Clinical Sequencing Exploratory Research Research Articles

Parents’ Perspectives on Secondary Genetic Ancestry Findings in Pediatric Genomic Medicine

With advances in genome sequencing technologies, large-scale genome-wide sequencing has advanced our understanding of disease risk and etiology and contributes to the rapidly expanding genomic health services in pediatric settings. Because it is possible to return ancestry estimates following clinical genomic sequencing, it is important to understand the interest in ancestry results among families who may have the option of receiving these results. We conducted 26 semi-structured qualitative telephone interviews of parents with children/newborns with likely genetic conditions from two studies of clinical genome sequencing. Using a purposive sampling approach, we selected parents from the SouthSeq cohort, Clinical Sequencing Evidence-Generating Research (CSER Phase 2) project active in Alabama, Mississippi, and Louisiana, or an earlier Clinical Sequencing Exploratory Research (CSER Phase 1) initiative based in the same region. Our interviews focused on parental knowledge about, attitudes on, interest in, and preferences for receiving genetic ancestry results following clinical genome sequencing in the neonatal intensive care unit or in pediatric clinics. Overall, parents prioritized clinical results or results that would help guide the diagnosis and treatment of their child, but they were also interested in any genetic result, including genetic ancestry, that potentially could enhance the meaning of information on disease risk, prevention and screening guidance, or family planning. While parents thought that ancestry results would help them learn about themselves and their heritage, the had concerns over the privacy, security, and accuracy of genetic ancestry information, although parents indicated that they had greater trust in ancestry findings provided as part of clinical care compared with those offered commercially. Parents also wanted ancestry results to be returned in a timely manner by knowledgeable staff, with kid-friendly materials and online tools available to aid, as needed, in the understanding of their results. Taken together, our results highlight that despite being in high-stress situations, such as having a newborn in the neonatal intensive care unit, parents were interested in receiving genetic ancestry results along with their clinically relevant findings.

Everolimus improves the efficacy of dasatinib in PDGFRα-driven glioma.

Pediatric and adult high-grade gliomas (HGGs) frequently harbor PDGFRA alterations. We hypothesized that cotreatment with everolimus may improve the efficacy of dasatinib in PDGFRα-driven glioma through combinatorial synergism and increased tumor accumulation of dasatinib. We performed dose-response, synergism, P-glycoprotein inhibition, and pharmacokinetic studies in in vitro and in vivo human and mouse models of HGG. Six patients with recurrent PDGFRα-driven glioma were treated with dasatinib and everolimus. We found that dasatinib effectively inhibited the proliferation of mouse and human primary HGG cells with a variety of PDGFRA alterations. Dasatinib exhibited synergy with everolimus in the treatment of HGG cells at low nanomolar concentrations of both agents, with a reduction in mTOR signaling that persisted after dasatinib treatment alone. Prolonged exposure to everolimus significantly improved the CNS retention of dasatinib and extended the survival of PPK tumor-bearing mice (mutant TP53, mutant PDGFRA, H3K27M). Six pediatric patients with glioma tolerated this combination without significant adverse events, and 4 patients with recurrent disease (n = 4) had a median overall survival of 8.5 months. Our results show that the efficacy of dasatinib treatment of PDGFRα-driven HGG was enhanced with everolimus and suggest a promising route for improving targeted therapy for this patient population.

Psychological outcomes related to exome and genome sequencing result disclosure: a meta-analysis of seven Clinical Sequencing Exploratory Research (CSER) Consortium studies

