Genetic counselors' views and experiences with the clinical integration of genome sequencing

Organizational Aspects of the Implementation and Use of Whole Genome Sequencing and Whole Exome Sequencing in the Pediatric Population in Italy: Results of a Survey

This study explores the organizational aspects of whole genome sequencing (WGS) implementation for pediatric patients with suspected genetic disorders in Italy, comparing it with whole exome sequencing (WES). Health professionals' opinions were collected through an internet-based survey and analyzed using a qualitative summative content analysis methodology. Among the 16 respondents, most were clinical geneticists performing only WES, while 5 also used WGS. The key differences identified include higher needs for analyzing genome rearrangements following WES, greater data storage and security requirements for WGS, and WGS only being performed in specific research studies. No difference was detected in centralization and decentralization issues. The main cost factors included genetic consultations, library preparation and sequencing, bioinformatic analysis, interpretation and confirmation, data storage, and complementary diagnostic investigations. Both WES and WGS decreased the need for additional diagnostic analyses when not used as last-resort tests. Organizational aspects were similar for WGS and WES, but economic evidence gaps may exist for WGS in clinical settings. As sequencing costs decline, WGS will likely replace WES and traditional genetic testing. Tailored genomic policies and cost-effectiveness analyses are needed for WGS implementation in health systems. WGS shows promise for enhancing genetics knowledge and expediting diagnoses for pediatric patients with genetic disorders.

Die Bedeutung der Hochdurchsatz-Sequenzierung in der medizinisch genetischen Diagnostik und Beratung

Next-Generation-Sequencing ist ein modernes diagnostisches Hochdurchsatz-Verfahren (Multi-Gen-Analysen), durch dessen Einsatz sowohl hereditäre Krebserkrankungen (Tumordispositionssyndrome, Keimbahndiagnostik) als auch somatische Alterationen in Tumoren besser abgeklärt werden können. Der breitere Einsatz dieser Technologie im medizinischen Alltag zeigt das tatsächliche Ausmaß der interindividuellen genetischen Variabilität. Wichtige Bedeutung hat dieses Verfahren für die Untersuchung von heterogenen genetischen Erkrankungen (z. B. Tumorerkrankungen, neurodegenerativen und -muskulären Erkrankungen) erlangt. Weitere Indikationsgebiete stellen die Pharmakogenetik sowie die nicht invasive Pränataldiagnostik dar. Es ist zu erwarten, dass dieses diagnostische Mittel eine breite klinische Anwendung finden wird. Mit der rasanten Zunahme und Komplexität genetischer Dateninformationen nimmt die richtige Interpretation und Übermittlung der Befunde in der humangenetischen Beratung (Keimbahndiagnostik) einen hohen Stellenwert ein. Die genetische Beratung muss entsprechend neu ausgerichtet und adaptiert werden.

Preferences for return of germline genome sequencing results for cancer patients and their genetic relatives in a research setting

Germline genome sequencing (GS) holds great promise for cancer prevention by identifying cancer risk and guiding prevention strategies, however research evidence is mixed regarding patient preferences for receiving GS results. The aim of this study was to discern preferences for return of results by cancer patients who have actually undergone GS. We conducted a mixed methods study with a cohort of cancer probands (n = 335) and their genetic relatives (n = 199) undergoing GS in a research setting. Both groups completed surveys when giving consent. A subset of participants (n = 40) completed semi-structured interviews. A significantly higher percentage of probands thought people would like to be informed about genetic conditions for which there is prevention or treatment that can change cancer risk compared to conditions for which there is no prevention or treatment (93% [311] versus 65% [216]; p < 0.001). Similar results were obtained for relatives (91% [180] versus 61% [121]; p < 0.001). Themes identified in the analysis of interviews were: (1) Recognised benefits of GS, (2) Balancing benefits with risks, (3) Uncertain results are perceived as unhelpful and (4) Competing obligations. While utility was an important discriminator in what was seen as valuable for this cohort, there was a variety of responses. In view of varied participant preferences regarding return of results, it is important to ensure patient understanding of test validity and identify individual choices at the time of consent to GS. The nature and value of the information, and a contextual understanding of researcher obligations should guide result return.

What's out there for parents? A systematic review of online information about prenatal microarray and exome sequencing

Objective

To identify what online patient information (presented in English) is available to parents about prenatal microarray (CMA) and exome sequencing (ES), and evaluate its content, quality, and readability.

