Molecular diagnosis of long QT syndrome at 10 days of life by rapid whole genome sequencing

The Advantages, Challenges, and Future of Human-Induced Pluripotent Stem Cell Lines in Type 2 Long QT Syndrome

Type 2 long QT syndrome (LQT2) is the second most common subtype of long QT syndrome and is caused by mutations in KCHN2 encoding the rapidly activating delayed rectifier potassium channel vital for ventricular repolarization. Sudden cardiac death is a sentinel event of LQT2. Preclinical diagnosis by genetic testing is potentially life-saving.Traditional LQT2 models cannot wholly recapitulate genetic and phenotypic features; therefore, there is a demand for a reliable experimental model. Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) meet this challenge. This review introduces the advantages of the hiPSC-CM model over the traditional model and discusses how hiPSC-CM and gene editing are used to decipher mechanisms of LQT2, screen for cardiotoxicity, and identify therapeutic strategies, thus promoting the realization of precision medicine for LQT2 patients.

Pediatric Electrophysiology Device Needs: A Survey from the Pediatric and Congenital Electrophysiology Society Taskforce on Pediatric‐Specific Devices

Background

There are few US Food and Drug Administration (FDA)–approved devices specifically aimed at the pediatric patient with arrhythmia. This has led to a high off‐label utilization of devices in this vulnerable population. The Pediatric and Congenital Electrophysiology Society (PACES), the international organization representing pediatric and congenital heart disease arrhythmia specialists, developed a task force to comprehensively address device development issues relevant to pediatric patients with congenital arrhythmia.

Methods and Results

As a first step, the taskforce developed a 26‐question survey for the pediatric arrhythmia community to assess providers’ understanding of the FDA approval process, specifically in regard to pediatric labeling. There were 92/211 respondents (44%) with a >90% completion rate. The vast majority of respondents believed there was a paucity of devices available for children (96%). More than 60% of respondents stated that they did not understand the FDA regulatory process and were not aware of whether the devices they used were labeled for pediatric use.

Conclusions

Pediatric electrophysiologists are keenly aware of the deficit of available pediatric devices for their patients. The majority do not understand the FDA approval process and could benefit from additional educational resources regarding this. A collaborative forum including PACES, FDA, patients and their families, and Industry would be an important next step in clarifying opportunities and priorities to serve this vulnerable population.

Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing

Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nanopore WGS that combines an optimized sample preparation protocol, distributing sequencing over 48 flow cells, near real-time base calling and alignment, accelerated variant calling and fast variant filtration for efficient manual review. Application to two example clinical cases identified a candidate variant in <8 h from sample preparation to variant identification. We show that this framework provides accurate variant calls and efficient prioritization, and accelerates diagnostic clinical genome sequencing twofold compared with previous approaches.

A streamlined sequencing process enables identification of disease-causing variants in the clinic within 8 hours.

Thyroid hormones regulate cardiac repolarization and QT-interval related gene expression in hiPSC cardiomyocytes

Prolongation of cardiac repolarization (QT interval) represents a dangerous and potentially life-threatening electrical event affecting the heart. Thyroid hormones (THs) are critical for cardiac development and heart function. However, little is known about THs influence on ventricular repolarization and controversial effects on QT prolongation are reported. Human iPSC-derived cardiomyocytes (hiPSC-CMs) and multielectrode array (MEA) systems were used to investigate the influence of 3,3',5-triiodo-L-Thyronine (T3) and 3,3',5,5'-tetraiodo-L-Thyronine (T4) on corrected Field Potential Duration (FPDc), the in vitro analog of QT interval, and on local extracellular Action Potential Duration (APD). Treatment with high THs doses induces a significant prolongation of both FPDc and APD, with the strongest increase reached after 24 h exposure. Preincubation with reverse T3 (rT3), a specific antagonist for nuclear TH receptor binding, significantly reduces T3 effects on FPDc, suggesting a TRs-mediated transcriptional mechanism. RNA-seq analysis showed significant deregulation in genes involved in cardiac repolarization pathways, including several QT-interval related genes. In conclusion, long-time administration of high THs doses induces FPDc prolongation in hiPSC-CMs probably through the modulation of genes linked to QT-interval regulation. These results open the way to investigate new potential diagnostic biomarkers and specific targeted therapies for cardiac repolarization dysfunctions.

