Undiagnosed Genetic Conditions Research Articles

EP425: Parental impact of genome sequencing during the neonatal period

Genome sequencing (GS) can shorten the diagnostic odyssey for infants and children with suspected genetic conditions, but is often not performed during the neonatal period. It is unknown what impact the use of GS in critically-ill infants could have on parents and families. In particular, it is unknown whether receiving a genetic diagnosis early in infancy affects parental experience of guilt for the child’s condition or affects parent-baby attachment. In SouthSeq, part of the Clinical Sequencing Evidence-Generating Research Consortium, we evaluated GS as a first-line diagnostic tool for critically-ill infants with suspected but undiagnosed genetic conditions. Infants with findings suggestive of a genetic condition underwent GS with Sanger confirmation in probands and in parent samples, when available, to determine inheritance. Enrollment took place at participating nurseries in Alabama, Mississippi, Louisiana, and Kentucky. Families were randomized to receive GS results from either a genetic counselor or a non-genetics provider, typically a neonatologist. Using a purposive sampling strategy designed to overrepresent groups historically under-represented in biomedical research, families were selected to participate in interviews one to six months following disclosure of results. Interviews focused on parental experiences with participating in GS during the neonatal period, often in the context of neonatal intensive care. Of 640 infants who underwent GS in SouthSeq, 62 families participated in interviews. Parents were given the option of participating in interviews together with the child’s other parent or separately. A number chose separate interviews, resulting in 76 total interviews being conducted. When asked whether they felt receipt of their child’s results took place too early in their journey, too late, or at about the right time, most parents reported that results were received at the right time, typically when the child was 2-4 months of age. Many felt that if results had been received earlier in their infant’s course, while the child’s condition was more acute, they would have been too overwhelmed to process the result adequately. Many parents reported difficulty bonding with their infant, although they were dismissive of the possibility that the genetic result impaired bonding. Instead, they cited emotional distancing as a form of self-preservation, an overwhelming NICU environment, and the inability to take their child home soon after birth. Those who received a genetic diagnosis found this information useful for a number of reasons, including understanding the etiology of their child’s condition, reproductive decision-making, and long-term planning for the care of the child. Parents valued access to GS during the neonatal period. Although guilt and difficulty bonding were common experiences, most parents rejected the idea that these challenges were exacerbated by GS results. Although follow-up interviews would be useful to develop a longitudinal understanding of the impact of GS during the neonatal period, these findings support the use of GS during this period. In particular, these findings do not support delaying genetic testing, including GS, in order to avoid interfering with parent-baby bonding or to avoid overwhelming families early in their journey caring for a child with a congenital condition.

The long-term impact of receiving incidental findings on parents undergoing genome-wide sequencing.

Genome-wide (exome or genome) sequencing (GWS) has the potential to detect incidental findings (IFs): variants unrelated to the primary indication for testing that may be of medical or personal utility. As GWS becomes increasingly common in clinical practice, it is important to understand the impact of IFs on the individuals and their families. Our goal was to explore the immediate and long-term lived experience of individuals who received IFs as part of diagnostic GWS. We interviewed parents who received an IF as part of the CAUSES translational research study at Children's and Women's Health Centre of British Columbia. Five hundred families were offered trio-based GWS for their child with a suspected, undiagnosed genetic condition. Nine hundred and one of the 1000 parents chose to find out about IFs and 21 parents received an IF for themselves. Twelve of these parents participated in this study. They were interviewed an average of 2.3years after the IFs were returned. Thematic analysis of transcribed interviews revealed that the participants' decisions and motivations to receive IFs were influenced by personal values and beliefs and by having a child with a suspected genetic condition. Participants' experiences were also influenced by the type of IF received, having a personal or family history of a related condition, their personal interpretation and perceived utility of the information, and the impact of the IF on other family members. Participants expressed either no regret or mild decisional regret on the Decisional Regret Scale. Two years post results, most participants reported little negative impact from receiving the IF. The utility of the information varied: some reported lifestyle changes and proactive screening, while others felt the information may be more relevant in the future. Understanding the immediate and longer term impact of receiving IFs from GWS can inform both pre- and post-test genetic counseling.