Method

Systematic searches (Google and Bing) were conducted, and websites were categorised according to their purpose. Websites categorised as patient information were included if they were: in English, directed at patients, or were a text, video, or online version of an information leaflet. Author‐developed content checklists, the DISCERN Genetics tool, and readability tests (the Flesch Reading Ease Score, the Gunning Fog Index, and the Simple Measure of Gobbledygook Index) were then used to assess those sources of patient information.

Results

Of the 665 websites screened, 18 met the criteria. A further 8 sources were found through a targeted search of professional organisations, resulting in 26 sources available for further evaluation. In general, this was found to be low in quality, omitted details recommended by national or international guidance, and was written at a level too advanced for average readers.

Conclusion

Improvements should be made to the content, quality, and readability of online information so that it both reinforces and complements the discussions between parents and clinicians about testing options during pregnancy.

What's already known about this topic?

The Internet is an important source of information for parents during pregnancy

Little is known about the availability and standard of online information about newer prenatal genetic tests like chromosomal microarray (CMA) and prenatal exome sequencing (ES)

What does this study add?

Our results revealed limited online information aimed at parents about CMA and ES

The information we did identify was lacking the details recommended by professional guidelines, had low quality scores, and was written at an advanced level

Improvements to online information for parents are needed to support informed decision‐making regarding prenatal genetic tests

Integration of genetic counsellors in genomic testing triage: Outcomes of a genomic consultation service in British Columbia, Canada

PURPOSE

Clinical diagnostic genome-wide (exome or genome) sequencing (GWS) in British Columbia requires funding approval by a provincial agency on a case-by-case basis. The CAUSES Clinic was a pediatric translational trio-based GWS study at BC Children's and Women's Hospitals. Referrals to the CAUSES Clinic were made through a Genomic Consultation Service (GCS), a multidisciplinary team led by genetic counsellors that provided advice regarding genomic testing for physicians considering GWS for their patients. Here we review the outcomes of the GCS, focusing on patients not recommended for the CAUSES Study.

METHODS

Demographic, clinical, and testing data were abstracted from patient charts. Logistic regression analysis was used to explore associations between demographic and clinical variables and two outcomes: the type of recommendation and referring physicians' decisions to follow the recommendation.

RESULTS

Of 972 GCS referrals, 248 patients were not referred to the CAUSES Study. GWS (vs. a targeted test; e.g. multi-gene panel) was more likely to be recommended to physicians of patients with ID than physicians of patients without ID (OR = 2.98; 95% CI = 1.46 to 6.27; n = 149). In total, 40% of physicians who were recommended to pursue clinical genomic testing submitted an application for funding approval; 71% of applications were approved for funding. Among approved tests, 50% resulted in a diagnosis, including 33% of targeted tests and 82% of GWS tests (χ² (1) = 5.0, p = 0.026).

CONCLUSION

The GCS provided an effective model in which physicians can interface with genetic specialists, including genetic counsellors, to facilitate appropriate genomic test selection.

A Centralized Approach for Practicing Genomic Medicine

Next-generation sequencing has revolutionized the diagnostic process, making broadscale testing affordable and applicable to almost all specialties; however, there remain several challenges in its widespread implementation. Barriers such as lack of infrastructure or expertise within local health systems and complex result interpretation or counseling make it harder for frontline clinicians to incorporate genomic testing in their existing workflow. The general population is more informed and interested in pursuing genetic testing, and this has been coupled with the increasing accessibility of direct-to-consumer testing. As a result of these changes, primary care physicians and nongenetics specialty providers find themselves seeing patients for whom genetic testing would be beneficial but managing genetic test results that are out of their scope of practice. In this report, we present a practical and centralized approach to providing genomic services through an independent, enterprise-wide clinical service model. We present 4 years of clinical experience, with >3400 referrals, toward designing and implementing the clinical service, maximizing resources, identifying barriers, and improving patient care. We provide a framework that can be implemented at other institutions to support and integrate genomic services across the enterprise.

Impact of patient education videos on genetic counseling outcomes after exome sequencing

OBJECTIVE

Growing use of clinical exome sequencing (CES) has led to an increased burden of genomic education. Self-guided educational tools can minimize the educational burden for genetic counselors (GCs). The effectiveness of these tools must be evaluated.

METHODS

Parents of patients offered CES were randomized to watch educational videos before their visit or to receive routine care. Parents and GCs were surveyed about their experiences following the sessions. The responses of the video (n = 102) and no-video (n = 105) groups were compared.

RESULTS

GCs reported no significant differences between parents in the video and no-video groups on genetics knowledge or CES knowledge. In contrast, parents' scores on genetics knowledge questions were lower in the video than no-video group (p = 0.007). Most parents reported the videos were informative, and the groups did not differ in satisfaction with GCs or decisions to have CES.

