Evaluation of a two-step model of opportunistic genomic screening.

Increasing use of diagnostic genomic sequencing is pushing health services to confront the issue of opportunistic genomic screening (OGS). To date, OGS has been offered concomitant with diagnostic testing. In contrast, we piloted a service offering OGS after return of diagnostic testing results. Evaluation was designed to provide insights for future models of service and included patient surveys at three time points, semi-structured interviews with genetic counsellors (GCs) and a focus group with medical scientists. Uptake was relatively low: 83 of 200 patients approached (42%) attended the OGS service, with 81 accepting OGS. Whilst many who declined to attend the service cited practical barriers, others gave reasons that indicated this was a considered decision. Despite specific genetic counselling, one third of patients did not understand the scope of re-analysis. Yet after post-test counselling, all respondents with novel pathogenic additional findings (AF) understood the implications and reported relevant follow-up. Recall was high: five months after last contact, 75% recalled being offered OGS without prompting. GC interviews and patient survey responses provide insights into complexities that influence patient support needs, including diagnostic status and AF result type. There was no consensus among patients or professionals about when to offer OGS. There was a clear preference for multiple, flexible methods of information provision; achieving this whilst balancing patient support needs and resource requirements is a challenge requiring further investigation. Decisions about whether, when and how to offer OGS are complex; our study shows the two-step approach warrants further exploration.

Secondary use of genomic data: patients' decisions at point of testing and perspectives to inform international data sharing.

International sharing of genomic data files arising from clinical testing of patients is essential to further improve genomic medicine. Whilst the general public are reluctant to donate DNA for research, the choices patients actually make about sharing their clinical genomic data for future re-use (research or clinical) are unknown. We ascertained the data-sharing choices of 1515 patients having genomic testing for inherited conditions or cancer treatment from clinical consent forms. To understand the experiences and preferences of these patients, surveys were administered after test consent (RR 73%). Almost all patients (98%) consented to share their data. Survey respondents' decision recall was high (90%), but poorer if English was an additional language (p < 0.001). Parents deciding on behalf of children were over-represented amongst data-sharing decliners (p = 0.047) and decliners were more likely to believe that stored data could be easily reidentified (p < 0.001). A quarter of respondents did not know if reidentification would be easy and 44% of them were concerned about this possibility. Of those willing to share data overseas (60%), 23% indicated the recipient researcher's country would affect their decision. Most respondents (89%) desired some ongoing control over research use of their data. Four preliminary data-sharing profiles emerged; their further development could inform tailored patient resources. Our results highlight considerations for establishment of systems to make clinical genomic data files available for reanalysis locally and across borders. Patients' willingness to share their data - and value of the resulting research - should encourage clinical laboratories to consider sharing data systematically for secondary uses.

Two-step offer and return of multiple types of additional genomic findings to families after ultrarapid trio genomic testing in the acute care setting: a study protocol.

INTRODUCTION: As routine genomic testing expands, so too does the opportunity to look for additional health information unrelated to the original reason for testing, termed additional findings (AF). Analysis for many different types of AF may be available, particularly to families undergoing trio genomic testing. The optimal model for service delivery remains to be determined, especially when the original test occurs in the acute care setting. METHODS AND ANALYSIS: Families enrolled in a national study providing ultrarapid genomic testing to critically ill children will be offered analysis for three types of AF on their stored genomic data: paediatric-onset conditions in the child, adult-onset conditions in each parent and reproductive carrier screening for the parents as a couple. The offer will be made 3-6 months after diagnostic testing. Parents will have access to a modified version of the Genetics Adviser web-based decision support tool before attending a genetic counselling appointment to discuss consent for AF. Parental experiences will be evaluated using qualitative and quantitative methods on data collected through surveys, appointment recordings and interviews at multiple time points. Evaluation will focus on parental preferences, uptake, decision support use and understanding of AF. Genetic health professionals' perspectives on acceptability and feasibility of AF will also be captured through surveys and interviews. ETHICS AND DISSEMINATION: This project received ethics approval from the Melbourne Health Human Research Ethics Committee as part of the Australian Genomics Health Alliance protocol: HREC/16/MH/251. Findings will be disseminated through peer-review journal articles and at conferences nationally and internationally.