PurposeAs exome and genome sequencing (ES/GS) enters the clinic, there is an urgent need to understand the psychological effects of test result disclosure. Through a Clinical Sequencing Exploratory Research (CSER), phase 1 (CSER1) Consortium collaboration, we evaluated participants’ psychological outcomes across multiple clinical settings. MethodsWe conducted a random effects meta-analysis of state anxiety (Hospital Anxiety and Depression Scale [HADS]/Generalized Anxiety Disorder 7-item), depressive symptoms (HADS/Personal Health Questionnaire 9-item), and multidimensional impact (i.e., test-related distress, uncertainty and positive impact: modified Multidimensional Impact of Cancer Risk Assessment/Feelings About Genomic Testing Results scale). ResultsAnxiety and depression did not increase significantly following test result disclosure. Meta-analyses examining mean differences from pre- to postdisclosure revealed an overall trend for a decrease in participants’ anxiety. We observed low levels of test-related distress and perceptions of uncertainty in some populations (e.g., pediatric patients) and a wide range of positive responses. ConclusionOur findings across multiple clinical settings suggest no clinically significant psychological harms from the return of ES/GS results. Some populations may experience low levels of test-related distress or greater positive psychological effects. Future research should further investigate the reasons for test-related psychological response variation.

Consent for clinical genome sequencing: considerations from the Clinical Sequencing Exploratory Research Consortium.

Implementing genome and exome sequencing in clinical practice presents challenges, including obtaining meaningful informed consent. Consent may be challenging due to test limitations such as uncertainties associated with test results and interpretation, complexity created by the potential for additional findings and high patient expectations. We drew on the experiences of research teams within the Clinical Sequencing Exploratory Research (CSER1) Consortium on informed consent for clinical genome and exome sequencing (CGES) to negotiate consensus considerations. We present six considerations for clinicians and 12 key points to communicate as they support patients in deciding whether to undergo CGES. These considerations and key points provide a helpful starting point for informed consent to CGES, grounded in the Clinical Sequencing Exploratory Research (CSER1) experience.

Secondary findings from clinical genomic sequencing: prevalence, patient perspectives, family history assessment, and health-care costs from a multisite study

PurposeClinical sequencing emerging in health care may result in secondary findings (SFs). MethodsSeventy-four of 6240 (1.2%) participants who underwent genome or exome sequencing through the Clinical Sequencing Exploratory Research (CSER) Consortium received one or more SFs from the original American College of Medical Genetics and Genomics (ACMG) recommended 56 gene-condition pair list; we assessed clinical and psychosocial actions. ResultsThe overall adjusted prevalence of SFs in the ACMG 56 genes across the CSER consortium was 1.7%. Initially 32% of the family histories were positive, and post disclosure, this increased to 48%. The average cost of follow-up medical actions per finding up to a 1-year period was $128 (observed, range: $0-$678) and $421 (recommended, range: $141-$1114). Case reports revealed variability in the frequency of and follow-up on medical recommendations patients received associated with each SF gene-condition pair. Participants did not report adverse psychosocial impact associated with receiving SFs; this was corroborated by 18 participant (or parent) interviews. All interviewed participants shared findings with relatives and reported that relatives did not pursue additional testing or care. ConclusionOur results suggest that disclosure of SFs shows little to no adverse impact on participants and adds only modestly to near-term health-care costs; additional studies are needed to confirm these findings.

Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience.

BackgroundClinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X‐linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed.MethodsRepresentatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project‐specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects.ResultsThe proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results.ConclusionFuture translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.

Clinical providers\u2019 experiences with returning results from genomic sequencing: an interview study

BackgroundCurrent medical practice includes the application of genomic sequencing (GS) in clinical and research settings. Despite expanded use of this technology, the process of disclosure of genomic results to patients and research participants has not been thoroughly examined and there are no established best practices.MethodsWe conducted semi-structured interviews with 21 genetic and non-genetic clinicians returning results of GS as part of the NIH funded Clinical Sequencing Exploratory Research (CSER) Consortium projects. Interviews focused on the logistics of sessions, participant/patient reactions and factors influencing them, how the sessions changed with experience, and resources and training recommended to return genomic results.ResultsThe length of preparation and disclosure sessions varied depending on the type and number of results and their implications. Internal and external databases, online resources and result review meetings were used to prepare. Respondents reported that participants’ reactions were variable and ranged from enthusiasm and relief to confusion and disappointment. Factors influencing reactions were types of results, expectations and health status. A recurrent challenge was managing inflated expectations about GS. Other challenges included returning multiple, unanticipated and/or uncertain results and navigating a rare diagnosis. Methods to address these challenges included traditional genetic counseling techniques and modifying practice over time in order to provide anticipatory guidance and modulate expectations. Respondents made recommendations to improve access to genomic resources and genetic referrals to prepare future providers as the uptake of GS increases in both genetic and non-genetic settings.ConclusionsThese findings indicate that returning genomic results is similar to return of results in traditional genetic testing but is magnified by the additional complexity and potential uncertainty of the results. Managing patient expectations, initially identified in studies of informed consent, remains an ongoing challenge and highlights the need to address this issue throughout the testing process. The results of this study will help to guide future providers in the disclosure of genomic results and highlight educational needs and resources necessary to prepare providers. Future research on the patient experience, understanding and follow-up of recommendations is needed to more fully understand the disclosure process.