CONCLUSION

GCs and parents perceived the videos to be beneficial. However, lower scores on genetics knowledge questions highlight the need for careful development of educational tools.

PRACTICE IMPLICATIONS

Educational tools should be developed and assessed for effectiveness with the input of all stakeholders before widespread implementation. Better measures of the effectiveness of these educational tools are needed.

Genetic Counseling and Surveillance Focused on Lynch Syndrome

Lynch syndrome is a hereditary cancer syndrome caused by germline mutations in one of several DNA mismatch repair genes. Lynch syndrome leads to an increased lifetime risk of various cancers, particularly colorectal, and endometrial cancers. After identifying patients suspected of having Lynch syndrome by clinical criteria, computational prediction models, and/or universal tumor testing, genetic testing is performed to confirm the diagnosis. Before and after genetic testing, genetic counseling should be provided. Genetic counseling should involve a detailed personal and family history, information on the disorder and genetic tests, discussion of the management and surveillance of the disease, career plan, family plan, and psychosocial support. Surveillance of colorectal cancer and other malignancies is of paramount importance for properly managing Lynch syndrome. This review focuses on important considerations in genetic counseling and the latest insights into the surveillance of individuals and families with Lynch syndrome.

Challenges to informed consent for exome sequencing: A best-worst scaling experiment

As exome sequencing expands as a diagnostic tool, patients and providers have voiced concerns about communicating the breadth and scope of potential results when obtaining informed consent. This study aimed to understand how genetic counselors prioritize essential components of the informed consent process and whether counselor factors influence these decisions. Development of a best-worst scaling experiment was informed by a systematic literature review and two focus groups. In all, 11 choice sets were created using a balanced incomplete block design, where participants selected the most and least important object in each set. Mean best-worst (BW) scores were calculated to summarize the relative importance of each object, and mediation analyses assessed whether responses were associated with genetic counselor factors and attitudes. In all, 342 members of the National Society of Genetic Counselors completed the online survey. Ranking of BW scores suggests that participants prioritize collaborative decision-making, assessing understanding and managing expectations, with the least emphasis placed on discussing technological complexities. Stratified analyses found that counselors more experienced with obtaining informed consent for exome sequencing and those reporting higher perceptions of patients' ability to manage information rated discussing variants of uncertain significance as significantly more important (p < .05). Our results suggest that genetic counselors report intentions to prioritize individual patient needs when obtaining informed consent for exome sequencing. Professional characteristics and attitudes may influence preemptive discussion of uncertain results.

Exploring genetic counselors' perceptions of usefulness and intentions to use refined risk models in clinical care based on the Technology Acceptance Model (TAM)

Pathogenic germline mutations in the BRCA1 or BRCA2 genes are associated with an elevated lifetime risk for breast (50%-85% risk) and ovarian cancer (20%-40% risk). Genome-wide association studies have identified over 100 genetic variants associated with modified breast and/or ovarian cancer risk in BRCA1 and BRCA2 carriers. Risk models generated based on these variants have shown that these genetic modifiers strongly influence absolute risk of developing breast or ovarian cancer in BRCA mutation carriers. There is a lack of understanding, however, about the clinical applicability and utility of these risk models. To investigate this gap, we collected survey data from 274 cancer genetic counselors (GCs) through the National Society of Genetic Counselors Cancer Special Interest Group. Questions assessed perceptions of usefulness and intentions of genetic counselors to use these refined risk models in clinical care based on the Technology Acceptance Model (TAM). We found that GCs' reactions to the estimates were largely positive, though they thought the possibility of changing management based on results was unlikely. Additionally, we found that more experienced GCs were more likely to consider refined risk estimates in clinic. Support also was provided for core predictions within the TAM, whereby the perceived usefulness (indirect effect est. = 0.08, 95% CI: [0.04, 0.13]) and perceived ease of use (indirect effect est. = 0.078, 95% CI: [0.04, 0.13]) of refined risk estimates were indirectly associated with intentions to use via attitudes.

Perspectives on facilitating whole exome sequencing for international patients at Mayo Clinic

Whole exome sequencing (WES) has become a fundamental component of genetic evaluation and diagnosing rare genetic diseases. This test is now offered to patients from a wide variety of cultural backgrounds and in various clinical and research settings. This commentary is a reflection of one group of clinical genetic counselors' experiences in facilitating WES for patients who come from outside the United States for genetic evaluation and pursue WES. This patient population in our clinic primarily consists of individuals from the Middle East and presents recurrent logistical and counseling challenges. We aim to describe our international patient population, illuminate the challenges we have faced and illustrate how we have addressed these challenges.

