A call to action: training pathology residents in genomics and personalized medicine

The challenges and opportunities of offering and integrating training in clinical molecular genetics and clinical cytogenetics: A survey of LGG Fellowship Program Directors

Purpose

The specialty of Laboratory Genetics and Genomics (LGG) was created in 2017 in an effort to reflect the increasing convergence in technologies and approaches between clinical molecular genetics and clinical cytogenetics. However, there has not yet been any formal evaluation of the merging of these disciplines and the challenges faced by Program Directors (PDs) tasked with ensuring the successful training of laboratory geneticists under the new model.

Methods

An electronic multi-question Qualtrics survey was created and was sent to the PD for each of the Accreditation Council for Graduate Medical Education-accredited LGG fellowship programs at the time. The data were collected, and the responses were aggregated for each question.

Results

All of the responding PDs had started training at least 1 LGG fellow. PDs noted challenges with funding, staff shortages, molecular/cytogenetics content integration, limited total training time, increased remote work, increased sendout testing, and a lack of prior cytogenetics knowledge among incoming fellows.

Conclusion

This survey attempted to assess the challenges that LGG PDs have been facing in offering and integrating clinical molecular genetics and clinical cytogenetics fellowship training. Common challenges between programs were noted, and a set of 6 concluding comments are provided to facilitate future discussion.

Implementation and evaluation of personal genetic testing as part of genomics analysis courses in German universities

PURPOSE

Due to the increasing application of genome analysis and interpretation in medical disciplines, professionals require adequate education. Here, we present the implementation of personal genotyping as an educational tool in two genomics courses targeting Digital Health students at the Hasso Plattner Institute (HPI) and medical students at the Technical University of Munich (TUM).

METHODS

We compared and evaluated the courses and the students' perceptions on the course setup using questionnaires.

RESULTS

During the course, students changed their attitudes towards genotyping (HPI: 79% [15 of 19], TUM: 47% [25 of 53]). Predominantly, students became more critical of personal genotyping (HPI: 73% [11 of 15], TUM: 72% [18 of 25]) and most students stated that genetic analyses should not be allowed without genetic counseling (HPI: 79% [15 of 19], TUM: 70% [37 of 53]). Students found the personal genotyping component useful (HPI: 89% [17 of 19], TUM: 92% [49 of 53]) and recommended its inclusion in future courses (HPI: 95% [18 of 19], TUM: 98% [52 of 53]).

CONCLUSION

Students perceived the personal genotyping component as valuable in the described genomics courses. The implementation described here can serve as an example for future courses in Europe.

ANALYSIS OF TECHNICAL TRAINING ON PHYSICAL FITNESS IN COLLEGE TENNIS PLAYERS

ABSTRACT Introduction: The stroke in tennis is a closed chain kinetic energy transfer starting from the lower limbs, through the trunk, to the upper limbs, and finally to the ball, requiring an upward coordinated muscular explosion. Due to its complex nature, it is believed that technical training can improve stability and accuracy in its players. Objective: Analyze the impacts of technical training on the physical fitness of college tennis players. Methods: Twenty tennis players from a tennis team at a university were selected and divided into an experimental group and a control group. The experiment lasted eight weeks. The experimental group received a technical training protocol on tennis strokes, while the control group received traditional physical training. Results: The hand-striking ability of the experimental group increased from 6.47 ± 2.02 to 8.67 ± 1.39 after four weeks and 10.56 ± 2.03 after eight weeks of training, while the control group increased from 4.42 ± 1.08 to 5.02 ± 0.59 in 4 weeks and 6.82 ± 1.46 after eight weeks of training. Conclusion: The application of technical movement training associated with traditional protocols is recommended to improve the physical fitness of athletes. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.

The Role of the Pathologist in the Next-Generation Era of Tumor Molecular Characterization

Current pathology practice is being shaped by the increasing complexity of modern medicine, in particular of precision oncology, and major technological advances. In the "next-generation technologies era", the pathologist has become the person responsible for the integration and interpretation of morphologic and molecular information and for the delivery of critical answers to diagnostic, prognostic and predictive queries, acquiring a prominent position in the molecular tumor boards.

A Stakeholders Approach for Curriculum Development of Master's Degree in Molecular Diagnostics

BACKGROUND

Curriculum development is a multi-processing activity that involves many academic and professional stakeholders. In order to detect the curriculum components, it is very helpful to determine the needs and expectations of the stakeholders concerning the graduate's competencies. The main objective of this work is to develop a curriculum for a master's degree in molecular diagnostics based on a survey of key stakeholders and according to the requirements of accreditation and certification, while maintaining its relevance with the rapidly advancing diverse techniques.

METHODS

Experts and supervisors including professors of molecular diagnostics at the various universities and consultants and supervisors at health-care centers performing molecular testing were surveyed to assess their expected cognitive and psychomotor molecular skills from a master's degree graduate. A validated questionnaire that included demographic information, current practiced molecular techniques, the level of expected expertise, and the educational requirements for each.

RESULTS

Thirty-six respondents, mostly with a doctorate degree and more than 10 years' experience, have successfully completed the questionnaire. More than 60% of the participating laboratories are commonly used or planned to be used within the next five years. About 57.4% required expert and familiar with skills and concepts. In general, the overall score of skills expectations was 2.8±5 0.out of four. The practice level for molecular techniques was in favor of a master's degree (53.8%). The level of skills expectation is very high for the specific managerial and quality activities with an overall value of 3.7±0.3 out of four.