Making community voices heard in a research-health service alliance, the evolving role of the Community Advisory Group: a case study from the members' perspective.

BACKGROUND: The Melbourne Genomics Health Alliance (the Alliance) is a collaboration of leading hospitals, research and academic organisations, supported by its member organisations and the Victorian Government. The Alliance was set up by its members in 2013 to steer the translation of genomics, making it an integral part of health care in Victoria, Australia. The Community Advisory Group (CAG) was formed soon after, to give input and advice across the program. This was to ensure consideration of community values, perspectives and priorities, and knowledge translation for patient care. The CAG was charged with providing a strong community voice for the duration of the program. Appointed members were experienced consumer advocates with developed connections to the community. MAIN BODY: The Alliance progressed from an initial Demonstration Project (2013-2015) to a multifaceted program (2016-2020). The CAG worked strategically to help address complex issues, for example, communication, privacy, informed consent, ethics, patient experience, measurement and evaluation standards and policies, data storage and re-use of genomic data. Many aspects of translating genomics into routine care have been tackled, such as communicating with patients invited to have genomic testing, or their caregivers, and obtaining informed consent, clinical questions across 16 areas of health care, training and education of health and laboratory professionals, genomic data management and data-sharing. Evidence generated around clinical utility and cost-effectiveness led to government funding of testing for complex genetic conditions in children. CONCLUSION: The CAG activities, recorded in a CAG-inspired Activity register, span the full spectrum of information sharing and consultation to co-design and partnership. The CAG were involved at multiple levels of participation and in all tiers of activity including governance, development of policies and procedures, program planning and evaluation. Working relationships were built up and a level of trust instilled to advance the Alliance work program in ensuring an effective patient-care model of delivery of genomics. CAG input into project deliverables has been tangible. Less tangible contributions included presentations at external meetings and conferences, direct interactions at meetings with Alliance members, interactions with visitors and external experts, taking part in consultations with experts, state and federal government.

Melbourne Genomics Health Alliance was established in 2013 to steer genomics into health care in Victoria, Australia. The Community Advisory Group (CAG) was formed soon after to provide advice and insights from the patient perspective. The CAG has added value to the Alliance's complex research-to-clinical service program of work over eight years to date. Following an explanation of the program, the CAG members identified priority areas and mechanisms for their involvement. Areas that members were involved in included: communication, visual identity and website, patient portal and its evaluation, information management, consent processes, laboratory requirements, tools for patient experience and quality of life measures, predictive health issues study, storage and sharing of data, databases, CAG Communication Plan, the Patient Guide, role with Victorian Government Department of Health and Human Services, implementation plan, workshop to upskill patient advocates, financial and strategic planning. Members also presented on the role of the CAG at conferences and symposia. The balanced, trusting relationship that developed between the CAG, the Program Team and its governance structure was of great value to and an achievement for the Alliance. CAG input into project deliverables and impact was recorded in a CAG inspired Activity Register and has been very tangible. Their less tangible contribution to the project is also important. Contributions included presentations at external meetings, direct interactions at annual meetings with Alliance members, interactions with visitors and external experts, taking part in consultations with experts, state and federal government. These provided opportunities to influence mindsets.

Clinical impact of genomic testing in patients with suspected monogenic kidney disease.

PURPOSE: To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. METHODS: We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. RESULTS: ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). CONCLUSION: In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design.

Utility of clinical comprehensive genomic characterization for diagnostic categorization in patients presenting with hypocellular bone marrow failure syndromes.

Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a heterogeneous clinical entity with a broad differential diagnosis including both inherited and acquired causes. Accurate diagnostic categorization is critical to optimal patient care and detection of genomic variants in these patients may provide this important diagnostic and prognostic information. We performed real-time, accredited (ISO15189) comprehensive genomic characterization including targeted sequencing and whole exome sequencing in 115 patients with BMF syndrome (median age 24 years, range 3 months - 81 years). In patients with clinical diagnoses of inherited BMF syndromes, acquired BMF syndromes or clinically unclassifiable BMF we detected variants in 52% (12/23), 53% (25/47) and 56% (25/45) respectively. Genomic characterization resulted in a change of diagnosis in 30/115 (26%) including the identification of germline causes for 3/47 and 16/45 cases with pre-test diagnoses of acquired and clinically unclassifiable BMF respectively. The observed clinical impact of accurate diagnostic categorization included choice to perform allogeneic stem cell transplantation, disease-specific targeted treatments, identification of at-risk family members and influence of sibling allogeneic stem cell donor choice. Multiple novel pathogenic variants and copy number changes were identified in our cohort including in TERT, FANCA, RPS7 and SAMD9. Whole exome sequence analysis facilitated the identification of variants in two genes not typically associated with a primary clinical manifestation of BMF but also demonstrated reduced sensitivity for detecting low level acquired variants. In conclusion, genomic characterization can improve diagnostic categorization of patients presenting with hypoplastic BMF syndromes and should be routinely performed in this group of patients.

"It's something I've committed to longer term": The impact of an immersion program for physicians on adoption of genomic medicine.

OBJECTIVE: To foster implementation of genomic testing in medical care by providing a cadre of physicians with 'hands on' experience in genomics, positioning them as opinion leaders in their medical speciality. This paper presents qualitative evaluation of immediate outcomes, in particular its impact on peer interactions. METHODS: Program design and delivery was informed by implementation science, behavior change and experiential learning theories. Inductive content analysis of transcribed audio-recordings from semi-structured post-project interviews with all participants (n = 12) was conducted. RESULTS: Participants reported the immersion experience improved their genomic capability, established them as credible genomic experts within their speciality and altered their practice in genomic medicine. Participants reported strengthening and widening of peer-to-peer and interdisciplinary communication, with both passive diffusion and active dissemination of information to peers. Some also became a resource for genetic professionals. CONCLUSIONS: Genomic immersion participants described elements which support sustained integration of an innovation, including immediate changes (e.g. use of genomic tests) and wider impacts (e.g. professional networks). PRACTICE IMPLICATIONS: This study supports a role for immersion as a successful strategy for enhancing engagement of non-geneticist physicians in genomics. Additional study is needed to understand how immersion experiences change the delivery of genomic services at the provider, practice and health system level.

Evaluating the resource implications of different service delivery models for offering additional genomic findings.

PURPOSE: To evaluate the resource implications of different delivery models for the provision of additional findings (AF) in genomics from a health-care purchaser perspective. METHODS: Data from the Additional Findings study were used to develop and validate a discrete event simulation model that represented the pathway of delivering AF. Resource implications were estimated by microcosting the consultations, sample verifications, bioinformatics, curation, and multidisciplinary case review meetings. A proof-of-concept model was used to generate costing, and then the simulation model was varied to assess the impact of an automated analysis pipeline, use of telehealth consultation, full automation with electronic decision support, and prioritizing case review for cases with pathogenic variants. RESULTS: For the proof-of-concept delivery model, the average total cost to report AF was US$430 per patient irrespective of result pathogenicity (95% confidence interval [CI] US$375-US$489). However, the cost of per AF diagnosis was US$4349 (95% CI US$3794-US$4953). Alternative approaches to genetic counseling (telehealth, decision support materials) and to multidisciplinary case review (pathogenic AF cases only) lowered the total per patient cost of AF analysis and reporting by 41-51%. CONCLUSION: Resources required to provide AF can be reduced substantially by implementing alternative approaches to counseling and multidisciplinary case review.

Social media usage in family communication about genetic information: 'I no longer speak with my sister but she needed to know'.

