interprofessional collaboration being central to an effective, mainstreamed molecular diagnostic service. Conclusions: Recommendations for streamlining precision medicine for patients with rare diseases include administrative improvements (e.g., streamlining of the consent process), educational improvements (e.g., rare disease training provided from undergraduate to postgraduate education alongside genomics training for non-genetic specialists) and analytical improvements (e.g., multidisciplinary collaboration and improved computational infrastructure).

An international genomics health workforce education priorities assessment

Aim: Global implementation of genomic medicine will require education of healthcare providers. There are limited international needs assessment data to guide curriculum development. Materials & methods: Genomics education experts developed and distributed a survey to individuals with knowledge of country-specific needs: 113 completed surveys (19% response rate) from 34 countries. A high percentage of respondents ranked non genetics physicians as the #1 target for genetics education. Over 70% indicated a need for moderate/extensive modification in physician training. The majority considered germline and somatic topics and targeting primary care and specialist providers equally important. Conclusion: Regardless of country economic level, there is a clear need for genomics education of healthcare providers. The study results can be used to focus future genomic medicine education efforts.

Reducing the Intimidation Factor of Teaching Genetics and Genomics in Nursing

BACKGROUND

Faculty-related barriers to increasing genetics and genomics content in undergraduate nursing education include knowledge deficits and a limited ability to embrace curricular changes.

METHOD

Faculty members at one school of nursing participated in an educational program designed to address these barriers and reduce the intimidation of teaching a challenging topic. Participants' perceptions of changes in their knowledge and confidence, as well as the quantity of potential curricular threads identified by participants were used to evaluate the program.

RESULTS

All of the participants indicated the program increased their knowledge of genetics and genomics, and the majority (68.2%) of participants reported their confidence in developing curricular content also had increased. Participants identified numerous potential genetics and genomics-related curricular threads, especially regarding nurses' professional responsibilities.

CONCLUSION

Faculty education shows promise as a strategy to increase knowledge, confidence, and ability to identify opportunities to increase genetics and genomics content in undergraduate nursing education. [J Nurs Educ. 2022;61(5):261-263.].

Factor's that impact on women's decision-making around prenatal genomic tests: An international discrete choice survey

OBJECTIVE

We conducted a survey-based discrete-choice experiment (DCE) to understand the test features that drive women's preferences for prenatal genomic testing, and explore variation across countries.

METHODS

Five test attributes were identified as being important for decision-making through a literature review, qualitative interviews and quantitative scoring exercise. Twelve scenarios were constructed in which respondents choose between two invasive tests or no test. Women from eight countries who delivered a baby in the previous 24 months completed a DCE presenting these scenarios. Choices were modeled using conditional logit regression analysis.

RESULTS

Surveys from 1239 women (Australia: n = 178; China: n = 179; Denmark: n = 88; Netherlands: n = 177; Singapore: n = 90; Sweden: n = 178; UK: n = 174; USA: n = 175) were analyzed. The key attribute affecting preferences was a test with the highest diagnostic yield (p < 0.01). Women preferred tests with short turnaround times (p < 0.01), and tests reporting variants of uncertain significance (VUS; p < 0.01) and secondary findings (SFs; p < 0.01). Several country-specific differences were identified, including time to get a result, who explains the result, and the return of VUS and SFs.

CONCLUSION

Most women want maximum information from prenatal genomic tests, but our findings highlight country-based differences. Global consensus on how to return uncertain results is not necessarily realistic or desirable.

The Development of Education of Public Health Nurses for Applying Genomics in Preventive Health Care

Genetics and genomics have become one of the most important development areas in healthcare. For this reason, it is essential that nursing professionals take their role to offer their skills in implementing genomics in health promotion. The education of public health nurses is taking vital steps in training the health promoters who are able to take the genome-based knowledge into account in precision healthcare. Tampere University of Applied Sciences managed to integrate genomics into the studies of public health nursing. This article describes the process of development and lays emphasis on the importance of genomic education of public health nurses.

Australian human research ethics committee members' confidence in reviewing genomic research applications

Human research ethics committees (HRECs) are evaluating increasing quantities of genomic research applications with complex ethical considerations. Genomic confidence is reportedly low amongst many non-genetics-experts; however, no studies have evaluated genomic confidence levels in HREC members specifically. This study used online surveys to explore genomic confidence levels, predictors of confidence, and genomics resource needs of members from 185 HRECs across Australia. Surveys were fully or partially completed by 145 members. All reported having postgraduate 94 (86%) and/or bachelor 15 (14%) degrees. Participants consisted mainly of researchers (n = 45, 33%) and lay members (n = 41, 30%), affiliated with either public health services (n = 73, 51%) or public universities (n = 31, 22%). Over half had served their HREC [Formula: see text]3 years. Fifty (44%) reviewed genomic studies [Formula: see text]3 times annually. Seventy (60%) had undertaken some form of genomic education. While most (94/103, 91%) had high genomic literacy based on familiarity with genomic terms, average genomic confidence scores (GCS) were moderate (5.7/10, n = 119). Simple linear regression showed that GCS was positively associated with years of HREC service, frequency of reviewing genomic applications, undertaking self-reported genomic education, and familiarity with genomic terms (p < 0.05 for all). Conversely, lay members and/or those relying on others when reviewing genomic studies had lower GCSs (p < 0.05 for both). Most members (n = 83, 76%) agreed further resources would be valuable when reviewing genomic research applications, and online courses and printed materials were preferred. In conclusion, even well-educated HREC members familiar with genomic terms lack genomic confidence, which could be enhanced with additional genomic education and/or resources.