Disruption of protein quality control of the human ether-à-go-go related gene K+ channel results in profound long QT syndrome

BACKGROUND

Long QT syndrome (LQTS) is a hereditary disease that predisposes patients to life-threatening cardiac arrhythmias and sudden cardiac death. Our previous study of the human ether-à-go-go related gene (hERG)-encoded K⁺ channel (K_v11.1) supports an association between hERG and RING finger protein 207 (RNF207) variants in aggravating the onset and severity of LQTS, specifically T613M hERG (hERG_T613M) and RNF207 frameshift (RNF207_G603fs) mutations. However, the underlying mechanistic underpinning remains unknown.

OBJECTIVE

The purpose of the present study was to test the role of RNF207 in the function of hERG-encoded K⁺ channel subunits.

METHODS

Whole-cell patch-clamp experiments were performed in human embryonic kidney (HEK 293) cells and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) together with immunofluorescent confocal and high resolution microscopy, auto-ubiquitinylation assays, and co-immunoprecipitation experiments to test the functional interactions between hERG and RNF207.

RESULTS

Here, we demonstrated that RNF207 serves as an E3 ubiquitin ligase and targets misfolded hERG_T613M proteins for degradation. RNF207_G603fs exhibits decreased activity and hinders the normal degradation pathway; this increases the levels of hERG_T613M subunits and their dominant-negative effect on the wild-type subunits, ultimately resulting in decreased current density. Similar findings are shown for hERG_A614V, a known dominant-negative mutant subunit. Finally, the presence of RNF207_G603fs with hERG_T613M results in significantly prolonged action potential durations and reduced hERG current in human-induced pluripotent stem cell-derived cardiomyocytes.

CONCLUSION

Our study establishes RNF207 as an interacting protein serving as a ubiquitin ligase for hERG-encoded K⁺ channel subunits. Normal function of RNF207 is critical for the quality control of hERG subunits and consequently cardiac repolarization. Moreover, our study provides evidence for protein quality control as a new paradigm in life-threatening cardiac arrhythmias in patients with LQTS.

A phenome-wide association study of 26 mendelian genes reveals phenotypic expressivity of common and rare variants within the general population

The clinical evaluation of a genetic syndrome relies upon recognition of a characteristic pattern of signs or symptoms to guide targeted genetic testing for confirmation of the diagnosis. However, individuals displaying a single phenotype of a complex syndrome may not meet criteria for clinical diagnosis or genetic testing. Here, we present a phenome-wide association study (PheWAS) approach to systematically explore the phenotypic expressivity of common and rare alleles in genes associated with four well-described syndromic diseases (Alagille (AS), Marfan (MS), DiGeorge (DS), and Noonan (NS) syndromes) in the general population.

Using human phenotype ontology (HPO) terms, we systematically mapped 60 phenotypes related to AS, MS, DS and NS in 337,198 unrelated white British from the UK Biobank (UKBB) based on their hospital admission records, self-administrated questionnaires, and physiological measurements. We performed logistic regression adjusting for age, sex, and the first 5 genetic principal components, for each phenotype and each variant in the target genes (JAG1, NOTCH2 FBN1, PTPN1 and RAS-opathy genes, and genes in the 22q11.2 locus) and performed a gene burden test.

Overall, we observed multiple phenotype-genotype correlations, such as the association between variation in JAG1, FBN1, PTPN11 and SOS2 with diastolic and systolic blood pressure; and pleiotropy among multiple variants in syndromic genes. For example, rs11066309 in PTPN11 was significantly associated with a lower body mass index, an increased risk of hypothyroidism and a smaller size for gestational age, all in concordance with NS-related phenotypes. Similarly, rs589668 in FBN1 was associated with an increase in body height and blood pressure, and a reduced body fat percentage as observed in Marfan syndrome.

Our findings suggest that the spectrum of associations of common and rare variants in genes involved in syndromic diseases can be extended to individual phenotypes within the general population.

Standard medical evaluation of genetic syndromes relies upon recognizing a characteristic pattern of signs or symptoms to guide targeted genetic testing for confirmation of the diagnosis. This may lead to missing diagnoses in patients with silent or a low expressed form of the syndrome. Here we take advantage of a rich electronic health record, various phenotypic measurements, and genetic information in 337,198 unrelated white British from the UKBB, to study the relation between single syndromic disease phenotypes and genes related to syndromic disease. We show multiple phenotype-genotype associations in concordance with phenotypes variations found in syndromic diseases. For example, we show that a commonly found variant in FBN1 was associated with high standing/sitting height ratio and reduced body fat percentage as observed in individuals with Marfan syndrome. Our findings suggest that common and rare alleles in syndromic disease genes are causative of individual component phenotypes present in a general population; further research is needed to characterize the pleiotropic effect of alleles in syndromic genes in persons without the syndromic disease.