Why Patients Decline Genomic Sequencing Studies: Experiences from the CSER Consortium.

Clinical and research settings are increasingly incorporating genomic sequencing (GS) technologies. Previous research has explored reasons for declining genetic testing and participation in genetic studies; however, there is a dearth of literature regarding why potential participants decline participation in GS research, and if any of these reasons are unique to GS. This knowledge is essential to promote informed decision-making and identify potential barriers to research participation and clinical implementation. We aggregated data from seven sites across the National Institutes of Health's Clinical Sequencing Exploratory Research (CSER) consortium on each project's procedures for recruitment, and rates of and reasons for decline. Data were analyzed using descriptive statistics. The decline rate for enrollment at the seven CSER sites ranged from 12 to 64% (median 28%) and varied based on age and disease status. Projects differed in their protocols for approaching potential participants and obtaining informed consent. Reasons for declining GS research were reported for 1088 potential participants. Commonly cited reasons were similar to those reported for clinical single gene testing and non-GS genetic research. The most frequently cited reason for decline was study logistics (35%); thus, addressing logistical barriers to enrollment may positively impact GS study recruitment. Privacy and discrimination concerns were cited by 13% of decliners, highlighting the need for researchers and providers to focus educational efforts in this area. The potential psychological burden of pursuing and receiving results from GS and not wanting to receive secondary findings, a concern specific to GS, have been cited as concerns in the literature. A minority of potential participants cited psychological impact (8%) or not wanting to receive secondary findings (2%) as reasons for decline, suggesting that these concerns were not major barriers to participation in these GS studies. Further research is necessary to explore the impact, if any, of different participant groups or study protocols on rates of decline for GS studies. Future studies exploring GS implementation should consider using standardized collection methods to examine reasons for decline in larger populations and more diverse healthcare settings.

Analysis of state laws on informed consent for clinical genetic testing in the era of genomic sequencing.

This article assesses the adequacy of informed consent to clinical genetic testing laws based on an examination of 15 states with institutions that had been involved in a National Institutes of Health-supported Clinical Sequencing Exploratory Research Consortium project. We identified relevant statutory provisions through a legal search engine and included statutes that describe the informed consent requirements for clinical genetic testing and/or the protections for genetic material, information, or data. We found that statutory definitions were often limited in problematic ways, such as focusing only on variants known to be associated with disease or negative health effects or associated with asymptomatic disease. Some statutes required complex levels of detail if applied to genomic technologies and set confusing disclosure standards for current use and future access. Others had exceptions from informed consent requirements for future research use, limited requirements for the destruction of specimens as opposed to derived data, or linked key definitional components to the evolving concept of "identifiability." Further reform and research are needed to ensure that state law protections advance as rapidly as the science they aspire to enable.

Gratitude, protective buffering, and cognitive dissonance: How families respond to pediatric whole exome sequencing in the absence of actionable results.