Readdressing Short Stature in India: The "Long and the Short" of it.

Readdressing Short Stature in India: The "Long and the Short" of it.

After genomic testing results: Parents' long-term views.

Many parents are motivated to pursue genome-wide (exome or genome) sequencing to find a diagnosis for their child with a suspected but undiagnosed genetic condition. However, the impact of the genomic test extends beyond the provision of results and the so-called 'diagnostic odyssey'. Our goal was to quantify post-test decisional regret and characterize long-term, post-test experiences and unmet needs of the parents of children with suspected genetic diseases after they had received the results of genome-wide sequencing. Study participants were parents of children who underwent trio genome-wide sequencing as part of the CAUSES research study at Children's & Women's Health Centre of British Columbia. About half of the participants received a definite or likely genetic diagnosis after clinical interpretation of the genome-wide sequencing results. Parents who participated in the current study (n=121) completed the Decisional Regret Scale four weeks after receiving results. A subset of these parents (n=32) had semi-structured interviews a median of 7months (range 3-20months) after results disclosure and post-test genetic counseling. Most parents expressed either no regret or mild regret about having undergone genome-wide sequencing on both the Decisional Regret Scale and in the interviews. Parents whose children did not receive a genetic diagnosis were slightly more likely to have decisional regret on this quantitative scale. Analysis of transcribed interviews revealed the following major themes: (a) a lack of decisional conflict around having the testing; (b) a lack of decisional regret post-testing; (c) expressions of both relief and continued uncertainty around the meaning of a genetic diagnosis; (d) expression of initial disappointment and evolving interpretation surrounding a result yielding no genetic diagnosis; and (e) needing time to absorb the test results. Our results suggest that parents need time to absorb the testing results and that long-term post-test counseling, including acknowledging feelings of relief, loss, and disappointment, may help parents adapt to the genomic test results and assist families to anticipate and plan for the next steps in their child's medical trajectory, whether or not a diagnosis is found.

'We don't know what tomorrow will bring': Parents' experiences of caring for a child with an undiagnosed genetic condition.

Families and healthcare professionals caring for a sick or disabled child without a definitive diagnosis face unique challenges, particularly in relation to managing uncertainty, access to healthcare and coordination of care. There has been little research exploring the impact this has on families, their support needs or their experience of health services. This qualitative interview study included interviews with 14 mothers of children with undiagnosed genetic conditions. Transcripts were analysed using thematic analysis. Four themes emerged, uncovering overlapping patterns in the data: (1) living with complexity amidst uncertainty-'We don't know what tomorrow will bring'; (2) parental role-'I do everything I can'; (3) parental role-'Not coping is not an option'; and (4) support needs-'There's lots of help that just isn't out there'. The results clearly demonstrate the stresses faced when caring for a child with an undiagnosed genetic condition. Some themes are shared with the experience of other families caring for children with complex needs. However, parents were doing all they could for their child in the context of a life of uncertainty, with the absence of a clear diagnosis clearly causing additional stress that impacted on the whole family. Impact on their emotional and physical well-being was evident; they described times of feeling stressed, worried and anxious. They were confused due to being overloaded with information and frustrated by a lack of care coordination. Parents did not appear to prioritize their own well-being and held back their emotions to protect themselves and others. As a result, they had many unmet needs, particularly relating to emotional support.

Supporting families of children with an undiagnosed genetic condition: Using co-design to ensure the right person is in the right post doing the right job.