Reevaluating the Mutation Classification in Genetic Studies of Bradycardia Using ACMG/AMP Variant Classification Framework

PURPOSE

Next-generation sequencing (NGS) has become more accessible, leading to an increasing number of genetic studies of familial bradycardia being reported. However, most of the variants lack full evaluation. The relationship between genetic factors and bradycardia should be summarized and reevaluated.

METHODS

We summarized genetic studies published in the PubMed database from 2008/1/1 to 2019/9/1 and used the ACMG/AMP classification framework to analyze related sequence variants.

RESULTS

We identified 88 articles, 99 sequence variants, and 34 genes after searching the PubMed database and classified ABCC9, ACTN2, CACNA1C, DES, HCN4, KCNQ1, KCNH2, LMNA, MECP2, LAMP2, NPPA, SCN5A, and TRPM4 as high-priority genes causing familial bradycardia. Most mutated genes have been reported as having multiple clinical manifestations.

CONCLUSIONS

For patients with familial CCD, 13 high-priority genes are recommended for evaluation. For genetic studies, variants should be carefully evaluated using the ACMG/AMP variant classification framework before publication.

Translating genomic testing results for pediatric critical care: Opportunities for genetic counselors

Genomic sequencing (GS), such as whole genome and exome sequencing, is rapidly being integrated into pediatric critical care settings. Results are being used to make high impact decisions including declarations of futility, withdrawal of care, and rationing of scarce resources. In this qualitative study, we conducted interviews with clinicians involved in the care of critically ill children with congenital heart disease (CHD) to investigate their views on implementation of GS into clinical practice. Interviews were transcribed and inductively analyzed for major themes using grounded theory and thematic analysis. Three major themes emerged surrounding the use of genomic information in the high-stakes, time pressured decision making that characterizes clinical care of critically ill children with CHD: (a) that clinicians felt they did not have sufficient training to accurately assess genetic results despite pressure to incorporate results into clinical decisions; (b), that they desire knowledge support from genetic specialists, such as genetic counselors, who both understand the critical care context and are available within the time constraints of critical care clinical pressures; and (c), that clinicians feel a pressing need for increased genetics education to be able to safely and appropriately incorporate GS results into clinical decisions Our data suggest that genetics specialists may need a stronger presence in the pediatric critical care setting.

Electrocardiographic Assessment and Genetic Analysis in Neonates: a Current Topic of Discussion

Background:

Sudden death of a newborn is a rare entity, which may be caused by genetic cardiac arrhythmias. Among these diseases, Long QT syndrome is the most prevalent arrhythmia in neonates, but other diseases such as Brugada syndrome, Short QT syndrome and Catecholaminergic Polymorphic Ventricular Tachycardia also cause sudden death in infants. All these entities are charac-terized by well-known alterations in the electrocardiogram and the first symptom of the disease may be an unexpected death. Despite the low prevalence of these diseases, the performance of an electro-cardiogram in the first hours or days after birth could help identify these electrical disruptions and adopt preventive measures. In recent years, there has been an important impulse by some experts in the scientific community towards the initiation of a newborn electrocardiogram-screening program, for the detection of these electrocardiographic abnormalities. In addition, the use of genetic analysis in neonates could identify the cause of these heart alterations. Identification of relatives carrying the ge-netic alteration associated with the disease allows adoption of measures to prevent lethal episodes.

Conclusion:

Recent technological advances enable a comprehensive genetic screening of a large number of genes in a cost-effective way. However, the interpretation of genetic data and its translation into clinical practice are the main challenges for cardiologists and geneticists. However, there is im-portant controversy as to the clinical value, and cost-effectiveness of the use of electrocardiogram as well as of genetic testing to detect these cases. Our review focuses on these current matters of argue.

Practical Aspects in Genetic Testing for Cardiomyopathies and Channelopathies

Genetic testing has an increasingly important role in the diagnosis and management of cardiac disorders, where it confirms the diagnosis, aids prognostication and risk stratification and guides treatment. A genetic diagnosis in the proband also enables clarification of the risk for family members by cascade testing. Genetics in cardiac disorders is complex where epigenetic and environmental factors might come into interplay. Incomplete penetrance and variable expressivity is also common. Genetic results in cardiac conditions are mostly probabilistic and should be interpreted with all available clinical information. With this complexity in cardiac genetics, testing is only indicated in patients with a strong suspicion of an inheritable cardiac disorder after a full clinical evaluation. In this review we discuss the genetics underlying the major cardiomyopathies and channelopathies, and the practical aspects of diagnosing these conditions in the laboratory.