An examination of the factors contributing to the expansion of subspecialty genetic counseling

In recent years, genetic counselors have moved into increasingly varied areas of patient care. Yet limited information is known about how these genetic counselors transitioned from more general clinical practice to subspecialized practice. This study was designed to answer three research questions: (1) What common factors establish a need for a genetic counselor in a subspecialty setting? (2) How do genetic counselors in subspecialties establish their positions? (3) Once established, how do the positions of these genetic counselors evolve as the subspecialty expands? Phone interviews with subspecialized genetic counselors led to the development of an online survey distributed through the National Society of Genetic Counselors ListServ. Sixty-eight of the 144 initial participants met eligibility criteria for participation as subspecialty genetic counselors in a clinical role. Physician interest in hiring a genetic counselor, clinical need, genetic counselor interest in subspecialty area, and available genetic testing were commonly reported as contributing factors to position creation. Most subspecialty genetic counseling positions were created as new positions, rather than evolved from a previous position. Over time, subspecialty positions drew more departmental funding and included increased clinical coordination or administrative responsibilities. The results of this study can encourage genetic counselors to collaborate with their medical institutions to utilize their skill-set in diverse areas of patient care.

Parental perceptions of prenatal whole exome sequencing (PPPWES) study

OBJECTIVE

The objective of the study is to investigate the experiences of couples who underwent prenatal whole-exome sequencing (WES) for fetal anomalies and the amount/type of information couples want from prenatal WES.

METHOD

Participants in the Fetal Sequencing Study who had genetic testing for fetal anomalies were invited for a semistructured interview about their experience with prenatal WES. A constructivist grounded theory approach with an inductive coding style was used for coding and analysis.

RESULTS

We interviewed 29 participants from 17 pregnancies. Two pregnancies had positive prenatal WES results, and 4 were terminated prior to receipt of WES results. The main themes were anxiety and stress around the time of diagnosis, education and consent for WES, coping and support while waiting for results, and receiving genetic testing results. In response to hypothetical scenarios probing the desire for uncertain results, 86% would like to be told about results for which the provider had some degree of uncertainty, and the percent desiring results decreased as the certainty of the results decreased.

CONCLUSION

Participants' experience with exome sequence was similar to other prenatal genetic diagnostic tests, except for the longer wait time for results. When probed with hypothetical scenarios, participants desired more results than were provided in the study, including uncertain results that might diagnose the fetal condition. This highlights the need for specialized prenatal genetic counseling to have nuanced discussions of multiple dimensions of uncertainty with implementation of prenatal WES.

The elusive ideal of inclusiveness: lessons from a worldwide survey of neurologists on the ethical issues raised by whole-genome sequencing

The anticipation of ethical issues that may arise with the clinical use of genomic technologies is crucial to envision their future implementation in a manner sensitive to local contexts. Yet, populations in low- and middle-income countries are underrepresented in studies that aim to explore stakeholders’ perspectives on the use of such technologies. Within the framework of a research project entitled “Personalized medicine in the treatment of epilepsy”, we sought to increase inclusiveness by widening the reach of our survey, inviting neurologists from around the world to share their views and practices regarding the use of whole-genome sequencing in clinical neurology and its associated ethics. We discuss herein the compelling scientific and ethical reasons that led us to attempt to recruit neurologists worldwide, despite the lack, in many low- or middle-income countries, of access to genomic technologies. Recruitment procedures and their results are presented and discussed, as well as the barriers we faced. We conclude that inclusive recruitment remains a challenging, albeit necessary and legitimate, endeavour.

How, who, and when: preferences for delivery of genome sequencing results among women diagnosed with breast cancer at a young age

Background

The increasing use of genome sequencing with patients raises a critical communication challenge: return of secondary findings. While the issue of what sequencing results should be returned to patients has been examined, much less attention has been paid to developing strategies to return these results in ways that meet patients' needs and preferences. To address this, we investigated delivery preferences (i.e., who, how, when) for individual genome sequencing results among women diagnosed with breast cancer at age 40 or younger.

Methods

We conducted 60 semistructured, in‐person individual interviews to examine preferences for the return of different types of genome sequencing results and the reasons underlying these preferences. Two coders independently coded interview transcripts; analysis was conducted using NVivo 10.

Results

The major findings from the study were that: (1) many participants wanted sequencing results as soon as possible, even at the time of breast cancer diagnosis; (2) participants wanted an opportunity for an in‐person discussion of results; and (3) they put less emphasis on the type of person delivering results than on the knowledge and communicative skills of that person. Participants also emphasized the importance of a results return process tailored to a patient's individual circumstances and one that she has a voice in determining.