Clinical genome and exome sequencing (CGES) may identify variants leading to targeted management of existing conditions. Yet, CGES often fails to identify pathogenic diagnostic variants and introduces uncertainties by detecting variants of uncertain significance (VUS) and secondary findings. This study investigated how families understand findings and adjust their perspectives on CGES. As part of NIH's Clinical Sequencing Exploratory Research Consortium, children were recruited from clinics at the Children's Hospital of Pennsylvania (CHOP) and offered exome sequencing. Primary pathogenic and possibly pathogenic, and some secondary findings were returned. Investigators digitally recorded results disclosure sessions and conducted 3-month follow up interviews with 10 adolescents and a parent. An interdisciplinary team coded all transcripts. Participants were initially disappointed with findings, yet reactions evolved within disclosure sessions and at 3-month interviews toward acceptance and satisfaction. Families erroneously expected, and prepared extensively, to learn about risk for common conditions. During disclosure sessions, parents and adolescents varied in how they monitored and responded to each others reactions. Several misinterpreted, or overestimated, the utility of findings to attribute meaning and achieve closure for the CGES experience. Participants perceived testing as an opportunity to improve disease management despite results that did not introduce new treatments or diagnoses. Future research may examine whether families experience cognitive dissonance regarding discrepancies between expectations and findings, and how protective buffering minimizes the burden of disappointment on loved ones. As CGES is increasingly integrated into clinical care providers must contend with tempering family expectations and interpretations of findings while managing complex medical care.

Pragmatic Tools for Sharing Genomic Research Results with the Relatives of Living and Deceased Research Participants.

Returning genomic research results to family members raises complex questions. Genomic research on life-limiting conditions such as cancer, and research involving storage and reanalysis of data and specimens long into the future, makes these questions pressing. This author group, funded by an NIH grant, published consensus recommendations presenting a framework. This follow-up paper offers concrete guidance and tools for implementation. The group collected and analyzed relevant documents and guidance, including tools from the Clinical Sequencing Exploratory Research (CSER) Consortium. The authors then negotiated a consensus toolkit of processes and documents. That toolkit offers sample consent and notification documents plus decision flow-charts to address return of results to family of living and deceased participants, in adult and pediatric research. Core concerns are eliciting participant preferences on sharing results with family and on choice of a representative to make decisions about sharing after participant death.

Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers.

PURPOSE:As massively parallel sequencing is increasingly being used for clinical decision-making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and have established a set of standards for variant calling in clinical sequencing applications.METHODS:To enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCid) to identify reduced coverage loci within genes or regions of particular interest. We used this framework to examine sequencing data from 500 patients generated in ten projects from sequencing centers in the NHGRI/NCI Clinical Sequencing Exploratory Research (CSER) Consortium.RESULTS:This approach identified reduced coverage regions in clinically relevant genes, including known clinically relevant loci that were uniquely missed at individual centers, in multiple centers, and in all centers.CONCLUSIONS:This report provides a process roadmap for clinical sequencing centers looking to perform similar analyses on their data.

How do providers discuss the results of pediatric exome sequencing with families?

This study provides preliminary data on the process and content of returning results from exome sequencing offered to children through one of the Clinical Sequencing Exploratory Research (CSER) projects. We recorded 25 sessions where providers returned diagnostic and secondary sequencing results to families. Data interpretation utilized inductive thematic analysis. Typically, providers followed a results report and discussed diagnostic findings using technical genomic and sequencing concepts. We identified four provider processes for returning results: teaching genetic concepts; assessing family response; personalizing findings; and strengthening patient-provider relationships. Sessions should reflect family interest in medical management and next steps, and minimize detailed genomic concepts. As the scope and complexity of sequencing increase, the traditional information-laden counseling model requires revision.

Navigating the research\u2013clinical interface in genomic medicine: analysis from the CSER Consortium

PurposeThe Clinical Sequencing Exploratory Research (CSER) Consortium encompasses nine National Institutes of Health–funded U-award projects investigating translation of genomic sequencing into clinical care. Previous literature has distinguished norms and rules governing research versus clinical care. This is the first study to explore how genomics investigators describe and navigate the research–clinical interface.MethodsA CSER working group developed a 22-item survey. All nine U-award projects participated. Descriptive data were tabulated and qualitative analysis of text responses identified themes and characterizations of the research–clinical interface.ResultsSurvey responses described how studies approached the research–clinical interface, including in consent practices, recording results, and using a research versus clinical laboratory. Responses revealed four characterizations of the interface: clear separation between research and clinical care, interdigitation of the two with steps to maintain separation, a dynamic interface, and merging of the two. All survey respondents utilized at least two different characterizations. Although research has traditionally been differentiated from clinical care, respondents pointed to factors blurring the distinction and strategies to differentiate the domains.ConclusionThese results illustrate the difficulty in applying the traditional bifurcation of research versus clinical care to translational models of clinical research, including in genomics. Our results suggest new directions for ethics and oversight.