Exome sequencing identifies a novel nonsense mutation of Ring Finger Protein 207 in a Chinese family with Long QT syndrome and syncope

Long QT syndrome (LQTS) is a rare inherited arrhythmia disease characterized by a prolonged QT interval on 12-lead electrocardiograms. It is the crucial factor to induce syncope, ventricular fibrillation, and even sudden cardiac death. Previous studies have proved that mutations of ion channels-related genes play an important role in LQTS patients. In this study, we enrolled a Chinese family with LQTS and syncope. With the help of whole-exome sequencing, we identified a novel nonsense mutation (c.439C>T/p.Q147X) of Ring Finger Protein 207 (RNF207) in this family. The novel mutation, resulting in a premature stop codon in exon 4 of the RNF207 gene, co-segregated with the affected individuals. Bioinformatics analysis and real-time PCR further proved that the newly identified mutation might induce nonsense-mediated mRNA decay. In mutation carriers, the level of RNF207 mRNA expression was much lower than controls, which may affect potassium channel KCNH2 and lead to LQTS and syncope. In this research, we reported a rare novel mutation of RNF207 in LQTS and syncope patients which further supports the significant role of RNF207 in potassium channel activation and expanded the spectrum of RNF207 mutations. These data may contribute to the genetic diagnosis and counseling of families with LQTS and syncope.

Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature

PURPOSE

Availability of clinical genomic sequencing (CGS) has generated questions about the value of genome and exome sequencing as a diagnostic tool. Analysis of reported CGS application can inform uptake and direct further research. This scoping literature review aims to synthesize evidence on the clinical and economic impact of CGS.

METHODS

PubMed, Embase, and Cochrane were searched for peer-reviewed articles published between 2009 and 2017 on diagnostic CGS for infant and pediatric patients. Articles were classified according to sample size and whether economic evaluation was a primary research objective. Data on patient characteristics, clinical setting, and outcomes were extracted and narratively synthesized.

RESULTS

Of 171 included articles, 131 were case reports, 40 were aggregate analyses, and 4 had a primary economic evaluation aim. Diagnostic yield was the only consistently reported outcome. Median diagnostic yield in aggregate analyses was 33.2% but varied by broad clinical categories and test type.

CONCLUSION

Reported CGS use has rapidly increased and spans diverse clinical settings and patient phenotypes. Economic evaluations support the cost-saving potential of diagnostic CGS. Multidisciplinary implementation research, including more robust outcome measurement and economic evaluation, is needed to demonstrate clinical utility and cost-effectiveness of CGS.

Cardiovascular Precision Medicine in the Genomics Era

Precision medicine strives to delineate disease using multiple data sources-from genomics to digital health metrics-in order to be more precise and accurate in our diagnoses, definitions, and treatments of disease subtypes. By defining disease at a deeper level, we can treat patients based on an understanding of the molecular underpinnings of their presentations, rather than grouping patients into broad categories with one-size-fits-all treatments. In this review, the authors examine how precision medicine, specifically that surrounding genetic testing and genetic therapeutics, has begun to make strides in both common and rare cardiovascular diseases in the clinic and the laboratory, and how these advances are beginning to enable us to more effectively define risk, diagnose disease, and deliver therapeutics for each individual patient.

Anticipating uncertainty and irrevocable decisions: provider perspectives on implementing whole-genome sequencing in critically ill children with heart disease

PURPOSE

To investigate the potential impacts of whole-genome sequencing (WGS) in the pediatric critical-care context, we examined how clinicians caring for critically ill children with congenital heart disease (CHD) anticipate and perceive the impact of WGS on their decision-making process and treatment recommendations.

METHODS

We conducted semistructured in-person and telephone interviews of clinicians involved in the care of critically ill children with CHD at a high-volume pediatric heart center. We qualitatively analyzed the transcribed interviews.

RESULTS

In total, 34 clinicians were interviewed. Three themes emerged: (i) uncertainty about the accuracy of WGS testing and adequacy of testing validation; (ii) the use of WGS to facilitate life-limiting decisions such as futility, rationing, and selective prenatal termination; and (iii) moral distress over using WGS with a lack of decision support.

CONCLUSION

Despite uncertainty about WGS testing, the interviewed clinicians were using, and anticipated expanding the use of, WGS results to justify declarations of futility, withdrawal of care, and rationing in critically ill children with CHD. This situation is causing moral distress in providers who have to make high-stakes decisions involving WGS results, with only partial understanding of them. Decision support for clinicians, and discussion with families of the risks of using WGS for rationing or withdrawal, is needed.