Families and professionals caring for a child without a definitive diagnosis face unique challenges, particularly in relation to managing uncertainty; access to healthcare; obtaining relevant information and support; and trying to navigate a healthcare system that is often fragmented. We used co-design to inform the establishment of the first UK specialist nursing post dedicated to working with children with undiagnosed genetic conditions and their families. (1) To understand what families and hospital staff want from the service; (2) To understand how the post should be operationalized in practice; (3) To develop the job description and person specification for the postholder. A range of approaches were used to collect data: interviews (nine parents and 10 hospital staff); a focus group (three parents); a creative workshop (six patients and siblings); and an online forum (81 parents). Data were analyzed using framework and thematic analysis. The strands of data were brought together and reviewed as a whole to formulate the postholder's job description and person specification. Stakeholders identified nine key elements to the role which were incorporated into the job description: practical support; point of contact; community liaison; signposting to other services; care coordination; supporting families; advocacy; raising awareness; and emotional support. Highlighted in this paper are the practical aspects of engaging and involving all relevant stakeholders in the process of co-designing a new post and subsequent staff recruitment. The flexibility employed in the setting and methods of data collection were instrumental in ensuring that the views of a diverse range of participants were ascertained. A major consideration is the resources required to undertake co-design, in terms of time and finances. We believe that the resources required for the co-design are offset by the advantages of having the right person in the right post, doing the right job.

Genome Sequencing as a Diagnostic Test in Children With Unexplained Medical Complexity

Children with medical complexity (CMC) represent a growing population in the pediatric health care system, with high resource use and associated health care costs. A genetic diagnosis can inform prognosis, anticipatory care, management, and reproductive planning. Conventional genetic testing strategies for CMC are often costly, time consuming, and ultimately unsuccessful. To evaluate the analytical and clinical validity of genome sequencing as a comprehensive diagnostic genetic test for CMC. In this cohort study of the prospective use of genome sequencing and comparison with standard-of-care genetic testing, CMC were recruited from May 1, 2017, to November 30, 2018, from a structured complex care program based at a tertiary care pediatric hospital in Toronto, Canada. Recruited CMC had at least 1 chronic condition, technology dependence (child is dependent at least part of each day on mechanical ventilators, and/or child requires prolonged intravenous administration of nutritional substances or drugs, and/or child is expected to have prolonged dependence on other device-based support), multiple subspecialist involvement, and substantial health care use. Review of the care plans for 545 CMC identified 143 suspected of having an undiagnosed genetic condition. Fifty-four families met inclusion criteria and were interested in participating, and 49 completed the study. Probands, similarly affected siblings, and biological parents were eligible for genome sequencing. Genome sequencing was performed using blood-derived DNA from probands and family members using established methods and a bioinformatics pipeline for clinical genome annotation. The primary study outcome was the diagnostic yield of genome sequencing (proportion of CMC for whom the test result yielded a new diagnosis). Genome sequencing was performed for 138 individuals from 49 families of CMC (29 male and 20 female probands; mean [SD] age, 7.0 [4.5] years). Genome sequencing detected all genomic variation previously identified by conventional genetic testing. A total of 15 probands (30.6%; 95% CI 19.5%-44.6%) received a new primary molecular genetic diagnosis after genome sequencing. Three individuals had novel diseases and an additional 9 had either ultrarare genetic conditions or rare genetic conditions with atypical features. At least 11 families received diagnostic information that had clinical management implications beyond genetic and reproductive counseling. This study suggests that genome sequencing has high analytical and clinical validity and can result in new diagnoses in CMC even in the setting of extensive prior investigations. This clinical population may be enriched for ultrarare and novel genetic disorders. Genome sequencing is a potentially first-tier genetic test for CMC.

Novel Mutations and Genes That Impact on Growth in Short Stature of Undefined Aetiology: The EPIGROW Study.

BackgroundChildren with short stature of undefined aetiology (SS-UA) may have undiagnosed genetic conditions.PurposeTo identify mutations causing short stature (SS) and genes related to SS, using candidate gene sequence data from the European EPIGROW study.MethodsFirst, we selected exonic single nucleotide polymorphisms (SNPs), in cases and not controls, with minor allele frequency (MAF) < 2%, whose carriage fitted the mode of inheritance. Known mutations were identified using Ensembl and gene-specific databases. Variants were classified as pathogenic, likely pathogenic, or variant of uncertain significance using criteria from the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. If predicted by ≥ 5/10 algorithms (eg, Polyphen2) to be deleterious, this was considered supporting evidence of pathogenicity. Second, gene-based burden testing determined the difference in SNP frequencies between cases and controls across all and then rare SNPs. For genotype/phenotype relationships, we used PLINK, based on haplotype, MAF > 2%, genotype present in > 75%, and Hardy Weinberg equilibrium P > 10–4.ResultsFirst, a diagnostic yield of 10% (27/263) was generated by 2 pathogenic (nonsense in ACAN) and a further 25 likely pathogenic mutations, including previously known missense mutations in FANCB, IGFIR, MMP13, NPR2, OBSL1, and PTPN11. Second, genes related to SS: all methods identified PEX2. Another 7 genes (BUB1B, FANCM, CUL7, FANCA, PTCH1, TEAD3, BCAS3) were identified by both gene-based approaches and 6 (A2M, EFEMP1, PRKCH, SOS2, RNF135, ZBTB38) were identified by gene-based testing for all SNPs and PLINK. ConclusionsSuch panels improve diagnosis in SS-UA, extending known disease phenotypes. Fourteen genes related to SS included some known to cause growth disorders as well as novel targets.