Discordance in selected designee for return of genomic findings in the event of participant death and estate executor.

BackgroundLegal and ethical questions arise regarding disseminating genetic research results to family members in the event of a research participant's death; failure to return or return to legal next of kin or estate executor may not reflect participant desires. We sought to determine participant preferences for whether and to whom they would like their data released in the case of their death prior to receiving genomic results, focusing on whether the person selected was also their estate executor.MethodsThe University of Washington NEXT Medicine Study of the Clinical Sequencing Exploratory Research program previously reported participant preferences regarding designating an individual to receive genomic results in the event of death, including whether they want results shared, and if so, with what person. Participants were also asked whether this designee is executor of their will or estate.ResultsTo date, 61 individuals were asked about the concordance of their study designee and legal representative: 42 (69%) reported having a will or estate plan and of these, 14 (33%) chose someone other than their executor to receive their results. For the 14 who chose someone other than their estate executor to receive genetic results, 12 (86%) chose a family member, typically a biological relative, as their designee. Those with a different genomic designee than their executor were less likely to be partnered (P = 0.0024). For those partnered participants without an estate plan, spouses were not always chosen for return of genomic results.ConclusionFor one‐third of our participants, the individual deemed most appropriate by the participant to receive their genomic results was not the executor. In the absence of an explicit designation, HIPAA may prohibit access to genomic results to persons other than the executor; hence asking for designation at the time of study enrollment (or initiation of clinical testing) is important.

Abstract 3169: The benefits and burdens of assaying matched normal tissue when sequencing cancer genomes

Abstract Targeted sequencing assays are increasingly used to identify tumor mutations that guide therapeutic decisions. Interpretation of a cancer variant's origin and therapeutic impact poses analytical challenges. Recent studies have indicated that jointly analyzing a tumor with its matched normal can accurately discriminate between tumor-specific (somatic) and inherited (germline) mutations. Moreover, a NHGRI/NCI Clinical Sequencing Exploratory Research Consortium Tumor Working Group just released a set of guidelines recommending that laboratories performing cancer sequencing tests should include germline variants. However, procurement of a matched sample is often logistically impractical. In the absence of a matched normal, large databases and analytical techniques are currently used to identify cancer variants in tumor sequencing data. Whether the benefits outweigh the additional burden of sequencing the matched normal for accurate detection of cancer-relevant mutations remains an open question. To compare tumor-only and tumor/normal analysis of cancer samples, we collected a set of >100 formalin-fixed (FFPE) and fresh frozen cancer samples of various tumor types, where matched normal blood or adjacent tissue was available. We performed augmented target enrichment sequencing (exome and large cancer gene panel) of both DNA and RNA. The data was analyzed using cancer bioinformatics pipelines that detect base substitutions, small insertions/deletions, copy number alterations, and gene fusions in both tumor-only and tumor/normal modes. Variants were annotated using described clinical actionability filtering strategies. Analysis of germline variants for secondary findings was performed. We find that 67% of mutations detected in tumor-only mode are reclassified as germline variants when analyzed together with the matched normal sample. These include mutations in hereditary cancer predisposition genes, such as BRCA1, VHL, and other genes with ACMG guidelines that warrant germline variant classification and appropriate management. Clinically actionable mutations may be miscalled as somatic when a matched normal is not available; however, we find the definition of ‘actionable’ can greatly impact the results of this analysis. Finally, the use of newly available large datasets, such as ExAC, substantially decreases the number of miscalled somatic variants in the absence of a matched normal. The effects of administering targeted therapies to patients with germline mutations in the relevant gene are largely unknown. Mutations of putative germline origin may be important for hereditary cancer knowledge and tumor treatment, and should be reported as such. For NGS-based cancer interpretation to guide clinical decisions in a practical and cost-effective manner, highly optimized tumor-only and tumor/normal analyses must be available with proper attention to germline consent, classification and education. Citation Format: Elena Helman, Michael J. Clark, Ravi Alla, Sean M. Boyle, Shujun Luo, Selene Virk, Deanna Church, Parin Sripakdeevong, Jason Harris, Mirian karbelashvili, Christian Haudenschild, John West, Richard Chen. The benefits and burdens of assaying matched normal tissue when sequencing cancer genomes. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3169.

