Integrating Germline Genetics Into Precision Oncology Practice in the Veterans Health Administration: Challenges and Opportunities.

OBJECTIVES: The advent of germline testing as a standard-of-care practice for certain tumor types and patients presents unique opportunities and challenges for the field of precision oncology. This article describes strategies to address workforce capacity, organizational structure, and genetics education needs within the US Department of Veterans Affairs (VA) with the expectation that these approaches may be applicable to other health care systems. OBSERVATIONS: Germline information can have health, reproductive, and psychosocial implications for veterans and their family members, which can pose challenges when delivering germline information in the setting of cancer care. Additional challenges include the complexity inherent in the interpretation of germline information, the national shortage of genetics professionals, limited awareness and knowledge about genetic principles among many clinicians, and organizational barriers, such as the inability to order genetic tests and receive results in the electronic health record. These challenges demand thoughtful implementation planning at the health care system level to develop sustainable strategies for the delivery of high-quality genetic services in precision oncology practice. CONCLUSIONS: The VA is uniquely positioned to address the integration of germline genetic testing into precision oncology practice due to its outsized role in treating veterans with cancer, training the health care workforce, and developing, testing, and implementing innovative models of clinical care.

A logic model for precision medicine implementation informed by stakeholder views and implementation science.

PURPOSE: Precision medicine promises to improve patient outcomes, but much is unknown about its adoption within health-care systems. A comprehensive implementation plan is needed to realize its benefits. METHODS: We convened 80 stakeholders for agenda setting to inform precision medicine policy, delivery, and research. Conference proceedings were audio-recorded, transcribed, and thematically analyzed. We mapped themes representing opportunities, challenges, and implementation strategies to a logic model, and two implementation science frameworks provided context. RESULTS: The logic model components included inputs: precision medicine infrastructure (clinical, research, and information technology), big data (from data sources to analytics), and resources (e.g., workforce and funding); activities: precision medicine research, practice, and education; outputs: precision medicine diagnosis; outcomes: personal utility, clinical utility, and health-care utilization; and impacts: precision medicine value, equity and access, and economic indicators. Precision medicine implementation challenges include evidence gaps demonstrating precision medicine utility, an unprepared workforce, the need to improve precision medicine access and reduce variation, and uncertain impacts on health-care utilization. Opportunities include integrated health-care systems, partnerships, and data analytics to support clinical decisions. Examples of implementation strategies to promote precision medicine are: changing record systems, data warehousing techniques, centralized technical assistance, and engaging consumers. CONCLUSION: We developed a theory-based, context-specific logic model that can be used by health-care organizations to facilitate precision medicine implementation.

Stakeholders' views on the value of outcomes from clinical genetic and genomic interventions.

PURPOSE: Robust evidence about the value of clinical genomic interventions (CGIs), such as genetic/genomic testing or clinical genetic evaluation, is limited. We obtained stakeholders' perspectives on outcomes from CGIs to help inform their value. METHODS: We used an adapted Delphi expert panel process. Two anonymous survey rounds assessed the value of 44 CGI outcomes and whether a third party should pay for them, with discussion in between rounds. RESULTS: Sixty-six panelists responded to the first-round survey and 60 to the second. Policy-makers/payers gave the lowest ratings for value and researchers gave the highest. Patients/consumers had the most uncertainty about value and payment by a third party. Uncertainty about value was observed when evidence of proven health benefit was lacking, potential harms outweighed benefits for reproductive outcomes, and outcomes had only personal utility for individuals or family members. Agreement about outcomes for which a third party should not pay included prevention through surgery with unproven health benefits, establishing ancestry, parental consanguinity, and paternity. CONCLUSION: Research is needed to understand factors contributing to uncertainty and stakeholder differences about the value of CGI outcomes. Reaching consensus will accelerate the creation of metrics to generate the evidence needed to inform value and guide policies that promote availability, uptake, and coverage of CGIs.

Electronic health record interventions at the point of care improve documentation of care processes and decrease orders for genetic tests commonly ordered by nongeneticists.

OBJECTIVE: To determine whether electronic health record (EHR) tools improve documentation of pre- and postanalytic care processes for genetic tests ordered by nongeneticists. METHODS: We conducted a nonrandomized, controlled, pre-/postintervention study of EHR point-of-care tools (informational messages and template report) for three genetic tests. Chart review assessed documentation of genetic testing processes of care, with points assigned for each documented item. Multiple linear and logistic regressions assessed factors associated with documentation. RESULTS: Preimplementation, there were no significant site differences (P > 0.05). Postimplementation, mean documentation scores increased (5.9 (2.1) vs. 5.0 (2.2); P = 0.0001) and records with clinically meaningful documentation increased (score >5: 59 vs. 47%; P = 0.02) at the intervention versus the control site. Pre- and postimplementation, a score >5 was positively associated with abnormal test results (OR = 4.0; 95% CI: 1.8-9.2) and trainee provider (OR = 2.3; 95% CI: 1.2-4.6). Postimplementation, a score >5 was also positively associated with intervention site (OR = 2.3; 95% CI: 1.1-5.1) and specialty clinic (OR = 2.0; 95% CI: 1.1-3.6). There were also significantly fewer tests ordered after implementation (264/100,000 vs. 204/100,000; P = 0.03), with no significant change at the control site (280/100,000 vs. 257/100,000; P = 0.50). CONCLUSIONS: EHR point-of-care tools improved documentation of genetic testing processes and decreased utilization of genetic tests commonly ordered by nongeneticists.Genet Med 19 1, 112-120.