Critical Trio Exome Benefits In-Time Decision-Making for Pediatric Patients With Severe Illnesses.

Critical illnesses caused by undiagnosed genetic conditions are challenging in PICUs. Whole-exome sequencing is a powerful diagnostic tool but usually costly and often fail to arrive at a final diagnosis in a short period. We assessed the feasibility of our whole-exome sequencing as a tool to improve the efficacy of rare diseases diagnosis for pediatric patients with severe illness. Observational analysis. We employed a fast but standard whole-exome sequencing platform together with text mining-assisted variant prioritization in PICU setting over a 1-year period. A tertiary referral Children's Hospital in Taiwan. Critically ill PICU patients suspected of having a genetic disease and newborns who were suspected of having a serious genetic disease after newborn screening were enrolled. None. Around 50,000 to 100,000 variants were obtained for each of the 40 patients in 5 days after blood sampling. Eleven patients were immediately found be affected by previously reported mutations after searching mutation databases. Another seven patients had a diagnosis among the top five in a list ranked by text mining. As a whole, 21 patients (52.5%) obtained a diagnosis in 6.2 ± 1.1 working days (range, 4.3-9 d). Most of the diagnoses were first recognized in Taiwan. Specific medications were recommended for 10 patients (10/21, 47.6%), transplantation was advised for five, and hospice care was suggested for two patients. Overall, clinical management was altered in time for 81.0% of patients who had a molecular diagnosis. The current whole-exome sequencing algorithm, balanced in cost and speed, uncovers genetic conditions in infants and children in PICU, which helps their managements in time and promotes better utilization of PICU resources.

OP64 Implementation Of Whole Exome Sequencing For Rare Diseases

IntroductionThe Victorian Department of Health and Human Services provided AUD 25 million (i.e. USD 17.3 million) over four years to determine the place of whole exome sequencing (WES) for patients attending public genetics clinics. Comparative analysis of WES and ‘usual care’ determined that WES increased diagnosis rate (from 14 to 58 percent), changed clinical management in one third of patients and identified relatives and couples at high risk of recurrence in future pregnancies. Translating this into routine care requires co-design with clinical and laboratory stakeholders.MethodsVictoria's clinical and laboratory genetics service system uses a ‘hub and spoke’ model. Representatives from these were invited to join a ‘Clinical Adoption Group’ (CAG) to oversight implementation of new government funding (AUD 2 million (i.e. USD 1.4 million) per year) to ensure statewide access to, and funding of, WES for children with rare undiagnosed genetic conditions. The CAG developed terms of reference, ‘traffic light’ evidence-based eligibility criteria, a pricing model and reporting mechanism, and recommended funding for sequencing, curation, curator training and multidisciplinary team (MDT) meetings to support implementation.ResultsFunding was distributed across hub and spoke sites reflecting clinical and laboratory demand and workforce requirements. All cases demonstrated clinical utility and were reviewed at MDT meetings. To date, 37 percent of patients have received a diagnosis changing management, with equity of access between metropolitan and regional areas demonstrated. Eligibility criteria are reviewed as new evidence is published to ensure new evidence is incorporated, although curation capacity limits turn-around-times.ConclusionsCo-designing a statewide and evidence-based clinical model has resulted in sector (i.e. clinician and laboratory) buy-in and supported broad access to funded WES. In addition, the sector has developed a better understanding of how evidence informs policy and funding decisions, which has resulted in delivering equitable WES that provides early diagnosis leading to changed clinical management and cessation of unnecessary interventions.