CONCLUSION

We gathered information on the standard requirements of the professional practice and on its anticipated future directions through surveys and interviews with the professional practitioners and educators to develop a curriculum for a master's degree in molecular diagnostics. The two major messages from the stakeholders are that both cognitive and psychomotor skills of the mentioned molecular techniques are required for the program and there is a need to include extensive laboratory training during the courses.

From helices to health: undergraduate medical education in genetics and genomics

Rapid advances in genomic technologies combined with drastic reductions in cost and a growing number of clinical genomic tests are transforming medical practice. While enthusiasm about applications of precision medicine is high, the existing clinical genetics workforce is insufficient to meet present demands and will fall increasingly short as the use of genetic and genomic testing becomes more routine. To address this shortage, physicians in all areas of medicine will require genomic literacy. Undergraduate medical students, therefore, need a solid foundation in genetics and genomics so they can apply genomic medicine across a range of specialties. Here, we review the current trends and challenges in undergraduate medical genetics education in North America, highlight innovations and offer recommendations.

Impacts of incorporating personal genome sequencing into graduate genomics education: a longitudinal study over three course years

BACKGROUND

To address the need for more effective genomics training, beginning in 2012 the Icahn School of Medicine at Mount Sinai has offered a unique laboratory-style graduate genomics course, "Practical Analysis of Your Personal Genome" (PAPG), in which students optionally sequence and analyze their own whole genome. We hypothesized that incorporating personal genome sequencing (PGS) into the course pedagogy could improve educational outcomes by increasing student motivation and engagement. Here we extend our initial study of the pilot PAPG cohort with a report on student attitudes towards genome sequencing, decision-making, psychological wellbeing, genomics knowledge and pedagogical engagement across three course years.

METHODS

Students enrolled in the 2013, 2014 and 2015 course years completed questionnaires before (T1) and after (T2) a prerequisite workshop (n = 110) and before (T3) and after (T4) PAPG (n = 66).

RESULTS

Students' interest in PGS was high; 56 of 59 eligible students chose to sequence their own genome. Decisional conflict significantly decreased after the prerequisite workshop (T2 vs. T1 p < 0.001). Most, but not all students, reported low levels of decision regret and test-related distress post-course (T4). Each year baseline decisional conflict decreased (p < 0.001) suggesting, that as the course became more established, students increasingly made their decision prior to enrolling in the prerequisite workshop. Students perceived that analyzing their own genome enhanced the genomics pedagogy, with students self-reporting being more persistent and engaged as a result of analyzing their own genome. More than 90% of respondents reported spending additional time outside of course assignments analyzing their genome.

CONCLUSIONS

Incorporating personal genome sequencing in graduate medical education may improve student motivation and engagement. However, more data will be needed to quantitatively evaluate whether incorporating PGS is more effective than other educational approaches.

Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma

Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA sequencing, and proteomics data of 538 lung adenocarcinoma patients from The Cancer Genome Atlas and used these to identify molecular pathways associated with histopathology patterns. We report cell-cycle regulation and nucleotide binding pathways underpinning tumor cell dedifferentiation, and we predicted histology grade using transcriptomics and proteomics signatures (area under curve >0.80). We built an integrative histopathology-transcriptomics model to generate better prognostic predictions for stage I patients (p = 0.0182 ± 0.0021) compared with gene expression or histopathology studies alone, and the results were replicated in an independent cohort (p = 0.0220 ± 0.0070). These results motivate the integration of histopathology and omics data to investigate molecular mechanisms of pathology findings and enhance clinical prognostic prediction.

Training Genetic Counsellors to Deliver an Innovative Therapeutic Intervention: their Views and Experience of Facilitating Multi-Family Discussion Groups

Innovations in clinical genetics have increased diagnosis, treatment and prognosis of inherited genetic conditions (IGCs). This has led to an increased number of families seeking genetic testing and / or genetic counselling and increased the clinical load for genetic counsellors (GCs). Keeping pace with biomedical discoveries, interventions are required to support families to understand, communicate and cope with their Inherited Genetic Condition. The Socio-Psychological Research in Genomics (SPRinG) collaborative have developed a new intervention, based on multi-family discussion groups (MFDGs), to support families affected by IGCs and train GCs in its delivery. A potential challenge to implementing the intervention was whether GCs were willing and able to undergo the training to deliver the MFDG. In analysing three multi-perspective interviews with GCs, this paper evaluates the training received. Findings suggests that MFDGs are a potential valuable resource in supporting families to communicate genetic risk information and can enhance family function and emotional well-being. Furthermore, we demonstrate that it is feasible to train GCs in the delivery of the intervention and that it has the potential to be integrated into clinical practice. Its longer term implementation into routine clinical practice however relies on changes in both organisation of clinical genetics services and genetic counsellors' professional development.

Educational strategies to enable expansion of pharmacogenomics-based care

PURPOSE

The current state of pharmacogenomics education for pharmacy students and practitioners is discussed, and resources and strategies to address persistent challenges in this area are reviewed.