Reporting genomic secondary findings: ACMG members weigh in.

PURPOSE: The aim of this study was to survey American College of Medical Genetics and Genomics members about secondary findings from clinical genome-scale sequencing. METHODS: A Web-based survey was mailed to 1,687 members of the American College of Medical Genetics and Genomics. Exploratory factor analysis identified underlying factors assessed by survey items. Linear regression assessed associations between factor scores and respondent characteristics. RESULTS: The response rate was 29%. Four factors explained 51% of the survey variance: best practices, patient preferences, guidance, and informed consent. Most agreed with "best practice" items describing seeking and reporting of secondary findings as consistent with medical standards, having sufficient evidence, and, for adults, the benefits generally outweighing potential harms. There was lack of agreement regarding benefits versus harms for children and impact on health-care resources. The majority agreed that patient preferences should be considered, including ability to opt out, and that informed consent was feasible and critical. Characteristics significantly associated with factor scores included country of residence, sequencing experience, and years in practice. CONCLUSION: The American College of Medical Genetics and Genomics should update a list of genes to be assessed when clinical genome-scale sequencing is performed. Informed consent is necessary, and reporting of secondary findings should be optional. Research on implementation of secondary findings reporting is needed.

Duodenal atresia in 17q12 microdeletion including HNF1B: a new associated malformation in this syndrome.

Deletions of chromosome 17q12 [OMIM 614527] encompass a wide range of phenotypes, including renal cysts, diabetes mellitus, pancreatic structural abnormalities, genital tract anomalies, developmental delay, learning difficulties, and more recently, autism spectrum disorder and schizophrenia. To date, gastrointestinal malformations have not been fully characterized in this syndrome. In this case report, we describe a four-year-old girl with a 17q12 microdeletion who was born with duodenal atresia, bilateral renal cysts, left kidney dysplasia, a midline cystic structure at the conus medullaris, and dysmorphic features. Both the patient and her affected father were found to have a deletion of 17q12, which encompasses the HNF1B (hepatocyte nuclear factor beta). It is hypothesized that HNF1B may play a role in intestinal differentiation and development. Our clinical report further expands the pre-and post-natal presentation of this rare microdeletion syndrome.

A cancer genetics toolkit improves access to genetic services through documentation and use of the family history by primary-care clinicians.

PURPOSE: We developed, implemented, and evaluated a multicomponent cancer genetics toolkit designed to improve recognition and appropriate referral of individuals at risk for hereditary cancer syndromes. METHODS: We evaluated toolkit implementation in the women's clinics at a large Veterans Administration medical center using mixed methods, including pre-post semistructured interviews, clinician surveys, and chart reviews, and during implementation, monthly tracking of genetic consultation requests and use of a reminder in the electronic health record. We randomly sampled 10% of progress notes 6 months before (n = 139) and 18 months during implementation (n = 677). RESULTS: The toolkit increased cancer family history documentation by almost 10% (26.6% pre- and 36.3% postimplementation). The reminder was a key component of the toolkit; when used, it was associated with a twofold increase in cancer family history documentation (odds ratio = 2.09; 95% confidence interval: 1.39-3.15), and the history was more complete. Patients whose clinicians completed the reminder were twice as likely to be referred for genetic consultation (4.1-9.6%, P < 0.0001). CONCLUSION: A multicomponent approach to the systematic collection and use of family history by primary-care clinicians increased access to genetic services.

Cleft Lip and Palate in a Patient with 5q35.2-q35.3 Microdeletion: The Importance of Chromosomal Microarray Testing in the Craniofacial Clinic.

We report on a 3½-year-old African American female with a 1.63 Mb microdeletion in 5q35.2-q35.3. This deletion includes NSD1, the gene that causes Sotos syndrome. The patient has unilateral cleft lip and palate (CLP) status postrepair, an unrepaired alveolar cleft, speech delay, global developmental delay, macrocephaly, mild cerebral palsy, and a patent ductus arteriosus status postrepair. Dysmorphic features include a prominent forehead and midface hypoplasia. This is one of the first cases of CLP associated with Sotos syndrome and emphasizes the utility of chromosomal microarray analysis in patients with more than isolated CLP in the Craniofacial Clinic.

Clinical findings associated with a de novo partial trisomy 10p11.22p15.3 and monosomy 7p22.3 detected by chromosomal microarray analysis.

We present the case of an 18-month-old boy with dysmorphic facial features, developmental delay, growth retardation, bilateral clubfeet, thrombocytopenia, and strabismus, whose array CGH analysis revealed concurrent de novo trisomy 10p11.22p15.3 and monosomy 7p22.3. We describe the patient's clinical presentation, along with his cytogenetic analysis, and we compare the findings to those of similar case reports in the literature. We also perform a bioinformatic analysis in the chromosomal regions of segmental aneuploidy to find genes that could potentially explain the patient's phenotype.

An exon 1 deletion in OTC identified using chromosomal microarray analysis in a mother and her two affected deceased newborns: implications for the prenatal diagnosis of ornithine transcarbamylase deficiency.

We describe the outcome of two consecutive pregnancies with a clinical presentation of ornithine transcarbamylase (OTC) deficiency (OTCD) without a molecular diagnosis. A 119kb deletion on Xp11.4 including the OTC gene was detected in the mother. The same deletion was identified in the blood spots from deceased male newborns. In patients with a clinical and biochemical presentation of OTCD and negative OTC sequencing, whole genome or targeted chromosomal microarray analysis (CMA) with coverage of the OTC and neighboring genes should be performed as a reflex test.