Conclusions

A critical goal for future transdisciplinary research including clinicians, patients, and communication researchers may be to develop decision‐making processes to help patients make decisions about how they would like various sequencing results returned.

While the issue of what genome sequencing results should be returned to patients has been examined, much less attention has been paid to developing strategies to return these results in ways that meet patients' needs and preferences. To address this, we investigated delivery preferences (i.e., who, how, when) for individual genome sequencing results among women diagnosed with breast cancer at age 40 or younger. The major findings from the study were that: (1) many participants wanted sequencing results as soon as possible, even at the time of breast cancer diagnosis; (2) participants wanted an opportunity for an in‐person discussion of results; and (3) they put less emphasis on the type of person delivering results than on the knowledge and communicative skills of that person.

Research participant interest in primary, secondary, and incidental genomic findings

PURPOSE

To define the frequency with which adult research participants consent to be offered clinically validated research genetic test results (RR) and incidental findings (IF).

METHODS

Consents were obtained from 506 adults enrolled in one of three studies within the National Cancer Institute Clinical Genetics Branch's Familial Cancer Research Program. A cross-sectional analysis was performed involving the choices indicated on study consents regarding receipt of RR and IF.

RESULTS

Ninety-seven percent opted to receive RR and IF. Participants who declined (n = 16) included two cancer survivors who were mutation-positive (1 = RR and 1 = both), eight who knew their primary mutation status (3 = RR; 4 = IF; 1 = both), three nonbloodline relatives (1 = RR; 2 = both), one untested but with the syndromic phenotype (1 = IF), and two parents of an affected child (2 = both). We speculate that these individuals either already had sufficient information, were not prepared to learn more, or felt that the information would not change their personal health-care decision making.

CONCLUSIONS

Adult research participants from families at high genetic risk for cancer overwhelmingly indicated their preference to receive both RR and IF. Future research will seek to identify the reasons for declining RR and IF and to study the impact of receipt of RR and IF on personal medical decision making.Genet Med 18 12, 1218-1225.

Unsolicited findings of next-generation sequencing for tumor analysis within a Dutch consortium: clinical daily practice reconsidered

Cancer patients participating in studies involving experimental or diagnostic next-generation sequencing (NGS) procedures are confronted with the possibility of unsolicited findings. The Center for Personalized Cancer Treatment (CPCT), a Dutch consortium of cancer centers, is offering centralized large-scale NGS for the discovery of somatic tumor mutations with their germline DNA as reference. The CPCT aims to give all cancer patients with advanced disease stages access to tumor DNA analysis in order to improve selection for experimental therapy. In this article, our experiences at the CPCT will serve as an example to discuss the ethical and practical aspects regarding the management of unsolicited findings in personalized cancer research and treatment. Generic issues, relevant for all researchers in this field are discussed and illustrated by description of three patients faced with an unsolicited DNA finding, while they intended to be candidate for future anticancer treatment by participating in a trial that included NGS of both somatic and germline DNA. As options for DNA analysis expand and costs decrease rapidly, more and more patients are offered large-scale NGS testing. After reviewing current recommendations in literature, we conclude that classical informed consent procedures need to be adapted to become more explicit in asking patients if they want to be informed about unsolicited findings and if so, what level of detail of genetic risk information exactly they want to be returned after the analysis.

Parents' Perspectives on Supporting Their Decision Making in Genome-Wide Sequencing

PURPOSE

The purpose of this study was to explore parents' perceptions of their decisional needs when considering genome-wide sequencing (GWS) for their child. This is a partial report and focuses on how parents prefer to receive education and information to support their decision making about GWS.

DESIGN

This study adopted an interpretive description qualitative methodological approach and used the concept of shared decision making and the Ottawa Decision Support Framework.

METHODS

Participants were parents who had already consented to GWS, and had children with undiagnosed conditions that were suspected to be genetic in origin. Fifteen parents participated in a focus group or individual interview. Transcriptions were analyzed concurrently with data collection, iteratively, and constantly compared to one another. Repeat interviews were conducted with five of the parents to confirm, challenge, or expand on the developing concepts.

FINDINGS

Participants felt that their decision to proceed with GWS for their child was an easy one. However, they expressed some unresolved decisional needs, including a lack of knowledge about certain topics that became relevant and important to them later and a need for more support and resources. Participants also had ongoing informational and psychosocial needs after the single clinical encounter where their decision making occurred.

CONCLUSIONS

Participants expressed unmet decisional needs, which may have influenced the quality of their decisions. The strategies that participants suggested may help create parent-tailored education, counseling, decision support, and informed consent processes.