SUMMARY

Consensus-based pharmacist competencies and guidelines have been published to guide pharmacogenomics knowledge attainment and application in clinical practice. Pharmacogenomics education is integrated into various pharmacy school courses and, increasingly, into Pharm.D. curricula in the form of required standalone courses. Continuing-education programs and a limited number of postgraduate training opportunities are available to practicing pharmacists. For colleges and schools of pharmacy, identifying the optimal structure and content of pharmacogenomics education remains a challenge; insufficient numbers of faculty members with pharmacogenomics expertise and the inadequate availability of practice settings for experiential education are other limiting factors. Strategies for overcoming those challenges include providing early exposure to pharmacogenomics through foundational courses and incorporating pharmacogenomics into practice-based therapeutics courses and introductory and advanced pharmacy practice experiences. For practitioner education, online resources, clinical decision support-based tools, and certificate programs can be used to supplement structured postgraduate training in pharmacogenomics. Recently published data indicate successful use of "shared curricula" and participatory education models involving opportunities for learners to undergo personal genomic testing.

CONCLUSION

The pharmacy profession has taken a leadership role in expanding student and practitioner education to meet the demand for increased pharmacist involvement in precision medicine initiatives. Effective approaches to teaching pharmacogenomics knowledge and driving its appropriate application in clinical practice are increasingly available.

Effects of Using Personal Genotype Data on Student Learning and Attitudes in a Pharmacogenomics Course

Objective. To evaluate the impact of personal genotyping and a novel educational approach on student attitudes, knowledge, and beliefs regarding pharmacogenomics and genomic medicine. Methods. Two online elective courses (pharmacogenomics and genomic medicine) were offered to student pharmacists at the University of Florida using a flipped-classroom, patient-centered teaching approach. In the pharmacogenomics course, students could be genotyped and apply results to patient cases. Results. Thirty-four and 19 student pharmacists completed the pharmacogenomics and genomic medicine courses, respectively, and 100% of eligible students (n=34) underwent genotyping. Student knowledge improved after the courses. Seventy-four percent (n=25) of students reported better understanding of pharmacogenomics based on having undergone genotyping. Conclusions. Completion of a novel pharmacogenomics elective course sequence that incorporated personal genotyping and genomic medicine was associated with increased student pharmacist knowledge and improved clinical confidence with pharmacogenomics.

Clinical Next Generation Sequencing for Precision Medicine in Cancer

Rapid adoption of next generation sequencing (NGS) in genomic medicine has been driven by low cost, high throughput sequencing and rapid advances in our understanding of the genetic bases of human diseases. Today, the NGS method has dominated sequencing space in genomic research, and quickly entered clinical practice. Because unique features of NGS perfectly meet the clinical reality (need to do more with less), the NGS technology is becoming a driving force to realize the dream of precision medicine. This article describes the strengths of NGS, NGS panels used in precision medicine, current applications of NGS in cytology, and its challenges and future directions for routine clinical use.

Using a Team-Based Learning Approach at National Meetings to Teach Residents Genomic Pathology

BACKGROUND

Accumulating data suggest that team-based learning (TBL) is more effective than lecture-based teaching strategies. Educational sessions at national meetings, however, tend to be lecture-based, and unlike most examples of TBL, involve participants who do not know each other or the instructor.

OBJECTIVE

We evaluated a 1-day TBL genomic pathology workshop for residents held at 3 national meetings.

METHODS

A committee of experts developed the workshop. Prior to attending, participants were provided access to readings and asked to answer preparation questions. Each of the 4 modules within the workshop consisted of a 60-minute TBL activity flanked by 15- to 30-minute preactivity and postactivity lectures. We used surveys to acquire participant evaluation of the workshop.

RESULTS

From 2013-2014, 86 pathology residents from 61 programs participated in 3 workshops at national meetings. All workshops were well received, with over 90% of attendees indicating that they would recommend them to other residents and that the material would help them as practicing pathologists. An incremental approach facilitated decreasing faculty presence at the workshops: the first 2 workshops had 7 faculty each (1 facilitator for each team and 1 circulating faculty member), while the final workshop involved only 2 faculty for 6 teams. For this final session, participants agreed that circulating faculty provided adequate support. Participant "buy-in" (requiring completion of a preworkshop survey) was critical in enabling a TBL approach.

CONCLUSIONS

These results demonstrate that TBL is a feasible and effective strategy for teaching genomic medicine that is acceptable to pathology residents at national meetings.

Design of a Genomics Curriculum: Competencies for Practicing Pathologists

CONTEXT

The field of genomics is rapidly impacting medical care across specialties. To help guide test utilization and interpretation, pathologists must be knowledgeable about genomic techniques and their clinical utility. The technology allowing timely generation of genomic data is relatively new to patient care and the clinical laboratory, and therefore, many currently practicing pathologists have been trained without any molecular or genomics exposure. Furthermore, the exposure that current and recent trainees receive in this field remains inconsistent.

OBJECTIVE

To assess pathologists' learning needs in genomics and to develop a curriculum to address these educational needs.

DESIGN

A working group formed by the College of American Pathologists developed an initial list of genomics competencies (knowledge and skills statements) that a practicing pathologist needs to be successful. Experts in genomics were then surveyed to rate the importance of each competency. These data were used to create a final list of prioritized competencies. A subset of the working group defined subtopics and tasks for each competency. Appropriate delivery methods for the educational material were also proposed.