Practical considerations for implementing genomic information resources. Experiences from eMERGE and CSER.

To understand opinions and perceptions on the state of information resources specifically targeted to genomics, and approaches to delivery in clinical practice. We conducted a survey of genomic content use and its clinical delivery from representatives across eight institutions in the electronic Medical Records and Genomics (eMERGE) network and two institutions in the Clinical Sequencing Exploratory Research (CSER) consortium in 2014. Eleven responses representing distinct projects across ten sites showed heterogeneity in how content is being delivered, with provider-facing content primarily delivered via the electronic health record (EHR) (n=10), and paper/pamphlets as the leading mode for patient-facing content (n=9). There was general agreement (91%) that new content is needed for patients and providers specific to genomics, and that while aspects of this content could be shared across institutions there remain site-specific needs (73% in agreement). This work identifies a need for the improved access to and expansion of information resources to support genomic medicine, and opportunities for content developers and EHR vendors to partner with institutions to develop needed resources, and streamline their use - such as a central content site in multiple modalities while implementing approaches to allow for site-specific customization.

Effect of Public Deliberation on Attitudes toward Return of Secondary Results in Genomic Sequencing

The increased use of genomic sequencing in clinical diagnostics and therapeutics makes imperative the development of guidelines and policies about how to handle secondary findings. For reasons both practical and ethical, the creation of these guidelines must take into consideration the informed opinions of the lay public. As part of a larger Clinical Sequencing Exploratory Research (CSER) consortium project, we organized a deliberative democracy (DD) session that engaged 66 participants in dialogue about the benefits and risks associated with the return of secondary findings from clinical genomic sequencing. Participants were educated about the scientific and ethical aspects of the disclosure of secondary findings by experts in medical genetics and bioethics, and then engaged in facilitated discussion of policy options for the disclosure of three types of secondary findings: 1) medically actionable results; 2) adult onset disorders found in children; and 3) carrier status. Participants' opinions were collected via surveys administered one month before, immediately following, and one month after the DD session. Post DD session, participants were significantly more willing to support policies that do not allow access to secondary findings related to adult onset conditions in children (Χ 2 (2, N=62)=13.300, p=0.001) or carrier status (Χ 2 (2, N=60)=11.375, p=0.003). After one month, the level of support for the policy denying access to secondary findings regarding adult-onset conditions remained significantly higher than the pre-DD level, although less than immediately post-DD (Χ 2 (1, N=60)=2.465, p=0.041). Our findings suggest that education and deliberation enhance public appreciation of the scientific and ethical complexities of genome sequencing.

Consideration of Cosegregation in the Pathogenicity Classification of Genomic Variants

The American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) recently published important new guidelines aiming to improve and standardize the pathogenicity classification of genomic variants. The Clinical Sequencing Exploratory Research (CSER) consortium evaluated the use of these guidelines across nine laboratories. One identified obstacle to consistent usage of the ACMG-AMP guidelines is the lack of a definition of cosegregation as criteria for pathogenicity classification. Cosegregation data differ from many other types of pathogenicity data in being quantitative. However, the ACMG-AMP guidelines do not define quantitative criteria for use of these data. Here, such quantitative criteria, in an easily implementable form, are proposed.

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it hasthus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germlineand cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.