CLINICAL RELEVANCE

Health care professionals who offer GWS for children should assess parents' values, priorities, and informational needs and tailor information accordingly. There are opportunities for nurses to become involved in supporting families who are considering GWS for their child.

The 3-I framework: a framework for developing public policies regarding pharmacogenomics (PGx) testing in Canada

The 3-I framework of analyzing the ideas, interests, and institutions around a topic has been used by political scientists to guide public policy development. In Canada, there is a lack of policy governing pharmacogenomics (PGx) testing compared to other developed nations. The goal of this study was to use the 3-I framework, a policy development tool, and apply it to PGx testing to identify and analyze areas where current policy is limited and challenges exist in bringing PGx testing into wide-spread clinical practice in Canada. A scoping review of the literature was conducted to determine the extent and challenges of PGx policy implementation at federal and provincial levels. Based on the 3-I analysis, contentious ideas related to PGx are (i) genetic discrimination, (ii) informed consent, (iii) the lack of knowledge about PGx in health care, (iv) the value of PGx testing, (v) the roles of health care workers in the coordination of PGx services, and (vi) confidentiality and privacy. The 3-I framework is a useful tool for policy makers, and applying it to PGx policy development is a new approach in Canadian genomics. Policy makers at every organizational level can use this analysis to help develop targeted PGx policies.

Evolving Roles for Physicians and Genetic Counselors in Managing Complex Genetic Disorders

Proponents of personalized medicine predict that genetic information will provide pivotal perspectives for the prevention and management of complex disorders. Personalized medicine differs from traditional Western medicine, in that it focuses on more complex disorders that require mechanistic disease modeling and outcome simulation by integrating genomic risk, environmental stressors, and biomarkers as indicators of disease state. This information could be useful to guide targeted therapy and prevent pathologic outcomes. However, gaps exist in the process of linking the pieces together; currently, genetic data are seldom used to assist physicians in clinical decision making. With rapid growth in genetic data and the requirements for new paradigms for complex disorders comes the need to train professionals to understand and manage the impact of genetic information on patients within these clinical settings. Here we describe the challenges, controversies, and opportunities for genetics and genetic counselors in managing complex disorders and discuss the rationale for modifications in genetic counselor training and function. We conclude that a major paradigm shift is underway and a compelling functional, ethical, and financial argument can be made for employing properly trained genetic counselors to be strategically positioned within the health-care industries that are responsible for managing complex disorders.

Reproductive genetic counseling challenges associated with diagnostic exome sequencing in a large academic private reproductive genetic counseling practice

OBJECTIVE

Diagnostic whole exome sequencing (WES) is rapidly entering clinical genetics, but experience with reproductive genetic counseling aspects is limited. The purpose of this study was to retrospectively review and report on our experience with preconception and prenatal genetic counseling for diagnostic WES.

METHOD

We performed a retrospective chart review over 34 months in a large private prenatal genetic counseling practice and analyzed data for referral indications, findings, and results of genetic counseling related to diagnostic WES.

RESULTS

Ten of 14 patients counseled about diagnostic WES for ongoing pregnancies pursued the test, resulting in identification of three pathogenic variants (30%). Five of 15 patients seeking counseling about familial WES results in an affected proband pursued prenatal diagnosis, resulting in identification of one affected fetus and five unaffected fetuses. We experienced challenges related to complexity and uncertainty of results, turnaround time, cost and insurance overage, and multidisciplinary fetal care coordination.

CONCLUSION

Despite having experienced complexity and identified challenges of the reproductive genetic counseling, availability of diagnostic WES contributed important information that aided in prenatal care planning and decision-making. Future enhanced provider education and larger studies to systematically study the integration of WES in reproductive genetic counseling and prenatal care will be important.

