“Possibly positive or certainly uncertain?”: participants’ responses to uncertain diagnostic results from exome sequencing

PurposeClinical genome sequencing produces uncertain diagnostic results, raising concerns about how to communicate the method’s inherent complexities in ways that reduce potential misunderstandings and harm. This study investigates clinicians’ communications and patient/participant responses to uncertain diagnostic results arising from a clinical exome sequencing research study, contributing empirical data to the debate surrounding disclosure of uncertain genomic information.MethodsWe investigated the communication and impact of uncertain diagnostic results using ethnographic observations of result disclosures with 21 adults and 11 parents of child patients, followed by two semistructured interviews with these same participants.ResultsParticipants understood their uncertain results in ways that were congruent with clinical geneticists’ communications. They followed recommendations for further consultation, although family testing to resolve uncertainty was not always done. Participants were prepared for learning an uncertain result and grasped the key concept that it should not be used to guide health-care or other decisions. They did not express regret for having learned the uncertain result; most regarded it as potentially valuable in the future.ConclusionThis study suggests that uncertain diagnostic results from genome sequencing can be relayed to patients in ways they can understand and consistent with providers’ interpretations, without causing undue harm.     

Combining exome/genome sequencing with data repository analysis reveals novel gene–disease associations for a wide range of genetic disorders

PurposeWithin this study, we aimed to discover novel gene–disease associations in patients with no genetic diagnosis after exome/genome sequencing (ES/GS).MethodsWe followed two approaches: (1) a patient-centered approach, which after routine diagnostic analysis systematically interrogates variants in genes not yet associated to human diseases; and (2) a gene variant centered approach. For the latter, we focused on de novo variants in patients that presented with neurodevelopmental delay (NDD) and/or intellectual disability (ID), which are the most common reasons for genetic testing referrals. Gene–disease association was assessed using our data repository that combines ES/GS data and Human Phenotype Ontology terms from over 33,000 patients.ResultsWe propose six novel gene–disease associations based on 38 patients with variants in the BLOC1S1, IPO8, MMP15, PLK1, RAP1GDS1, and ZNF699 genes. Furthermore, our results support causality of 31 additional candidate genes that had little published evidence and no registered OMIM phenotype (56 patients). The phenotypes included syndromic/nonsyndromic NDD/ID, oral–facial–digital syndrome, cardiomyopathies, malformation syndrome, short stature, skeletal dysplasia, and ciliary dyskinesia.ConclusionOur results demonstrate the value of data repositories which combine clinical and genetic data for discovering and confirming gene–disease associations. Genetic laboratories should be encouraged to pursue such analyses for the benefit of undiagnosed patients and their families.     

Payer decision making for next-generation sequencing–based genetic tests: insights from cell-free DNA prenatal screening

PurposeCell-free DNA (cfDNA) prenatal screening tests have been rapidly adopted into clinical practice, due in part to positive insurance coverage. We evaluated the framework payers used in making coverage decisions to describe a process that should be informative for other sequencing tests.MethodsWe analyzed coverage policies from the 19 largest US private payers with publicly available policies through February 2016, building from the University of California San Francisco TRANSPERS Payer Coverage Policy Registry.ResultsAll payers studied cover cfDNA screening for detection of trisomies 21, 18, and 13 in high-risk, singleton pregnancies, based on robust clinical validity (CV) studies and modeled evidence of clinical utility (CU). Payers typically evaluated the evidence for each chromosomal abnormality separately, although results are offered as part of a panel. Starting in August 2015, 8 of the 19 payers also began covering cfDNA screening in average-risk pregnancies, citing recent CV studies and updated professional guidelines. Most payers attempted, but were unable, to independently assess analytic validity (AV).ConclusionPayers utilized the standard evidentiary framework (AV/CV/CU) when evaluating cfDNA screening but varied in their interpretation of the sufficiency of the evidence. Professional guidelines, large CV studies, and decision analytic models regarding health outcomes appeared highly influential in coverage decisions.Genet Med advance online publication 22 September 2016     

AUDIOME: a tiered exome sequencing–based comprehensive gene panel for the diagnosis of heterogeneous nonsyndromic sensorineural hearing loss

PurposeHereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing loss (NSHL) using an exome sequencing (ES) platform and targeted analysis for the curated genes.MethodsA tiered strategy was implemented for this test. Tier 1 includes combined Sanger and targeted deletion analyses of the two most common NSHL genes and two mitochondrial genes. Nondiagnostic tier 1 cases are subjected to ES and array followed by targeted analysis of the remaining AUDIOME genes.ResultsES resulted in good coverage of the selected genes with 98.24% of targeted bases at >15 ×. A fill-in strategy was developed for the poorly covered regions, which generally fell within GC-rich or highly homologous regions. Prospective testing of 33 patients with NSHL revealed a diagnosis in 11 (33%) and a possible diagnosis in 8 cases (24.2%). Among those, 10 individuals had variants in tier 1 genes. The ES data in the remaining nondiagnostic cases are readily available for further analysis.ConclusionThe tiered and ES-based test provides an efficient and cost-effective diagnostic strategy for NSHL, with the potential to reflex to full exome to identify causal changes outside of the AUDIOME test.     