RESULTS

A final list of 32 genomics competency statements was developed. A prioritized curriculum was created with designated subtopics and tasks associated with each competency.

CONCLUSIONS

We present a genomics curriculum designed as a first step toward providing practicing pathologists with the competencies needed to practice successfully.

Preparing the next generation of genomicists: a laboratory-style course in medical genomics

The growing gap between the demand for genome sequencing and the supply of trained genomics professionals is creating an acute need to develop more effective genomics education. In response we developed “Practical Analysis of Your Personal Genome”, a novel laboratory-style medical genomics course in which students have the opportunity to obtain and analyze their own whole genome. This report describes our motivations for and the content of a “practical” genomics course that incorporates personal genome sequencing and the lessons we learned during the first three iterations of this course.

The Evolving Role of the Laboratory Professional in the Age of Genome Sequencing: A Vision of the Association for Molecular Pathology

In conclusion, to maximize the benefit of the genomic era, the molecular laboratory director will continue to be essential in the generation, analysis, and interpretation of patient results, which now include genomic data obtained through NGS approaches. That includes integrating this information as part of the complete care of the patient and communicating and interacting with professionals across disciplines. In addition, the molecular laboratory director must continue to provide training and education to current and future colleagues, within and outside of molecular pathology and molecular genetics. Professionalism includes volunteerism in professional organizations and education and advocacy to policy makers, health administrators, payers, and the public. It also includes efforts to increase visibility of the profession to our colleagues from other medical disciplines and the public at large. Thus, the role of the molecular laboratory professional is multifaceted, but, above all, it is to ensure the access to and quality of molecular pathology testing, the responsible implementation of expanded test modalities such as genome sequencing, and the interpretation thereof to aid the clinician in the medical management of the patient and ultimately to benefit the society by providing precision patient care.

Genomics in the clinic: ethical and policy challenges in clinical next-generation sequencing programs at early adopter USA institutions

Next-generation sequencing (NGS) technologies are poised to revolutionize clinical diagnosis and treatment, but raise significant ethical and policy challenges. This review examines NGS program challenges through a synthesis of published literature, website and conference presentation content, and interviews at early-adopting institutions in the USA. Institutions are proactively addressing policy challenges related to the management and technical aspects of program development. However, ethical challenges related to patient-related aspects have not been fully addressed. These complex challenges present opportunities to develop comprehensive and standardized regulations across programs. Understanding the strengths, weaknesses and current practices of evolving NGS program approaches are important considerations for institutions developing NGS services, policymakers regulating or funding NGS programs and physicians and patients considering NGS services.

Genomic oncology education: an urgent need, a new approach

Genomic testing has entered oncology practice. With reduced cost and faster turnaround times, clinical applications for next-generation sequencing-based assays will only continue to increase. As such, there is an urgent need for health professional education to allow implementation of these new diagnostic tools. However, current medical school, residency, and fellowship training has had limited success in educating physicians in the fundamentals of single-gene testing, let alone genomic methods. In this review, we describe the novel approach the pathology community has taken in genomic education and the potential for application to oncology trainees.

How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study

PURPOSE

Health-care professionals need to be trained to work with whole-genome sequencing (WGS) in their practice. Our aim was to explore how students responded to a novel genome analysis course that included the option to analyze their own genomes.

METHODS

This was an observational cohort study. Questionnaires were administered before (T3) and after the genome analysis course (T4), as well as 6 months later (T5). In-depth interviews were conducted at T5.

RESULTS

All students (n = 19) opted to analyze their own genomes. At T5, 12 of 15 students stated that analyzing their own genomes had been useful. Ten reported they had applied their knowledge in the workplace. Technical WGS knowledge increased (mean of 63.8% at T3, mean of 72.5% at T4; P = 0.005). In-depth interviews suggested that analyzing their own genomes may increase students' motivation to learn and their understanding of the patient experience. Most (but not all) of the students reported low levels of WGS results-related distress and low levels of regret about their decision to analyze their own genomes.

CONCLUSION

Giving students the option of analyzing their own genomes may increase motivation to learn, but some students may experience personal WGS results-related distress and regret. Additional evidence is required before considering incorporating optional personal genome analysis into medical education on a large scale.

Ethical considerations regarding classroom use of personal genomic information

Rapidly decreasing costs of genetic technologies-especially next-generation sequencing-and intensifying need for a clinical workforce trained in genomic medicine have increased interest in having students use personal genomic information to motivate and enhance genomics education. Numerous ethical issues attend classroom/pedagogical use of students' personal genomic information, including their informed decision to participate, pressures to participate, privacy concerns, and psychosocial sequelae of learning genomic information. This paper addresses these issues, advocates explicit discussion of these issues to cultivate students' ethical reasoning skills, suggests ways to mitigate potential harms, and recommends collection of ethically relevant data regarding pedagogical use of personal genomic information.

Clinical laboratory immunology: an indispensable player in laboratory medicine

OBJECTIVES

Clinical laboratory immunology affects practically every aspect of medicine. Accordingly, appropriately trained, board-certified clinical laboratory immunologists are key contributors to the diagnosis and management of patients with various immune-mediated conditions. This review highlights the availability of postdoctoral level training programs for clinical laboratory immunology and identifies possible career tracks.