The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants

Genetic disorders are a leading cause of morbidity and mortality in infants in neonatal and pediatric intensive care units (NICU/PICU). While genomic sequencing is useful for genetic disease diagnosis, results are usually reported too late to guide inpatient management. We performed an investigator-initiated, partially blinded, pragmatic, randomized, controlled trial to test the hypothesis that rapid whole-genome sequencing (rWGS) increased the proportion of NICU/PICU infants receiving a genetic diagnosis within 28 days. The participants were families with infants aged <4 months in a regional NICU and PICU, with illnesses of unknown etiology. The intervention was trio rWGS. Enrollment from October 2014 to June 2016, and follow-up until November 2016. Of all, 26 female infants, 37 male infants, and 2 infants of undetermined sex were randomized to receive rWGS plus standard genetic tests (n = 32, cases) or standard genetic tests alone (n = 33, controls). The study was terminated early due to loss of equipoise: 73% (24) controls received genomic sequencing as standard tests, and 15% (five) controls underwent compassionate cross-over to receive rWGS. Nevertheless, intention to treat analysis showed the rate of genetic diagnosis within 28 days of enrollment (the primary end-point) to be higher in cases (31%, 10 of 32) than controls (3%, 1 of 33; difference, 28% [95% CI, 10-46%]; p = 0.003). Among infants enrolled in the first 25 days of life, the rate of neonatal diagnosis was higher in cases (32%, 7 of 22) than controls (0%, 0 of 23; difference, 32% [95% CI, 11-53%];p = 0.004). Median age at diagnosis (25 days [range 14-90] in cases vs. 130 days [range 37-451] in controls) and median time to diagnosis (13 days [range 1-84] in cases, vs. 107 days [range 21-429] in controls) were significantly less in cases than controls (p = 0.04). In conclusion, rWGS increased the proportion of NICU/PICU infants who received timely diagnoses of genetic diseases.

A primer to clinical genome sequencing

PURPOSE OF REVIEW

Genome sequencing is now available as a clinical diagnostic test. There is a significant knowledge and translation gap for nongenetic specialists of the processes necessary to generate and interpret clinical genome sequencing. The purpose of this review is to provide a primer on contemporary clinical genome sequencing for nongenetic specialists describing the human genome project, current techniques and applications in genome sequencing, limitations of current technology, and techniques on the horizon.

RECENT FINDINGS

As currently implemented, genome sequencing compares short pieces of an individual's genome with a reference sequence developed by the human genome project. Genome sequencing may be used for obtaining timely diagnostic information, cancer pharmacogenomics, or in clinical cases when previous genetic testing has not revealed a clear diagnosis. At present, the implementation of clinical genome sequencing is limited by the availability of clinicians qualified for interpretation, and current techniques in used clinical testing do not detect all types of genetic variation present in a single genome.

SUMMARY

Clinicians considering a genetic diagnosis have wide array of testing choices which now includes genome sequencing. Although not a comprehensive test in its current form, genome sequencing offers more information than gene-panel or exome sequencing and has the potential to replace targeted single-gene or gene-panel testing in many clinical scenarios.

Genetic Testing in Inherited Heart Diseases: Practical Considerations for Clinicians

PURPOSE OF REVIEW

Genetic testing has become an important element in the care of patients with inherited cardiac conditions (ICCs). The purpose of this review is to provide clinicians with insights into the utility of genetic testing as well as challenges associated with interpreting results.

RECENT FINDINGS

Genetic testing may be indicated for individuals who are affected with or who have family histories of various ICCs. Various testing options are available and determining the most appropriate test for any given clinical scenario is key when interpreting results. Newly published guidelines as well as various publicly accessible tools are available to clinicians to help with interpretation of genetic findings; however the subjectivity with respect to variant classification can make accurate assessment challenging. Genetic information can provide highly useful and relevant information for patients, their family members, and their healthcare providers. Given the potential ramifications of variant misclassification, expertise in both clinical phenotyping and molecular genetics is imperative in order to provide accurate diagnosis, management recommendations, and family risk assessment for this patient population.

Deep sequencing of atrial fibrillation patients with mitral valve regurgitation shows no evidence of mosaicism but reveals novel rare germline variants

BACKGROUND

Atrial fibrillation (AF) is the most common cardiac arrhythmia. Valvular heart disease is a strong predictor, yet the underlying molecular mechanisms are unknown.

OBJECTIVE

The purpose of this study was to investigate the prevalence of somatic variants in AF candidate genes in an AF patient population undergoing surgery for mitral valve regurgitation (MVR) to determine whether these patients are genetically predisposed to AF.