Burden or benefit? Effects of providing education about and the option to request additional genomic findings from diagnostic exome sequencing: A randomized controlled trial

ObjectiveMany people prefer to learn secondary or “additional” findings from genomic sequencing, including findings with limited medical actionability. Research has investigated preferences for and effects of learning such findings, but not psychosocial and behavioral effects of receiving education about them and the option to request them, which could be burdensome or beneficial (e.g., causing choice overload or satisfying strong preferences, respectively).Methods335 adults with suspected genetic disorders who had diagnostic exome sequencing in a research study and were randomized to receive either diagnostic findings only (DF; n = 171) or diagnostic findings plus education about additional genomic findings and the option to request them (DF + EAF; n = 164). Assessments occurred after enrollment (Time 1), after return of diagnostic results and—for DF + EAF—the education under investigation (Time 2), and three and six months later (Times 3, 4).ResultsTime 2 test-related distress, test-related uncertainty, and generalized anxiety were lower in the DF + EAF group (ps = 0.025–0.043). There were no other differences.ConclusionsFindings show limited benefits and no harms of providing education about and the option to learn additional findings with limited medical actionability.Practice implicationsFindings can inform recommendations for returning additional findings from genomic sequencing (e.g., to research participants or after commercial testing).     

Improving hearing loss gene testing: a systematic review of gene evidence toward more efficient next-generation sequencing–based diagnostic testing and interpretation

PurposeWith next generation sequencing technology improvement and cost reductions, it has become technically feasible to sequence a large number of genes in one diagnostic test. This is especially relevant for diseases with large genetic and/or phenotypic heterogeneity, such as hearing loss. However, variant interpretation remains the major bottleneck. This is further exacerbated by the lack in the clinical genetics community of consensus criteria for defining the evidence necessary to include genes on targeted disease panels or in genomic reports, and the consequent risk of reporting variants in genes with no relevance to disease.MethodsWe describe a systematic evidence-based approach for assessing gene–disease associations and for curating relevant genes for different disease aspects, including mode of inheritance, phenotypic severity, and mutation spectrum.ResultsBy applying this approach to clinically available hearing loss gene panels with a total of 163 genes, we show that a significant number (45%) of genes lack sufficient evidence of association with disease and thus are expected to increase uncertainty and patient anxiety, in addition to intensifying the interpretation burden. Information about all curated genes is summarized. Our retrospective analysis of 539 hearing loss cases tested by our previous OtoGenomeV2 panel demonstrates the impact of including genes with weak disease association in laboratory wet-bench and interpretation processes.ConclusionOur study is, to our knowledge, the first to highlight the urgent need for defining the clinical validity of gene–disease relationships for more efficient and accurate clinical testing and reporting.     

Children with genetic conditions in the United States: Prevalence estimates from the 2016-2017 National Survey of Children’s Health

PurposeEstimating the overall prevalence of genetic conditions among children in the United States and the burden of these conditions on children and their families has been challenging. The redesigned National Survey of Children’s Health provides an opportunity to examine the prevalence and burden.MethodsWe used the combined 2016-2017 National Survey of Children’s Health to estimate the prevalence of genetic conditions among children aged 0 to 17 years (N = 71,522). Bivariate analyses were used to assess differences in sociodemographic characteristics, health-related characteristics, and health care utilization between children with and without genetic conditions.ResultsIn 2016-2017, the prevalence of children aged 0 to 17 years with a reported genetic condition was approximately 0.039, roughly equating to 2.8 million children. A greater percentage of children with genetic conditions had a physical (50.9% vs 24.8%), mental (27.9% vs 5.8%), or behavioral/developmental/intellectual condition (55.6% vs 14.4%) than children without a genetic condition. Furthermore, they used more care and had more unmet health needs (7.6% vs 2.9%).ConclusionThis study provides an estimate of the overall prevalence of children living with genetic conditions in the United States based on a nationally representative sample. It also highlights the physical, mental, and behavioral health needs among children with genetic conditions and their unmet health care needs.     

KIR alloreactivity based on the receptor–ligand model is associated with improved clinical outcomes of allogeneic hematopoietic stem cell transplantation: Result of single center prospective study

Receptors on natural killer (NK) cells, named killer immunoglobulin-like receptors (KIRs), recognize HLA class I alleles. Patients (n = 59) who received allogeneic hematopoietic stem cell transplantation (HSCT) from either a related (n = 17) or unrelated donor (n = 42) in Samsung Medical Center (Seoul, South Korea) were included. KIR mismatch was defined as incompatibility between the donor KIR and recipient KIR ligand (receptor–ligand model), and all cases were classified into the two broad haplotypes of KIR A and B. Patients with acute leukemia (n = 51, 86.4%) or myelodysplastic syndrome (n = 8, 13.6%) were included. Peripheral blood was used as the source of stem cells in all patients. Kaplan–Meier survival curves for overall survival (OS), disease-free survival (DFS), and cumulative incidence of relapse (CIR) favored recipients with a KIR-mismatched donor, although the differences were not statistically significant. In multivariate analysis, KIR mismatch was an independent prognostic indicator of a better OS (P = 0.010, HR = 0.148, 95% CI 0.034–0.639), DFS (P = 0.022, HR = 0.237, 95% CI 0.069–0.815), and CIR (P = 0.031, HR = 0.117, 95% CI 0.017–0.823). OS, DFS, and CIR did not differ significantly between the KIR A and B haplotypes.