METHODS

Fundamental elements for doctoral level clinical laboratory immunologists are identified and the critical components of diagnostic immunology training as well as career opportunities in and out of academia are described.

RESULTS

Relative to other disciplines in laboratory medicine, little emphasis has been given to clinical laboratory immunology in medical, graduate, and postgraduate training. Formal postgraduate fellowship programs and board certification examinations are available, yet there remains a significant lack of awareness in the medical education community about the value and necessity of training in this field.

CONCLUSIONS

It is anticipated that sharing this knowledge will increase awareness of the discipline of clinical laboratory immunology at the postdoctoral level with implications for the practice of laboratory medicine.

The current state of resident training in genomic pathology: a comprehensive analysis using the resident in-service examination

OBJECTIVES

To determine the current state of pathology resident training in genomic and molecular pathology.

METHODS

The Training Residents in Genomics (TRIG) Working Group developed survey and knowledge questions for the 2013 pathology Resident In-Service Examination (RISE). Sixteen demographic questions related to amount of training, current and predicted future use, and perceived ability in molecular pathology vs genomic medicine were included, along with five genomic pathology and 19 molecular pathology knowledge questions.

RESULTS

A total of 2,506 pathology residents took the 2013 RISE, with approximately 600 individuals per postgraduate year (PGY). For genomic medicine, 42% of PGY-4 respondents stated they had no training, compared with 7% for molecular pathology (P < .001). PGY-4 residents' perceived ability, comfort in discussing results, and predicted future use as a practicing pathologist were reported to be less in genomic medicine than in molecular pathology (P < .001). Based on PGY, knowledge question scores showed a greater increase in molecular pathology than in genomic pathology.

CONCLUSIONS

The RISE is a powerful tool for assessing the state of resident training in genomic pathology and current results suggest a significant deficit. The results also provide a baseline to assess future initiatives to improve genomics education for pathology residents such as those developed by the TRIG Working Group.

A Balanced Look at the Implications of Genomic (and Other "Omics") Testing for Disease Diagnosis and Clinical Care

The tremendous increase in DNA sequencing capacity arising from the commercialization of "next generation" instruments has opened the door to innumerable routes of investigation in basic and translational medical science. It enables very large data sets to be gathered, whose interpretation and conversion into useful knowledge is only beginning. A challenge for modern healthcare systems and academic medical centers is to apply these new methods for the diagnosis of disease and the management of patient care without unnecessary delay, but also with appropriate evaluation of the quality of data and interpretation, as well as the clinical value of the insights gained. Most critically, the standards applied for evaluating these new laboratory data and ensuring that the results and their significance are clearly communicated to patients and their caregivers should be at least as rigorous as those applied to other kinds of medical tests. Here, we present an overview of conceptual and practical issues to be considered in planning for the integration of genomic methods or, in principle, any other type of "omics" testing into clinical care.

Progress and potential: training in genomic pathology

CONTEXT

Genomic medicine is revolutionizing patient care. Physicians in areas as diverse as oncology, obstetrics, and infectious disease have begun using next-generation sequencing assays as standard diagnostic tools.

OBJECTIVE

To review the role of pathologists in genomic testing as well as current educational programs and future training needs in genomic pathology.

DATA SOURCES

Published literature as well as personal experience based on committee membership and genomic pathology curricular design.

CONCLUSIONS

Pathologists, as the directors of the clinical laboratories, must be prepared to integrate genomic testing into their practice. The pathology community has made significant progress in genomics-related education. A continued coordinated and proactive effort will ensure a future vital role for pathologists in the evolving health care system and also the best possible patient care.

Engaging the next generation of healthcare professionals in genomics: planning for the future

There is broad agreement that healthcare professionals require fundamental training in genomics to keep pace with scientific advancement. Strong models that promote effective genomic education, however, are lacking. Furthermore, curricula at many institutions are now straining to adapt to the integration of additional material on next-generation sequencing and the bioethical and legal issues that will accompany clinical genomic testing. This article advocates for core competencies focused on job function, which will best prepare providers to be end-users of healthcare information. In addition, it argues in favor of online and blended learning models that incorporate student genotyping and specific training in the ethical, legal and social issues raised by genomic testing.

Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study

Background

Multiple laboratories now offer clinical whole genome sequencing (WGS). We anticipate WGS becoming routinely used in research and clinical practice. Many institutions are exploring how best to educate geneticists and other professionals about WGS. Providing students in WGS courses with the option to analyze their own genome sequence is one strategy that might enhance students’ engagement and motivation to learn about personal genomics. However, if this option is presented to students, it is vital they make informed decisions, do not feel pressured into analyzing their own genomes by their course directors or peers, and feel free to analyze a third-party genome if they prefer. We therefore developed a 26-hour introductory genomics course in part to help students make informed decisions about whether to receive personal WGS data in a subsequent advanced genomics course. In the advanced course, they had the option to receive their own personal genome data, or an anonymous genome, at no financial cost to them. Our primary aims were to examine whether students made informed decisions regarding analyzing their personal genomes, and whether there was evidence that the introductory course enabled the students to make a more informed decision.

Methods

This was a longitudinal cohort study in which students (N = 19) completed questionnaires assessing their intentions, informed decision-making, attitudes and knowledge before (T1) and after (T2) the introductory course, and before the advanced course (T3). Informed decision-making was assessed using the Decisional Conflict Scale.