METHODS

DNA was extracted from blood and left atrial tissue from 44 AF patients with MVR. Using next-generation sequencing, we investigated 110 genes using the HaloPlex Target Enrichment System. MuTect software was used for identification of somatic point variants. We functionally characterized selected variants using electrophysiologic techniques.

RESULTS

No somatic variants were identified in the cardiac tissue. Thirty-three patients (75%) had a rare germline variation in ≥1 candidate genes. Fourteen variants were novel. Fifteen variants were predicted damaging or likely damaging in ≥6 in silico predictions. We identified rare variants in genes never directly associated with AF: KCNE4, SCN4B, NEURL1, and CAND2. Interestingly, 7 patients (16%) had variants in genes involved in cellular potassium handling. The variants KCNQ1 (p.G272S) and KCNH2 (p.A913V) resulted in gain of function due to faster activation (KCNQ1) and slowed deactivation kinetics (KCNQ1, KCNH2).

CONCLUSION

We did not find any somatic variants in patients with AF and MVR. Surprisingly, we found that our cohort of non-lone AF patients might, like lone AF patients, be predisposed to AF by rare germline variants. Our findings emphasize the extent of still unknown factors in the pathogenesis of AF.

Towards precision medicine

There is great potential for genome sequencing to enhance patient care through improved diagnostic sensitivity and more precise therapeutic targeting. To maximize this potential, genomics strategies that have been developed for genetic discovery - including DNA-sequencing technologies and analysis algorithms - need to be adapted to fit clinical needs. This will require the optimization of alignment algorithms, attention to quality-coverage metrics, tailored solutions for paralogous or low-complexity areas of the genome, and the adoption of consensus standards for variant calling and interpretation. Global sharing of this more accurate genotypic and phenotypic data will accelerate the determination of causality for novel genes or variants. Thus, a deeper understanding of disease will be realized that will allow its targeting with much greater therapeutic precision.

Sudden infant death syndrome due to long QT syndrome: a brief review of the genetic substrate and prevalence

The pathophysiological mechanisms which lead to sudden infant death syndrome (SIDS) are not completely understood. Cardiac channelopathies are a well-established causative factor with long QT syndrome (LQTS) being the most frequent one, accounting for approximately 12% of SIDS cases. The genetic substrate of the above arrhythmogenic syndrome has been thoroughly described but only specific gene mutations or polymorphisms have been identified as SIDS causative. The review will focus on the prevalence of LQTS-induced SIDS or near-SIDS cases and the mutations held responsible. A literature search was performed in PubMed and Scopus electronic databases. Search terms used were: long QT syndrome, channelopathies, QT prolongation, cardiac ion channels. The above-mentioned search terms were always combined with the term: sudden infant death syndrome. Study types considered eligible were: case–control, family pedigree analysis, case reports. The prevalence of LQTS-induced SIDS according to six broad genetic studies ranges from 3.9 to 20.6%, with an average of 12%. Since LQTS can be effectively managed, LQTS-related SIDS cases could be prevented, provided that a screening method is efficient enough to detect all the affected infants.

Early somatic mosaicism is a rare cause of long-QT syndrome

Somatic mosaicism, the occurrence and propagation of genetic variation in cell lineages after fertilization, is increasingly recognized to play a causal role in a variety of human diseases. We investigated the case of life-threatening arrhythmia in a 10-day-old infant with long QT syndrome (LQTS). Rapid genome sequencing suggested a variant in the sodium channel Na_V1.5 encoded by SCN5A, NM_000335:c.5284G > T predicting p.(V1762L), but read depth was insufficient to be diagnostic. Exome sequencing of the trio confirmed read ratios inconsistent with Mendelian inheritance only in the proband. Genotyping of single circulating leukocytes demonstrated the mutation in the genomes of 8% of patient cells, and RNA sequencing of cardiac tissue from the infant confirmed the expression of the mutant allele at mosaic ratios. Heterologous expression of the mutant channel revealed significantly delayed sodium current with a dominant negative effect. To investigate the mechanism by which mosaicism might cause arrhythmia, we built a finite element simulation model incorporating Purkinje fiber activation. This model confirmed the pathogenic consequences of cardiac cellular mosaicism and, under the presenting conditions of this case, recapitulated 2:1 AV block and arrhythmia. To investigate the extent to which mosaicism might explain undiagnosed arrhythmia, we studied 7,500 affected probands undergoing commercial gene-panel testing. Four individuals with pathogenic variants arising from early somatic mutation events were found. Here we establish cardiac mosaicism as a causal mechanism for LQTS and present methods by which the general phenomenon, likely to be relevant for all genetic diseases, can be detected through single-cell analysis and next-generation sequencing.