Supporting teachers to use genomics as a context in the classroom: an evaluation of learning resources for high school biology

As genomics becomes embedded into healthcare, public genomic health literacy is critical to support decision-making for personal and family health decisions and enable citizens to engage with related social issues. School science education has the potential to establish the foundations of genetic and genomic literacy. The concept of literacy extends beyond conceptual understanding of biological principles to familiarity with the applications and implications of genetics, critical thinking skills, and socioscientific reasoning. We developed and evaluated a suite of resources for teaching genetics and genomics in the Australian senior biology syllabus for students aged 16-18 years. The aim was to increase teachers' knowledge and confidence to teach genetic and genomic content, and their capacity to develop robust genetic literacy in their students. Resources, including an inquiry-based task and five associated lesson plans, were developed and made freely available to teachers online. Evaluation was undertaken between December 2019 and March 2020 with a post-use survey emailed to teachers who had accessed the resources. The 56 teachers who responded rated the resources as high quality, engaging, and well-aligned with the syllabus. Teachers who used the resources self-reported increases in their knowledge and confidence in teaching. They also perceived positive outcomes in their students, reporting that the resources deepened their students understanding of genetic concepts, helped them to consider social and ethical issues, and developed their higher order thinking skills. Findings may inform future interactions with high schools to improve genetic literacy.

Increasing Genomic Literacy Through National Genomic Projects

Genomics is an advancing field of medicine, science, ethics, and legislation. Keeping up to date with this challenging discipline requires continuous education and exchange of knowledge between many target groups. Specific challenges in genomic education include tailoring complex topics to diverse audiences ranging from the general public and patients to highly educated professionals. National genomic projects face many of the same challenges and thus offer many opportunities to highlight common educational strategies for improving genomic literacy. We have reviewed 41 current national genomic projects and have identified 16 projects specifically describing their approach to genomic education. The following target groups were included in the educational efforts: the general public (nine projects), patients (six projects), and genomic professionals (16 projects), reflecting the general overall aims of the projects such as determining normal and pathological genomic variation, improving infrastructure, and facilitating personalized medicine. The national genomic projects aim to increase genomic literacy through supplementing existing national education in genomics as well as independent measures specifically tailored to each target group, such as training events, research collaboration, and online resources for healthcare professionals, patients, and patient organizations. This review provides the current state of educational activities within national genomic projects for different target groups and identifies good practices that could contribute to patient empowerment, public engagement, proficient healthcare professionals, and lend support to personalized medicine.

Physician awareness, preparedness, and opinions toward consumer-initiated genetic testing in Thailand: Views from a changing landscape

Consumer-initiated genetic tests have captured public interest in recent years, including in low-to-middle-income countries (LMICs) such as Thailand. Due to limited resources and personnel, physicians will most likely bear the burden of increasing service needs from the public as consumer-initiated genetic tests become popularized. The primary objective of this study was to describe (a) awareness, (b) preparedness to provide counseling about the consumer-initiated genetic test, and (c) opinions on the usefulness of consumer-initiated genetic tests among physicians at an academic hospital in Bangkok, Thailand. The secondary objective was to describe factors that were associated with the awareness, preparedness, and opinion of the participants. Paper questionnaires were sent out to participants which included internal medicine residents, fellows, and faculty staff members. The questionnaires assessed awareness, preparedness to discuss consumer-initiated genetic test results, and opinion on the usefulness of consumer-initiated genetic tests and included both closed- and open-ended questions. Responses were anonymous. Among 308 participants, there were 223 (72.4%) residents, 14 (4.5%) fellows, and 71 (23.1%) staff members. Only 15% of participants were aware of consumer-initiated genetic tests, mostly from the internet, and only 7% were prepared to provide counseling regarding consumer-initiated genetic tests. However, 60% agreed that consumer-initiated genetic tests may be clinically useful. Many participants, including trainees, expressed concerns about the interpretation of consumer-initiated genetic test results, application into clinical practice, appropriate counseling, and patient referral to geneticists. Multivariate logistic regression revealed that years of work experience was independently associated with awareness of consumer-initiated genetic tests, while male gender and less work experience were independently associated with favorable opinion toward the usefulness of consumer-initiated genetic tests. Our results pointed to an urgent need for genetic counselors in Thailand. Also, physicians, particularly trainees, need appropriate training to prepare them for a rapidly evolving environment where consumer-initiated genetic tests become commonplace.