Results

At the start of the introductory course (T1), most (17/19) students intended to receive their personal WGS data in the subsequent course, but many expressed conflict around this decision. Decisional conflict decreased after the introductory course (T2) indicating there was an increase in informed decision-making, and did not change before the advanced course (T3). This suggests that it was the introductory course content rather than simply time passing that had the effect. In the advanced course, all (19/19) students opted to receive their personal WGS data. No changes in technical knowledge of genomics were observed. Overall attitudes towards WGS were broadly positive.

Conclusions

Providing students with intensive introductory education about WGS may help them make informed decisions about whether or not to work with their personal WGS data in an educational setting.

Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era

Background

The revolution in DNA sequencing technology continues unabated, and is affecting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively influencing research and development efforts to advance genome biology. Here we present a cross-disciplinary course that provides undergraduate students with practical experience in running a next generation sequencing instrument through to the analysis and annotation of the generated DNA sequences.

Results

Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research. The students conducted the work flow from DNA extraction, library preparation, running the sequencing instrument, to the extraction and analysis of the data. They sequenced microbes, metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores.

Conclusions

Students learned important skills for their future education and career opportunities, and a perceived increase in students’ ability to conduct independent scientific research was measured. DNA sequencing is rapidly expanding in the life sciences. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life.

Personal genotypes are teachable moments

There is an urgent need for effective genomics education for healthcare professionals. Recent analysis of an experimental genomics curriculum showed that medical students' examinations of their own genotypes provide a valuable learning experience. Such experiential learning has a long tradition in medical education and its application to genomics is enabled by increasingly powerful and decreasingly costly genome science and technology. Personal genotyping is an important option to consider when designing educational programs for healthcare professionals.

Personal genome testing in medical education: student experiences with genotyping in the classroom

BACKGROUND

Direct-to-consumer (DTC) personal genotyping services are beginning to be adopted by educational institutions as pedagogical tools for learning about human genetics. However, there is little known about student reactions to such testing. This study investigated student experiences and attitudes towards DTC personal genome testing.

METHODS

Individual interviews were conducted with students who chose to undergo personal genotyping in the context of an elective genetics course. Ten medical and graduate students were interviewed before genotyping occurred, and at 2 weeks and 6 months after receiving their genotype results. Qualitative analysis of interview transcripts assessed the expectations and experiences of students who underwent personal genotyping, how they interpreted and applied their results; how the testing affected the quality of their learning during the course, and what were their perceived needs for support.

RESULTS

Students stated that personal genotyping enhanced their engagement with the course content. Although students expressed skepticism over the clinical utility of some test results, they expressed significant enthusiasm immediately after receiving their personal genetic analysis, and were particularly interested in results such as drug response and carrier testing. However, few reported making behavioral changes or following up on specific results through a healthcare provider. Students did not report utilizing genetic counseling, despite feeling strongly that the 'general public' would need these services. In follow-up interviews, students exhibited poor recall on details of the consent and biobanking agreements, but expressed little regret over their decision to undergo genotyping. Students reported mining their raw genetic data, and conveyed a need for further consultation support in their exploration of genetic variants.

CONCLUSIONS

Personal genotyping may improve students' self-reported motivation and engagement with course material. However, consultative support that is different from traditional genetic counseling will be necessary to support students. Before incorporating personal genotyping into coursework, institutions should lead multi-disciplinary discussion to anticipate issues and incorporate teaching mechanisms that engage the ethical, legal, and social implications of personal genotyping, including addressing those found in this study, to go beyond what is offered by commercial providers.

Clinical integration of next-generation sequencing technology

Recent advances in next-generation sequencing (NGS) methods and technology have substantially reduced costs and operational complexity leading to production of benchtop sequencers and commercial software solutions for implementation in small research and clinical laboratories. This article addresses requirements and limitations to successful implementation of these systems, including (1) calibration and validation of the instrumentation, experimental paradigm, and primary readout, (2) secure data transfer, storage, and secondary processing, (3) implementation of software tools for targeted analysis, and (4) training of research and clinical personnel to evaluate data fidelity and interpret the molecular significance of the genomic output.

Teaching residents genomic pathology: a novel approach for new technology

Genomics-based diagnostics have become part of patient care. As pathologists have the expertise in clinical laboratory testing as well as access to patient samples, all genomic medicine is genomic pathology. This article will review the evidence that there is a critical need for pathology resident training in genomics. Several individual program curricula are described as well as the progress of the Training Residents in Genomics Working Group. This group has made significant advances toward developing, implementing, and evaluating a national curriculum in genomics for pathology residents. The novel approach of the Training Residents in Genomics Working Group can be used as a model for training pathology professionals in any new technology.