Young adults' attitudes toward pediatric whole-genome sequencing

AIM

To characterize the views of young adults toward integrating whole-genome sequencing (WGS) into standard pediatric care, particularly when used as a supplement to newborn screening.

MATERIALS & METHODS

This mixed methods descriptive study assessed the perspectives of a diverse group of 18- and 19-year olds (n = 145) in the USA using an informational video and online survey.

RESULTS

Young adults typically recommended disclosing WGS results to both parents and children during childhood. In the qualitative analysis, most participants emphasized the anticipated health benefits of pediatric WGS, while a minority discussed possible negative emotional and developmental impacts.

CONCLUSION

Differing preferences for pediatric WGS emphasize the importance that clinicians adopt responsive approaches when providing WGS and disclosing results to families.

Comorbid Epilepsy and Developmental Disorders in Congenital Long QT Syndrome With Life-Threatening Perinatal Arrhythmias

OBJECTIVES

Given the association of long QT syndrome (LQTS) and neurological disorders, we speculated that the more severe LQTS phenotype, perinatal LQTS, would exhibit more frequent comorbid neurodevelopmental anomalies than LQTS without perinatal arrhythmias (nonperinatal LQTS).

BACKGROUND

Congenital LQTS with life-threatening perinatal arrhythmias (perinatal LQTS) has a poor life prognosis.

METHODS

Twenty-one consecutive LQTS patients diagnosed before 1 year of age at our institution and 3 previously reported perinatal LQTS patients with neurological seizures were enrolled. In total, the clinical course was evaluated in 24 patients.

RESULTS

Among 21 infantile LQTS patients, 5 of 6 with perinatal LQTS (83%) were diagnosed with epilepsy and 4 (67%) with developmental disorders, but none with nonperinatal LQTS were. The total development quotient by Kinder Infant Development Scale scores was 17 to 72 (median 67) in 5 epileptic perinatal LQTS. In the 8 perinatal LQTS patients with neurological disorders, including 3 previously reported cases, epileptic seizures occurred at 2 days to 2.5 years of age and 5 had developmental disorders. Mutations in these 8 patients were located in the transmembrane loop of KCNH2, and D3/S4-S5 linker, D4/S4, or the D4/S6 segment of SCN5A.

CONCLUSIONS

A high comorbidity of neurodevelopmental anomalies was observed in perinatal LQTS. Mutations in patients with neurological comorbidities were in loci linked to LQTS with a severe cardiac phenotype. These observations indicate the possibility that neurological disorders in perinatal LQTS are manifested as neurological phenotypes associated with severe cardiac phenotypes, while we could not completely exclude another possibility that those were caused by a brain perfusion injury.

Medical implications of technical accuracy in genome sequencing

Background

As whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for sequencing methods and analysis pipelines to be technically accurate. The Genome in a Bottle Consortium has recently published a set of benchmark SNV, indel, and homozygous reference genotypes for the pilot whole genome NIST Reference Material based on the NA12878 genome.

Methods

We examine the relationship between human genome complexity and genes/variants reported to be associated with human disease. Specifically, we map regions of medical relevance to benchmark regions of high or low confidence. We use benchmark data to assess the sensitivity and positive predictive value of two representative sequencing pipelines for specific classes of variation.

Results

We observe that the accuracy of a variant call depends on the genomic region, variant type, and read depth, and varies by analytical pipeline. We find that most false negative WGS calls result from filtering while most false negative WES variants relate to poor coverage. We find that only 74.6 % of the exonic bases in ClinVar and OMIM genes and 82.1 % of the exonic bases in ACMG-reportable genes are found in high-confidence regions. Only 990 genes in the genome are found entirely within high-confidence regions while 593 of 3,300 ClinVar/OMIM genes have less than 50 % of their total exonic base pairs in high-confidence regions. We find greater than 77 % of the pathogenic or likely pathogenic SNVs currently in ClinVar fall within high-confidence regions. We identify sites that are prone to sequencing errors, including thousands present in publicly available variant databases. Finally, we examine the clinical impact of mandatory reporting of secondary findings, highlighting a false positive variant found in BRCA2.

Conclusions

Together, these data illustrate the importance of appropriate use and continued improvement of technical benchmarks to ensure accurate and judicious interpretation of next-generation DNA sequencing results in the clinical setting.

Electronic supplementary material

The online version of this article (doi:10.1186/s13073-016-0269-0) contains supplementary material, which is available to authorized users.