The use of social media has become a ubiquitous form of communication. Little is known about whether social media is used in families to assist with the communication of genetic information. This study aimed to understand if and why individuals use social media to communicate genetic information to at-risk relatives. Individuals with either a pathogenic variant in a cancer-predisposing gene or a heterozygous pathogenic variant in an autosomal or X-linked recessive gene were surveyed about communicating genetic information to their at-risk relatives and their use of social media to assist this process. Surveys were sent to 323 individuals from a reproductive carrier screening program and 250 individuals from a familial cancer center. The 128 responses (response rate 25.2%) showed that while most participants (79.0%) did not use social media to communicate genetic information, those that did use social media (21.0%) found it to be helpful as it was easy, accessible and allowed individuals to overcome communication barriers. Genetic professionals should be aware that social media is being used by individuals to assist family communication about genetic information and should discuss this method of communication with individuals who are faced with communicating genetic information with their family.

Exome sequencing in newborns with congenital deafness as a model for genomic newborn screening: the Baby Beyond Hearing project.

PURPOSE: Genomic newborn screening raises practical and ethical issues. Evidence is required to build a framework to introduce this technology safely and effectively. We investigated the choices made by a diverse group of parents with newborns when offered tiered genomic information from exome sequencing. METHODS: This population-derived cohort comprised infants with congenital deafness. Parents were offered exome sequencing and choice regarding the scope of analysis. Options were choice A, diagnostic analysis only; choice B, diagnostic analysis plus childhood-onset diseases with medical actionability; or choice C, diagnostic analysis plus childhood-onset diseases with or without medical actionability. RESULTS: Of the 106 participants, 72 (68%) consented to receive additional findings with 29 (27.4%) selecting choice B and 43 (40.6%) opting for choice C. Family size, ethnicity, and age of infant at time of recruitment were the significant predictors of choice. Parents who opted to have additional findings analysis demonstrated less anxiety and decisional conflict. CONCLUSIONS: These data provide evidence from a culturally diverse population that choice around additional findings is important and the age of the infant when this choice is offered impacts on their decision. We found no evidence that offering different levels of genomic information to parents of newborns has a negative psychological impact.

Prospective Evaluation of the Utility of Whole Exome Sequencing in Dilated Cardiomyopathy.

Background Dilated cardiomyopathy may be heritable but shows extensive genetic heterogeneity. The utility of whole exome sequencing as a first-line genetic test for patients with dilated cardiomyopathy in a contemporary "real-world" setting has not been specifically established. Using whole exome sequencing with rigorous, evidence-based variant interpretation, we aimed to identify the prevalence of a molecular diagnosis in patients with dilated cardiomyopathy in a clinical setting. Methods and Results Whole exome sequencing was performed in eligible patients (n=83) with idiopathic or familial dilated cardiomyopathy. Variants were prioritized for curation in up to 247 genes and classified using American College of Medical Genetics and Genomics-based criteria. Ten (12%) had a pathogenic or likely pathogenic variant. Eight (10%) participants had truncating TTN variants classified as variants of uncertain significance. Five (6%) participants had variants of unknown significance according to strict American College of Medical Genetics and Genomics criteria but classified as either pathogenic or likely pathogenic by other clinical laboratories. Pathogenic or likely pathogenic variants were found in 8 genes (all within tier 1 genes), 2 (20%) of which are not included in a standard commercially available dilated cardiomyopathy panel. Using our bioinformatics pipeline, there was an average of 0.74 variants of uncertain significance per case with ≈0.75 person-hours needed to interpret each of these variants. Conclusions Whole exome sequencing is an effective diagnostic tool for patients with dilated cardiomyopathy. With stringent classification using American College of Medical Genetics and Genomics criteria, the rate of detection of pathogenic variants is lower than previous reports. Efforts to improve adherence to these guidelines will be important to prevent erroneous misclassification of nonpathogenic variants in dilated cardiomyopathy genetic testing and inappropriate cascade screening.

Exome sequencing in infants with congenital hearing impairment: a population-based cohort study.