Clinical reassessment of post-laboratory variant call format (VCF) files

Background: Next-generation sequencing has been leading the genetic study of human disease for the past 10 years, generating a huge amount of sequence variant data, which are stored in variant call format (VCF) files. The aim of the study was to reassess the utility of VCF files for reanalysis. Methodology: This is a descriptive observational study of Saudi patients with undiagnosed genetic conditions. VCF files from 20 samples were referred to the molecular laboratory by physicians for reanalysis using variant interpretation software. Results: Seven cases (n = 20) have been reported differently from the outside laboratory. This accounts for almost 35% of all cases and is mainly due to the ability to gather more information about the patient's phenotype. One whole-genome sequence (WGS) case changed from inconclusive to negative. In addition, we identified variants related to the patient's phenotype in six cases; two of them were WGS and four were whole-exome sequence, all reported as negative before the reanalysis. Conclusion: Comprehensive phenotyping of individuals is a crucial step in identifying candidate phenotype-related variants. We outline the benefit obtained from access to the patient's medical records and communication with referring physicians.

Genetic Testing among Children in a Complex Care Program.

Little is known about the pattern of genetic testing and frequency of genetic diagnoses among children enrolled in structured complex care programs (CCPs). Such information may inform the suitability of emerging genome diagnostics for this population. The objectives were to describe the proportion of children with undiagnosed genetic conditions despite genetic testing and measure the testing period, types and costs of genetic tests used. A retrospective analysis of 420 children enrolled in Toronto’s Hospital for Sick Children’s CCP from January 2010 until June 2014 was conducted. Among those who underwent genetic testing (n = 319; 76%), a random sample of 20% (n = 63) was further analyzed. A genetic diagnosis was confirmed in 48% of those who underwent testing. Those with no genetic diagnosis underwent significantly more genetic tests than those with a confirmed genetic diagnosis [median interquartile range (IQR): six tests (4–9) vs. three tests (2–4), p = 0.002], more sequence-level tests and a longer, more expensive testing period than those with a genetic diagnosis [median (IQR): length of testing period: 4.12 years (1.73–8.42) vs. 0.35 years (0.12–3.04), p < 0.001; genetic testing costs C$8496 ($4399–$12,480) vs. C$2614 ($1605–$4080), p < 0.001]. A genetic diagnosis was not established for 52% of children. Integrating genome-wide sequencing into clinical care may improve diagnostic efficiency and yield in this population.

Association of a Novel ACTA1 Mutation With a Dominant Progressive Scapuloperoneal Myopathy in an Extended Family.

New genomic strategies can now be applied to identify a diagnosis in patients and families with previously undiagnosed rare genetic conditions. The large family evaluated in the present study was described in 1966 and now expands the phenotype of a known neuromuscular gene. To determine the genetic cause of a slowly progressive, autosomal dominant, scapuloperoneal neuromuscular disorder by using linkage and exome sequencing. Fourteen affected individuals in a 6-generation family with a progressive scapuloperoneal disorder were evaluated. Participants were examined at pediatric, neuromuscular, and research clinics from March 1, 2005, to May 31, 2014. Exome and linkage were performed in genetics laboratories of research institutions. Examination and evaluation by magnetic resonance imaging, ultrasonography, electrodiagnostic studies, and muscle biopsies (n = 3). Genetic analysis included linkage analysis (n = 17) with exome sequencing (n = 7). Clinical findings included progressive muscle weakness in an initially scapuloperoneal and distal distribution, including wrist extensor weakness, finger and foot drop, scapular winging, mild facial weakness, Achilles tendon contractures, and diminished or absent deep tendon reflexes. Both age at onset and progression of the disease showed clinical variability within the family. Muscle biopsy specimens demonstrated type I fiber atrophy and trabeculated fibers without nemaline rods. Analysis of exome sequences within the linkage region (4.8 megabases) revealed missense mutation c.591C>A p.Glu197Asp in a highly conserved residue in exon 4 of ACTA1. The mutation cosegregated with disease in all tested individuals and was not present in unaffected individuals. This family defines a new scapuloperoneal phenotype associated with an ACTA1 mutation. A highly conserved protein, ACTA1 is implicated in multiple muscle diseases, including nemaline myopathy, actin aggregate myopathy, fiber-type disproportion, and rod-core myopathy. To our knowledge, mutations in Glu197 have not been reported previously. This residue is highly conserved and located in an exposed position in the protein; the mutation affects the intermolecular and intramolecular electrostatic interactions as shown by structural modeling. The mutation in this residue does not appear to lead to rod formation or actin accumulation in vitro or in vivo, suggesting a different molecular mechanism from that of other ACTA1 diseases.