How should whole-genome sequencing be implemented in children? A consideration of the current limitations

In children, whole-genome sequencing (WGS) is envisioned as a tool to improve diagnosis of undiagnosed diseases and to improve population-based screening. Pilot applications have shown benefits: genomic information has been used as a diagnostic aid; pharmacogenomics can reduce medicine-related adverse events; advanced knowledge of the potential for later-onset disease can target tests and appropriate therapies. However, emerging technical, conceptual and ethical challenges may limit WGS from fulfilling the current vision for future applications. WGS platforms still struggle with reliability and accuracy. The role of the genome in long-term organismal function and disease is still being established. Ethical implications of WGS in both undiagnosed disease and population screening, particularly potential impacts of testing on children and their families are still unresolved.

A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

While the cost of whole genome sequencing (WGS) is approaching the realm of routine medical tests, it remains too tardy to help guide the management of many acute medical conditions. Rapid WGS is imperative in light of growing evidence of its utility in acute care, such as in diagnosis of genetic diseases in very ill infants, and genotype-guided choice of chemotherapy at cancer relapse. In such situations, delayed, empiric, or phenotype-based clinical decisions may meet with substantial morbidity or mortality. We previously described a rapid WGS method, STATseq, with a sensitivity of >96 % for nucleotide variants that allowed a provisional diagnosis of a genetic disease in 50 h. Here improvements in sequencing run time, read alignment, and variant calling are described that enable 26-h time to provisional molecular diagnosis with >99.5 % sensitivity and specificity of genotypes. STATseq appears to be an appropriate strategy for acutely ill patients with potentially actionable genetic diseases.

Emergency medical genomes: a breakthrough application of precision medicine

Today there exist two medical applications where relatively strong evidence exists to support the broad adoption of genome-informed precision medicine. These are the differential diagnosis of single gene diseases and genotype-based selection of patients for targeted cancer therapies. However, despite the availability of the $1000 genome and $700 exome for research, there is as yet little broad uptake of genomic medicine, even in these applications. Significant impediments to mainstream adoption exist, including unavailability in many institutions, lack of scalability in others, a dearth of physician understanding of interpreted genome or exome results or knowledge of how to translate consequent precision medicine care plans, and a lack of test reimbursement. In short, genomic medicine lacks a breakthrough application. Rapid genome sequencing of acutely ill infants with suspected genetic diseases (STATseq) may become that application when scaled to dozens of trios per day without loss of timeliness or accuracy. Also critical for broad adoption is embedding STATseq in software for timely patient ascertainment, augmented intelligence for interpretation, explanation of results for generalist physicians, and dynamic precision medicine decision support.

Genetics of long-QT syndrome

Congenital long QT syndrome (LQTS) is an inherited arrhythmia syndrome characterized by a prolonged QT interval in the 12-lead ECG, torsades de pointes and not negligible prevalence of sudden cardiac death. The genetic testing plays an important role in the diagnosis of LQTS. A total of 15 genes have been reported for autosomal-dominant forms of Romano-Ward-type congenital LQTS and 2 genes for autosomal-recessive forms of the Jervell and Lange-Nielsen syndrome. In this review, we summarize the recent advances in genetics of LQTS and briefly describe forward perspectives of LQTS investigation.

Parent and public interest in whole-genome sequencing

OBJECTIVE

The aim of this study was to assess the baseline interest of the public in whole-genome sequencing (WGS) for oneself, parents' interest in WGS for their youngest children, and factors associated with such interest.

METHODS

A random sample of adults from a probability-based nationally representative online panel was surveyed. All participants were provided basic information about WGS and then asked about their interest in WGS for themselves. Those participants who were parents were additionally asked about their interest in WGS for their children. The order in which parents were asked about their interest in WGS for themselves and for their child was randomized. The relationship between parent/child characteristics and interest in WGS was examined.

RESULTS

The overall response rate was 62% (55% among parents). 58.6% of the total population (parents and nonparents) was interested in WGS for themselves. Similarly, 61.8% of the parents were interested in WGS for themselves and 57.8% were interested in WGS for their youngest children. Of note, 84.7% of the parents showed an identical interest level in WGS for themselves and their youngest children. Mothers as a group and parents whose youngest children had ≥2 health conditions had significantly more interest in WGS for themselves and their youngest children, while those with conservative political ideologies had considerably less.

CONCLUSIONS

While US adults have varying interest levels in WGS, parents appear to have similar interests in genome testing for themselves and their youngest children. As WGS technology becomes available in the clinic and private market, clinicians should be prepared to discuss WGS risks and benefits with their patients.