Congenital hearing impairment (HI) is the most common sensory impairment and can be isolated or part of a syndrome. Diagnosis through newborn hearing screening and management through early intervention, hearing aids and cochlear implantation is well established in the Australian setting; however understanding the genetic basis of congenital HI has been missing. This population-derived cohort comprised infants with moderate-profound bilateral HI born in the 2016-2017 calendar years, detected through newborn hearing screening. Participants were recruited through an integrated paediatric, otolaryngology and genetics HI clinic and offered whole exome sequencing (WES) on a HiSeq4000 or NextSeq500 (Illumina) platform with a targeted average sequencing depth of 100x and chromosome microarray on the Illumina Infinium core exome-24v1.2 platform. Of those approached, 68% (106/156) consented to participate. The rate of genetic diagnosis was 56% (59/106), significantly higher than standard of care (GJB2/6 sequencing only), 21% (22/106). There were clinical implications for the 106 participants: 36% required no further screening, 9% had tailored screening initiated, 2% were offered treatment and 4% had informed care for a complex neurodevelopmental syndrome. WES in this cohort demonstrates the range of diagnoses associated with congenital HI and confirms the genetic heterogeneity of congenital HI. The high diagnostic yield and clinical implications emphasises the need for genomic sequencing to become standard of care.

A novel approach to offering additional genomic findings-A protocol to test a two-step approach in the healthcare system.

Internationally, the practice of offering additional findings (AFs) when undertaking a clinically indicated genomic test differs. In the USA, the recommendation is to include analysis for AFs alongside diagnostic analysis, unless a patient opts-out, whereas European and Canadian guidelines recommend opt-in models. These guidelines all consider the offer of AFs as an activity concurrent with the offer of diagnostic testing. This paper describes a novel two-step model for managing AFs within the healthcare system in Victoria, Australia and presents the study protocol for its evaluation. Adults who have received results of diagnostic whole exome sequencing undertaken within the healthcare system are invited to attend a genetic counseling appointment to consider reanalysis of their stored genomic data for AFs. The evaluation protocol addresses uptake, decision-making, understanding, counseling challenges, and explores preferences for future models of care. Recruitment commenced in November 2017 and will cease when 200 participants have been approached. When the study is concluded, the evaluation results will contribute to the evidence base guiding approaches to counseling and models of care for AFs.

Genetic Counseling in the Era of Genomics: What's all the Fuss about?

As genomic sequencing becomes more widely available in clinical settings for diagnostic purposes, a number of genetic counseling issues are gaining precedence. The ability to manage these issues will be paramount as genetic and non-genetic healthcare professionals navigate the complexities of using genomic technologies to facilitate diagnosis and inform patient management. Counseling issues arising when counseling for diagnostic genomic sequencing were identified by four genetic counselors with 10 years of collective experience providing genetic counseling in this setting. These issues were discussed and refined at a meeting of genetic counselors working in clinical genomics settings in Melbourne, Australia. Emerging counseling issues, or variations of established counseling issues, were identified from the issues raised. Illustrative cases were selected where pre- and post-test genetic counseling was provided in clinical settings to individuals who received singleton or trio WES with targeted analysis. Counseling issues discussed in this paper include a reappraisal of how genetic counselors manage hope in the genomic era, informed consent for secondary use of genomic data, clinical reanalysis of genomic data, unexpected or unsolicited secondary findings, and trio sequencing. The authors seek to contribute to the evolving understanding of genetic counseling for diagnostic genomic sequencing through considering the applicability of existing genetic counseling competencies to managing emerging counseling issues and discussing genetic counseling practice implications.

A protocol for whole-exome sequencing in newborns with congenital deafness: a prospective population-based cohort.