Balancing personalized medicine and personalized care

The current description of personalized medicine by the National Institutes of Health is "the science of individualized prevention and therapy." Although physicians are beginning to see the promise of genetic medicine coming to fruition, the rapid pace of sequencing technology, informatics, and computer science predict a revolution in the ability to care for patients in the near future. The enthusiasm expressed by researchers is well founded, but the expectations voiced by the public do not center on advancing technology. Rather, patients are asking for personalized care: a holistic approach that considers physical, mental, and spiritual well-being. This perspective considers psychological, religious, and ethical challenges that may arise as the precision of preventive medicine improves. Psychological studies already highlight the barriers to single gene testing and suggest significant barriers to the predictive testing envisioned by personalized medicine. Certain religious groups will likely mount opposition if they believe personalized medicine encourages embryo selection. If the technology prompts cost-containment discussions, those concerned about the sanctity of life may raise ethical objections. Consequently, the availability of new scientific developments does not guarantee advances in treatment because patients may prove unwilling to receive and act on personalized genetic information. This perspective highlights current efforts to incorporate personalized medicine and personalized care into the medical curriculum, genetic counseling, and other aspects of clinical practice. Because these efforts are generally independent, the authors offer recommendations for physicians and educators so that personalized medicine can be implemented in a manner that meets patient expectations for personalized care.

Integration of genomic medicine into pathology residency training: the stanford open curriculum

Next-generation sequencing methods provide an opportunity for molecular pathology laboratories to perform genomic testing that is far more comprehensive than single-gene analyses. Genome-based test results are expected to develop into an integral component of diagnostic clinical medicine and to provide the basis for individually tailored health care. To achieve these goals, rigorous interpretation of high-quality data must be informed by the medical history and the phenotype of the patient. The discipline of pathology is well positioned to implement genome-based testing and to interpret its results, but new knowledge and skills must be included in the training of pathologists to develop expertise in this area. Pathology residents should be trained in emerging technologies to integrate genomic test results appropriately with more traditional testing, to accelerate clinical studies using genomic data, and to help develop appropriate standards of data quality and evidence-based interpretation of these test results. We have created a genomic pathology curriculum as a first step in helping pathology residents build a foundation for the understanding of genomic medicine and its implications for clinical practice. This curriculum is freely accessible online.

Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics

The Human Genome Project (HGP) provided the initial draft of mankind's DNA sequence in 2001. The HGP was produced by 23 collaborating laboratories using Sanger sequencing of mapped regions as well as shotgun sequencing techniques in a process that occupied 13 years at a cost of ~$3 billion. Today, Next Generation Sequencing (NGS) techniques represent the next phase in the evolution of DNA sequencing technology at dramatically reduced cost compared to traditional Sanger sequencing. A single laboratory today can sequence the entire human genome in a few days for a few thousand dollars in reagents and staff time. Routine whole exome or even whole genome sequencing of clinical patients is well within the realm of affordability for many academic institutions across the country. This paper reviews current sequencing technology methods and upcoming advancements in sequencing technology as well as challenges associated with data generation, data manipulation and data storage. Implementation of routine NGS data in cancer genomics is discussed along with potential pitfalls in the interpretation of the NGS data. The overarching importance of bioinformatics in the clinical implementation of NGS is emphasized.[7] We also review the issue of physician education which also is an important consideration for the successful implementation of NGS in the clinical workplace. NGS technologies represent a golden opportunity for the next generation of pathologists to be at the leading edge of the personalized medicine approaches coming our way. Often under-emphasized issues of data access and control as well as potential ethical implications of whole genome NGS sequencing are also discussed. Despite some challenges, it's hard not to be optimistic about the future of personalized genome sequencing and its potential impact on patient care and the advancement of knowledge of human biology and disease in the near future.

Use of a wiki as an interactive teaching tool in pathology residency education: Experience with a genomics, research, and informatics in pathology course

Background:

The need for informatics and genomics training in pathology is critical, yet limited resources for such training are available. In this study we sought to critically test the hypothesis that the incorporation of a wiki (a collaborative writing and publication tool with roots in “Web 2.0”) in a combined informatics and genomics course could both (1) serve as an interactive, collaborative educational resource and reference and (2) actively engage trainees by requiring the creation and sharing of educational materials.

Materials and Methods:

A 2-week full-time course at our institution covering genomics, research, and pathology informatics (GRIP) was taught by 36 faculty to 18 second- and third-year pathology residents. The course content included didactic lectures and hands-on demonstrations of technology (e.g., whole-slide scanning, telepathology, and statistics software). Attendees were given pre- and posttests. Residents were trained to use wiki technology (MediaWiki) and requested to construct a wiki about the GRIP course by writing comprehensive online review articles on assigned lectures. To gauge effectiveness, pretest and posttest scores for our course were compared with scores from the previous 7 years from the predecessor course (limited to informatics) given at our institution that did not utilize wikis.

Results:

Residents constructed 59 peer-reviewed collaborative wiki articles. This group showed a 25% improvement (standard deviation 12%) in test scores, which was greater than the 16% delta recorded in the prior 7 years of our predecessor course (P = 0.006).

Conclusions:

Our use of wiki technology provided a wiki containing high-quality content that will form the basis of future pathology informatics and genomics courses and proved to be an effective teaching tool, as evidenced by the significant rise in our resident posttest scores. Data from this project provide support for the notion that active participation in content creation is an effective mechanism for mastery of content. Future residents taking this course will continue to build on this wiki, keeping content current, and thereby benefit from this collaborative teaching tool.

The future of genomics in pathology

The recent advances in technology and the promise of cheap and fast whole genomic data offer the possibility to revolutionise the discipline of pathology. This should allow pathologists in the near future to diagnose disease rapidly and early to change its course, and to tailor treatment programs to the individual. This review outlines some of these technical advances and the changes needed to make this revolution a reality.