An approach to pediatric exome and genome sequencing.

Exome and genome sequencing have recently emerged as clinical tools to resolve undiagnosed genetic conditions. Protocols are critically needed to identify proper patients for testing, select a test and laboratory, engage parents in shared decision-making, and for the return of results. Among well selected patients, the likelihood for identifying the causative gene change may be as high as 30%. It is key for pediatricians to consider whether sequencing should be the primary line of pursuit of a molecular diagnosis. Parents should understand the uncertainties inherent in this sequencing and the preference-based nature of testing. Pediatricians can engage in shared decision-making for this process and work to help parents make decisions consistent with their priorities and values. Upon receipt of a pathogenic mutation, discussion of the likelihood for future treatment is paramount to parents, as are the implications for recurrence within the family. Uncertainties inherent to genomic results need to be explained in the context of the likelihood of future research and discoveries. Pediatricians should make a deliberate decision with each patient whether to manage genomic testing on their own, refer the patient for such testing, or initiate the process and refer simultaneously. Regardless of which approach is taken, understanding the basics of this testing will allow the pediatrician to support the parents through the diagnostic process.

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions.

Diagnostic exome sequencing was immediately successful in diagnosing patients in whom traditional technologies were uninformative. Herein, we provide the results from the first 500 probands referred to a clinical laboratory for diagnostic exome sequencing. Family-based exome sequencing included whole-exome sequencing followed by family inheritance-based model filtering, comprehensive medical review, familial cosegregation analysis, and analysis of novel genes. A positive or likely positive result in a characterized gene was identified in 30% of patients (152/500). A novel gene finding was identified in 7.5% of patients (31/416). The highest diagnostic rates were observed among patients with ataxia, multiple congenital anomalies, and epilepsy (44, 36, and 35%, respectively). Twenty-three percent of positive findings were within genes characterized within the past 2 years. The diagnostic rate was significantly higher among families undergoing a trio (37%) as compared with a singleton (21%) whole-exome testing strategy. Overall, we present results from the largest clinical cohort of diagnostic exome sequencing cases to date. These data demonstrate the utility of family-based exome sequencing and analysis to obtain the highest reported detection rate in an unselected clinical cohort, illustrating the utility of diagnostic exome sequencing as a transformative technology for the molecular diagnosis of genetic disease.

Clinical application of exome sequencing in undiagnosed genetic conditions

BackgroundThere is considerable interest in the use of next-generation sequencing to help diagnose unidentified genetic conditions, but it is difficult to predict the success rate in a clinical setting that...

Klinefelter Syndrome: Awareness and Index of Suspicion

A.H., a 15-year-old boy, presents for an annual health maintenance visit. The child and family have struggled with his speech, language, and learning issues since the age of 3 years. The patient has recently been treated with antidepressants and mood stabilizers because of an uneven temperament ranging from extreme passivity and sadness to outward aggression. He is very tall for his age, has limited upper body strength, and complains of persistent fatigue. This patient exhibits signs and symptoms of a frequently undiagnosed genetic condition. A karyotype reveals a supernumerary X chromosome. A.H. is a male with 47 XXY chromosomes, and the diagnosis of Klinefelter syndrome is confirmed.

An unusual cause of collapse and neck pain

Following a collapse at home, a previously well 24-year-old Ukrainian man living in Ireland was brought to the emergency department. He complained of neck pain and cervical spine radiographs revealed...