INTRODUCTION: The aetiology of congenital hearing loss is heterogeneous, and in many infants a genetic cause is suspected. Parents face a diagnostic odyssey when searching for a cause of their infant's hearing loss. Through the Melbourne Genomics Health Alliance, a prospective cohort of infants will be offered whole-exome sequencing (WES) with targeted analysis in conjunction with chromosome microarray to determine the genetic causes of congenital hearing loss. Parents will also be offered the opportunity to receive additional results from their infant's WES. METHODS: Eligible infants will be identified through the Victorian Infant Hearing Screening Program and offered an appointment in a paediatrician-run clinic, a genetics assessment and enrolment in the Victorian Childhood Hearing Impairment Longitudinal Databank. If parents consent to WES, genes causing deafness will be analysed and they can choose to obtain additional findings. For the additional results component, a modified laboratory protocol has been designed for reporting of results in the absence of a relevant phenotype. Parents' experience of being offered WES will be evaluated using surveys. DISCUSSION: This project will provide descriptive analysis of the genetic aetiology of congenital hearing loss in this cohort and may provide data on genotype-phenotype correlations. Additionally, choices regarding additional findings will be analysed. Participants will represent a diverse cross section of the population, increasing the ability to generalise results beyond the study group. Evaluation surveys will allow analysis of preferences around counselling, usefulness of a decision aid and adequacy of information provision.

Ownership of uncertainty: healthcare professionals counseling and treating women from hereditary breast and ovarian cancer families who receive an inconclusive BRCA1/2 genetic test result.

AIM: The aim of this study was to understand more fully how healthcare professionals deal with the uncertainty intrinsic in counseling and treating women from hereditary breast/ovarian cancer families who receive inconclusive BRCA1/2 genetic test results (genetic tests that do not find a mutation to account for the family history). METHODS: We conducted a small, qualitative, exploratory study using open-ended semistructured interviews of 12 geneticists, genetic counselor/nurses, oncologists, gynecologists, and breast surgeons at a major UK cancer center. We asked questions about how these professionals dealt with the large amount of uncertainty raised by an inconclusive result, how they communicated the uncertainty involved, their feelings about presenting medical management options based on information fraught with uncertainty, the role of the media, differences in perspectives by specialty, and personal feelings about the uncertainty. RESULTS: Based on themes generated by the data, we proposed the concept "ownership of uncertainty" (sole, shared, diffused, normalized, transferred) to explain how the professionals in this study dealt with this high degree of uncertainty. A shared ownership of uncertainty was the dominant model during the presentation of information given by the professionals as part of their consultation with their patients. However, the final decision for management was left primarily to the woman seeking advice, even though several of the professionals reported feeling uneasy about this. CONCLUSION: The concept "ownership of uncertainty" helps advance the understanding of how the healthcare professionals deal with the uncertainty intrinsic to an inconclusive BRCA1/2 genetic test result within the current social context.

Is no news good news? Inconclusive genetic test results in BRCA1 and BRCA2 from patients and professionals' perspectives.

BACKGROUND: Women from families with a high risk of breast or ovarian cancer in which genetic testing for mutations in the BRCA1/2 genes is inconclusive are a vulnerable and understudied group. Furthermore, there are no studies of the professional specialists who treat them - geneticists, genetic counsellors/nurses, oncologists, gynaecologists and breast surgeons. METHODS: We conducted a small qualitative study that investigated women who had developed breast cancer under the age of 45 and who had an inconclusive BRCA1/2 genetic diagnostic test (where no mutations or unclassified variants were identified). We arranged three focus groups for affected women and their close female relatives - 13 women took part. We also interviewed 12 health professionals who were involved in the care of these women. RESULTS: The majority of the women had a good grasp of the meaning of their own or a family member's inconclusive result, but a few indicated some misunderstanding. Most of the women in this study underwent the test for the benefit of others in the family and none mentioned that they were having the test purely for themselves. A difficult issue for sisters of affected women was whether or not to undertake prophylactic breast surgery. The professionals were sensitive to the difficulties in explaining an inconclusive result. Some felt frustrated that technology had not as yet provided them with a better tool for prediction of risk. CONCLUSIONS: Some of the women were left with the dilemma of what decision to make regarding medical management of their cancer risk. For the most part, the professionals believed that the women should be supported in whatever management decisions they considered best, provided these decisions were based on a complete and accurate understanding of the genetic test that had taken place in the family.