TRIG on TRACK: educating pathology residents in genomic medicine

Genomic technologies are dramatically changing the practice of medicine. Next-generation sequencing has allowed prognostic stratification of cancer patients, personalized drug therapy and the identification of genetic risk factors for a multitude of diseases. As the physicians who oversee tissue- and laboratory-based diagnostic testing, pathologists must understand and utilize this new technology for the benefit of patients; however, only a minority of pathology residency programs currently provide training in genomics. In response to this urgent need, the Training Residents in Genomics (TRIG) Working Group has made significant progress towards creating, implementing, evaluating and disseminating a national curriculum in genomic pathology. Although presented in the context of pathology training, the approach described in this review can serve as model for education in genomic medicine of students, trainees or professionals in other areas of healthcare.

Clinical Requests for Molecular Tests: The 3-Step Evidence Check

Laboratory tests performed by molecular methods are increasing in volume and complexity at an unprecedented rate. Molecular tests have a broad set of applications, and most recently have been advocated as the mechanism by which providers can further tailor treatments to the individual patient. As the momentum behind molecular testing continues to increase, pathology practices may find themselves unprepared for the new wave of molecular medicine. This special article has been developed in an effort to provide pathologists who have limited molecular training with a simple and quick algorithm for determining whether a requested molecular test is appropriate for a patient. Additional recommendations for a more intensive and proactive review and management of molecular requests also are included. The principles discussed can easily be applied to requests for any test, including those not using molecular methods, which would be sent to an outside reference laboratory. This special article was developed from a Webinar for the College of American Pathologists targeting education for pathologists about the transformation of pathology practice in the new molecular and digital age.

Swabbing students: should universities be allowed to facilitate educational DNA testing?

Recognizing the profound need for greater patient and provider familiarity with personalized genomic medicine, many university instructors are including personalized genotyping as part of their curricula. During seminars and lectures students run polymerase chain reactions on their own DNA or evaluate their experiences using direct-to-consumer genetic testing services subsidized by the university. By testing for genes that may influence behavioral or health-related traits, however, such as alcohol tolerance and cancer susceptibility, certain universities have stirred debate on the ethical concerns raised by educational genotyping. Considering the potential for psychosocial harm and medically relevant outcomes, how far should university-facilitated DNA testing be permitted to go? The analysis here distinguishes among these learning initiatives and critiques their approaches to the ethical concerns raised by educational genotyping.

Commentary: to genotype or not to genotype? Addressing the debate through the development of a genomics and personalized medicine curriculum

As technologic innovation helps broaden and refine our knowledge base of genetic associations, a growing interest in translating these genetic discoveries to clinically useful laboratory tests has given rise to the potential of personalized medicine. To fully realize this potential, medical schools must educate trainees on genetic and genomic testing in clinical settings. An emerging debate in academic medical centers is not about the need for this education but, rather, the most effective educational models that should be deployed. At Stanford School of Medicine, several proposals to offer personal genotyping in the educational curriculum argued that learning genetics and the attendant cutting-edge molecular techniques would be more powerful and sustained if students were applying their knowledge to their personal genotypes. Given the complex ethical, legal, and social issues involved in implementing such a program, a schoolwide task force was formed to evaluate the risks and benefits of offering personal genotyping to students and residents. In this commentary, the authors discuss the salient issues raised by the task force and describe the safeguards adopted into the ultimate approval and implementation of the course, which included the opportunity for students to analyze their own genomes.

Molecular pathology of breast cancer: the journey from traditional practice toward embracing the complexity of a molecular classification

CONTEXT

Adenocarcinoma of the breast is the most frequent cancer affecting women in both developed and developing regions of the world. From the moment of clinical presentation until the time of pathologic diagnosis, patients affected by this disease will face daunting questions related to prognosis and treatment options. While improvements in targeted therapies have led to increased patient survival, these same advances have created the imperative to accurately stratify patients to achieve maximum therapeutic efficacy while minimizing side effects. In this evolving era of personalized medicine, there is an ever-increasing need to overcome the limitations of traditional diagnostic practice.

OBJECTIVE

To summarize the molecular diagnostics traditionally used to guide prognostication and treatment of breast carcinomas, to highlight published data on the molecular classification of these tumors, and to showcase molecular assays that will supplement traditional methods of categorizing the disease.

DATA SOURCES

A review of the literature covering the molecular diagnostics of breast carcinomas with a focus on the gene expression and array studies used to characterize the molecular signatures of the disease. Special emphasis is placed on summarizing evolving technologies useful in the diagnosis and characterization of breast carcinoma.

CONCLUSIONS

Available and emerging molecular resources will allow pathologists to provide superior diagnostic, prognostic, and predictive information about individual breast carcinomas. These advances should translate into earlier identification and tailored therapy and should ultimately improve outcome for patients affected by this disease.

Using electronic health records to drive discovery in disease genomics

If genomic studies are to be a clinically relevant and timely reflection of the relationship between genetics and health status--whether for common or rare variants--cost-effective ways must be found to measure both the genetic variation and the phenotypic characteristics of large populations, including the comprehensive and up-to-date record of their medical treatment. The adoption of electronic health records, used by clinicians to document clinical care, is becoming widespread and recent studies demonstrate that they can be effectively employed for genetic studies using the informational and biological 'by-products' of health-care delivery while maintaining patient privacy.