Mapping the Educational Environment of Genomics and Pharmacogenomics in the United Arab Emirates: A Mixed-Methods Triangulated Design

Pharmacogenomics (PGx) education is crucial to support the effective delivery of PGx services in any health care system. We mapped the current educational environment of genomics and PGx in the United Arab Emirates (UAE) and assessed the readiness of the accredited higher education system to move forward with the implementation of PGx in the country. We employed a mixed-methods triangulated approach to map the PGx educational environment in UAE. We used two qualitative methods and one quantitative method. University curricula inspection, interviews, and questionnaires were the main resources of data. PGx was taught in 6 out of 21 accredited universities, but only for pharmacy majors. Only three out of six PGx courses were stand-alone. Majority of academia exhibited positive attitudes toward the availability and accessibility of genetic testing, with 89% agreeing that the government should invest more money into its development. Interviews with academics and, importantly, the commissioners who oversee the accreditation process of universities in UAE revealed recurrent themes that included recognizing the importance of genomic medicine and PGx and called for translational and implementational research, including recruitment of experts in the field. We recommend, as supported by our findings in this study, the creation of standardized curriculum of genomics and PGx for each health science field, using the blended teaching approach, and benchmarking internationally accredited universities to foster international collaboration and improve the education and practice of genomics in the clinic and public health systems. An 11-item genomics and PGx strategy is presented herein. Finally, the mixed-methods study design employed in this research may also serve as a model conceptual frame for other science education mapping efforts at country or multi-institutional scales in the future.

Mainstreaming genomics: training experience of hospital medical officers at the Royal Melbourne Hospital

The rapid evolution and wide applicability of genomic testing means that medical practitioners outside the field are not appropriately skilled to understand the utility of genomics for their patients. Rotating junior doctors through genomic medicine provides them with the hands-on experience necessary to understand the complexities in this field. In this study, we analysed the training experience of 12 hospital medical officers who rotated through genomic medicine at the Royal Melbourne Hospital. Here, we demonstrate that immersion in clinical genomics aids in mainstreaming genomics knowledge.

Queensland Consumers' Awareness and Understanding of Clinical Genetics Services

As genetic testing becomes increasingly utilized in health care, consumer awareness and understanding is critical. Both are reported to be low in Australia, though there are limited studies to date. A consumer survey assessed perceived knowledge, awareness and attitudes toward genetic medicine, prior to consumers’ genomics forums in Queensland in 2018 and 2019. Data was analyzed using t-test and Mann-Whitney U tests analysis to detect any associations between sociodemographic factors and familiarity or attitudes. This highly educated and experienced health consumer cohort reported they were significantly more familiar with the healthcare system generally than genetic medicine specifically (p < 0.0001). Consumers perceived that genetic testing would be significantly more important in the future than it is currently (p < 0.00001). Consumers agreed that genetic testing should be promoted (91.4%), made available (100%), better funded (94.2%), and offered to all pregnant women (81.6%). The preferred learning modality about genetics was internet sites (62.7%) followed by talks/presentations (30.8%). Benefits of genetic testing, reported in qualitative responses, included the potential for additional information to promote personal control and improve healthcare. Perceived concerns included ethical implications (including privacy and discrimination), and current limitations of science, knowledge and/or practice. This study demonstrates that even knowledgeable consumers have little familiarity with genetic medicine but are optimistic about its potential benefits. Ethical concerns, particularly concerns regarding genetic discrimination should inform legislation and policy. Consumers are supportive of online resources in increasing genomic literacy.

The importance of chain context in assessing small nucleotide variants in titin: in silico case study of the I10-I11 tandem and its arrhythmic right ventricular cardiomyopathy linked position T2580

Non-synonymous small nucleotide variations (nsSNVs) in the giant muscle protein, titin, have key roles in the development of several myopathologies. Although there is considerable motive to screen at-risk individuals for nsSNVs, to identify patients in early disease stages while therapeutic intervention is still possible, the clinical significance of most titin variations remains unclear. Therefore, there is a growing need to establish methods to classify nsSNVs in a simple, economic and rapid manner. Due to its strong correlation to arrhythmogenic right ventricular cardiomyopathy (ARVC), one particular mutation in titin-T2580I, located in the I10 immunoglobulin domain-has received considerable attention. Here, we use the I10-I11 tandem as a case study to explore the possible benefits of considering the titin chain context-i.e. domain interfaces-in the assessment of titin nsSNVs. Specifically, we investigate which exchanges mimic the conformational molecular phenotype of the T2580I mutation at the I10-I11 domain interface. Then, we computed a residue stability landscape for domains alone and in tandem to define a Domain Interface Score (DIS) which identifies several hotspot residues. Our findings suggest that the T2580 position is highly sensitive to exchange and that any variant found in this position should be considered with care. Furthermore, we conclude that the consideration of the higher order structure of the titin chain is important to gain accurate insights into the vulnerability of positions in linker regions and that titin nsSNV prediction benefits from a contextual analysis. Communicated by Ramaswamy H. Sarma.