Malignant hyperthermia: a review

Malignant hyperthermia (MH) is a pharmacogenetic disorder of skeletal muscle that presents as a hypermetabolic response to potent volatile anesthetic gases such as halothane, sevoflurane, desflurane, isoflurane and the depolarizing muscle relaxant succinylcholine, and rarely, in humans, to stressors such as vigorous exercise and heat. The incidence of MH reactions ranges from 1:10,000 to 1: 250,000 anesthetics. However, the prevalence of the genetic abnormalities may be as great as one in 400 individuals. MH affects humans, certain pig breeds, dogs and horses. The classic signs of MH include hyperthermia, tachycardia, tachypnea, increased carbon dioxide production, increased oxygen consumption, acidosis, hyperkalaemia, muscle rigidity, and rhabdomyolysis, all related to a hypermetabolic response. The syndrome is likely to be fatal if untreated. An increase in end-tidal carbon dioxide despite increased minute ventilation provides an early diagnostic clue. In humans the syndrome is inherited in an autosomal dominant pattern, while in pigs it is autosomal recessive. Uncontrolled rise of myoplasmic calcium, which activates biochemical processes related to muscle activation leads to the pathophysiologic changes. In most cases, the syndrome is caused by a defect in the ryanodine receptor. Over 400 variants have been identified in the RYR1 gene located on chromosome 19q13.1, and at least 34 are causal for MH. Less than 1 % of variants have been found in CACNA1S but not all of these are causal. Diagnostic testing involves the in vitro contracture response of biopsied muscle to halothane, caffeine, and in some centres ryanodine and 4-chloro-m-cresol. Elucidation of the genetic changes has led to the introduction of DNA testing for susceptibility to MH. Dantrolene sodium is a specific antagonist and should be available wherever general anesthesia is administered. Increased understanding of the clinical manifestation and pathophysiology of the syndrome, has lead to the mortality decreasing from 80 % thirty years ago to <5 % in 2006.

Genomic analysis in the clinic: benefits and challenges for health care professionals and patients in Brazil

Despite significant advances in the diagnosis and treatment of genetic diseases in the last two decades, there is still a significant proportion where a causative mutation cannot be identified and a definitive genetic diagnosis remains elusive. New genome-wide or high-throughput multiple gene tests have brought new hope to the field, since they can offer fast, cost-effective and comprehensive analysis of genetic variation. This is particularly interesting in disorders with high genetic heterogeneity. There are, however, limitations and concerns regarding the implementation of genomic analysis in everyday clinical practice, including some particular to emerging and developing economies, as Brazil. They include the limited number of actionable genetic variants known to date, difficulties in determining the clinical validity and utility of novel variants, growth of direct-to-consumer genetic testing using a genomic approach and lack of proper training of health care professionals to adequately request, interpret and use genetic information. Despite all these concerns and limitations, the availability of genomic tests has grown at an extremely rapid pace and commercially available services include initiatives in almost all areas of clinical genetics, including newborn and carrier screening. We discuss the benefits and limitations of genomic testing, as well as the ethical implications and the challenges for genetic education and enough available and qualified health care professionals, to ensure the adequate process of informed consent, meaningful interpretation and use of genomic data and definition of a clear regulatory framework in the particular context of Brazil.

Compare and contrast: a cross-national study across UK, USA and Greek experts regarding return of incidental findings from clinical sequencing

Return of incidental findings (IFs) from clinical sequencing has become a hotly debated topic over the past year. Efforts are being made by several bodies to provide guidance at both national and international levels; however, no studies comparing attitudes of experts across different countries have been published so far. Our goal was to investigate attitudes towards return of IFs from clinical sequencing across UK, USA and Greek experts. Thirty in-depth interviews were conducted with genetics and genomic experts with different backgrounds. Our study revealed more differences when experts were compared according to their professional background than their country. General principles guiding the decision-making and the feedback process were common across all experts but the details of integrating these tests might vary as different professionals reported different needs and attitudes.

Impact of a prospective review program for reference laboratory testing requests

OBJECTIVES

To control the cost of reference laboratory testing, to ensure that its usage is medically appropriate, and to review the contribution of reference testing to patient care at our institution.

METHODS

A multidisciplinary institutional committee was convened to manage the utilization of reference testing. A subset of tests was designated to be reviewed in real time by a team of clinical pathologists in consultation with clinical subject matter experts.

RESULTS

Twelve percent of testing requests, accounting for approximately 18% of send-out costs, were determined to be clinically unnecessary or would not produce actionable results at that point during that patient's care and were therefore not performed. This intervention, combined with insourcing of frequently requested tests, resulted in a reduction in the costs of reference testing to less than half of that predicted by the rate of growth from 2005 to 2009. Molecular diagnostic tests displayed a higher cost per test than other forms of testing but had a similar degree of clinical impact.

CONCLUSIONS

Formal prospective review of reference laboratory testing requests resulted in substantial cost containment and improved the efficiency of patient care.

Evolution of genetic techniques: past, present, and beyond

Genetics is the study of heredity, which means the study of genes and factors related to all aspects of genes. The scientific history of genetics began with the works of Gregor Mendel in the mid-19th century. Prior to Mendel, genetics was primarily theoretical whilst, after Mendel, the science of genetics was broadened to include experimental genetics. Developments in all fields of genetics and genetic technology in the first half of the 20th century provided a basis for the later developments. In the second half of the 20th century, the molecular background of genetics has become more understandable. Rapid technological advancements, followed by the completion of Human Genome Project, have contributed a great deal to the knowledge of genetic factors and their impact on human life and diseases. Currently, more than 1800 disease genes have been identified, more than 2000 genetic tests have become available, and in conjunction with this at least 350 biotechnology-based products have been released onto the market. Novel technologies, particularly next generation sequencing, have dramatically accelerated the pace of biological research, while at the same time increasing expectations. In this paper, a brief summary of genetic history with short explanations of most popular genetic techniques is given.

Practical considerations in the clinical application of whole-exome sequencing

Despite the exciting advent of whole-exome sequencing (WES) in medical genetics practices, the optimal interpretation of results requires further actions such as reconsidering clinical information and obtaining further laboratory testing. There are no published data to guide clinicians in this process. In a retrospective study on 93 patients who underwent clinical WES, we set out to assess and resolve these practical challenges. With the laboratories reporting a molecular diagnostic rate of 25.8%, the medical geneticists and the laboratories were 90% concordant in their interpretation of the WES results. Divergence occurred when the medical geneticist reconsidered clinical information and/or additional information regarding pathogenicity of a variant. Variants of uncertain significance were reported in 86% of patients, with 53.7% needing follow-up, such as additional laboratory tests and genotyping of family members. By layering clinical data (e.g. mode of inheritance and phenotypic fit) on to the laboratory results, we developed clinical categories for the WES results. These categories of definite diagnosis (14/93), likely diagnosis (8/93), possible diagnosis (13/93) and no diagnosis (58/93) could be used to convey results to patients uniformly. Our framework for a clinically informed interpretation of the results enhances the utility of WES within medical genetics practices.

Personalized medicine in oncology: ethical implications for the delivery of healthcare

While personalized medicine brings benefits for the treatment of cancer, there are still key ethical issues at stake in developing personalized medicine in oncology. We propose an ethical analysis of personalized medicine in oncology that highlights the particularities of cancer care, critically assesses the scientific advances behind personalized medicine in oncology and emphasizes fairness in resource allocation in the delivery of personalized healthcare. This allows for a broader understanding of the real impacts on both recipients and the healthcare system.

Developing patient-friendly genetic and genomic test reports: formats to promote patient engagement and understanding

With the emergence of electronic medical records and patient portals, patients are increasingly able to access their health records, including laboratory reports. However, laboratory reports are usually written for clinicians rather than patients, who may not understand much of the information in the report. While several professional guidelines define the content of test reports, there are no guidelines to inform the development of a patient-friendly laboratory report. In this Opinion, we consider patient barriers to comprehension of lab results and suggest several options to reformat the lab report to promote understanding of test results and their significance to patient care, and to reduce patient anxiety and confusion. In particular, patients’ health literacy, genetic literacy, e-health literacy and risk perception may influence their overall understanding of lab results and affect patient care. We propose four options to reformat lab reports: 1) inclusion of an interpretive summary section, 2) a summary letter to accompany the lab report, 3) development of a patient user guide to be provided with the report, and 4) a completely revised patient-friendly report. The complexity of genetic and genomic test reports poses a major challenge to patient understanding that warrants the development of a report more appropriate for patients.

Comparative effectiveness of next generation genomic sequencing for disease diagnosis: design of a randomized controlled trial in patients with colorectal cancer/polyposis syndromes

Whole exome and whole genome sequencing are applications of next generation sequencing transforming clinical care, but there is little evidence whether these tests improve patient outcomes or if they are cost effective compared to current standard of care. These gaps in knowledge can be addressed by comparative effectiveness and patient-centered outcomes research. We designed a randomized controlled trial that incorporates these research methods to evaluate whole exome sequencing compared to usual care in patients being evaluated for hereditary colorectal cancer and polyposis syndromes. Approximately 220 patients will be randomized and followed for 12 months after return of genomic findings. Patients will receive findings associated with colorectal cancer in a first return of results visit, and findings not associated with colorectal cancer (incidental findings) during a second return of results visit. The primary outcome is efficacy to detect mutations associated with these syndromes; secondary outcomes include psychosocial impact, cost-effectiveness and comparative costs. The secondary outcomes will be obtained via surveys before and after each return visit. The expected challenges in conducting this randomized controlled trial include the relatively low prevalence of genetic disease, difficult interpretation of some genetic variants, and uncertainty about which incidental findings should be returned to patients. The approaches utilized in this study may help guide other investigators in clinical genomics to identify useful outcome measures and strategies to address comparative effectiveness questions about the clinical implementation of genomic sequencing in clinical care.