Whole exome sequencing in a large pedigree with DCM identifies a novel mutation in RBM20

Background: Familial dilated cardiomyopathy (DCM) is genetically heterogeneous and is associated with mutations in at least 40 different genes. Apart from TTN encoding the giant protein Titin, none of these genes have an expected diagnostic yield of more than 5% complicating genetic diagnosis. Whole exome sequencing (WES) is a powerful alternative for the identification of the causal gene, however variant interpretation remains challenging. We report on WES in a large family with autosomal dominant DCM complicated by end stage heart failure and non-sustained ventricular arrhythmias in whom no causative mutation was identified using a targeted gene panel including 28 genes.Methods and results: WES was applied on 2 affected cousins. Stringent filtering of the identified genetic variants was performed including population variant frequencies, in silico analysis, orthologous and paralogous conservation. Subsequently Sanger sequencing was performed for 10 potential disease causing variants in order to confirm the presence of the variant and to evaluate co-segregation. Only one variant in exon 9 of the RBM20 gene (c.2714T > A, p.Met950Lys, NM_001334363) showed full co-segregation in the 7 affected family members resulting in a maximum 2-point LOD score of 2.1 and suggesting this as the pathogenic mutation responsible for the phenotype. Recently mutations in RBM20 have been linked to arrhythmogenic dilated cardiomyopathy caused by defective splicing of the giant sarcomere protein titin and abnormal calcium handling.Conclusions: We report the identification of a novel mutation in RBM20 by WES in a large pedigree with DCM.

Community-based recruitment and exome sequencing indicates high diagnostic yield in adults with intellectual disability

BACKGROUND

Establishing a genetic diagnosis for individuals with intellectual disability (ID) benefits patients and their families as it may inform the prognosis, lead to appropriate therapy, and facilitate access to medical and supportive services. Exome sequencing has been successfully applied in a diagnostic setting, but most clinical exome referrals are pediatric patients, with many adults with ID lacking a comprehensive genetic evaluation.

METHODS

Our unique recruitment strategy involved partnering with service and education providers for individuals with ID. We performed exome sequencing and analysis, and clinical variant interpretation for each recruited family.

RESULTS

All five families enrolled in the study opted-in for the return of genetic results. In three out of five families exome sequencing analysis identified pathogenic or likely pathogenic variants in KANSL1, TUSC3, and MED13L genes. Families discussed the results and any potential medical follow-up in an appointment with a board certified clinical geneticist.

CONCLUSION

Our study suggests high yield of exome sequencing as a diagnostic tool in adult patients with ID who have not undergone comprehensive sequencing-based genetic testing. Research studies including an option of return of results through a genetic clinic could help minimize the disparity in exome diagnostic testing between pediatric and adult patients with ID.

Free-ranging horse management in Australia, New Zealand and the United States: socio-ecological dimensions of a protracted environmental conflict

Management of free-ranging horses (Equus ferus caballus) is a complex socio-ecological issue in Australia (AU), New Zealand (NZ), and the United States (US). In these countries, horses are the results of colonial introductions and occupy very harsh rangeland environments exerting a grazing disturbance that has generated ecological concerns. Although many social and ecological concerns are similar, each country also has nuances. In 2018, we conducted a field-based comparison of AU, NZ, and US using an inductive approach to identify similarities, differences, and emerging themes through conversations with >100 individuals from New South Wales Australia, the North Island of New Zealand, and the western US. Additional data sources included field observations and archival documents. Consistent emergent themes identified included: strong public emotion, politicization of management, population growth concerns, negative ecological impact concerns, agreement that horses should be treated humanely, disagreement as to what practices were the most humane, interest and scepticism about fertility control, the need for transparency, compromise to accommodating horses and acknowledgement of social values, and recognition that collaboration is the only means to achieve both healthy rangelands and healthy horses. Unique themes identified included: NZ empowering advocate groups to become part of the solution, conflict between horses and livestock is a mostly US conflict, equids originated in the US, concern about the sustainability of adoption programs, different expectations/options for management on private lands, cultural history such as brumby running in AU, permanent branding of horses in the US, litigation as a uniquely US strategy (although a judgement on recent AU litigation is pending), government data accepted to guide removals in NZ but not always in AU or US, and complex heterogeneous land surface ownership patterns makes management difficult in the US. The difficulty of horse management in these countries is attributed to social intricacies rather than biological/ecological gaps of knowledge.

A diagnostic ceiling for exome sequencing in cerebellar ataxia and related neurological disorders

Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.

Rare variants in SLC5A10 are associated with serum 1,5-anhydroglucitol (1,5-AG) in the Atherosclerosis Risk in Communities (ARIC) Study

Serum 1,5-anhydroglucitol (1,5-AG) is an emerging biomarker used to monitor glycemic control in persons with diabetes. We performed whole-exome sequencing, examining the association between rare, coding genetic variants and 1,5-AG among European ancestry (N = 6,589) and African ancestry (N = 2,309) participants without diagnosed diabetes in the Atherosclerosis Risk in Communities (ARIC) Study. Five variants representing 3 independent signals on chromosome 17 in SLC5A10, a glucose transporter not previously known to transport 1,5-AG, were associated with 1,5-AG levels up to 10.38 µg/mL lower per allele (1,5-AG range 3.4–32.8 µg/mL) in the European ancestry sample and validated in the African ancestry sample. Together these variants explained 6% of the variance in 1,5-AG. Two of these variants (rs61741107, p = 8.85E-56; rs148178887, p = 1.13E-36) were rare, nonsynonymous, and predicted to be damaging or deleterious by multiple algorithms. Gene-based SKAT-O analysis supported these results (SLC5A10 p = 5.13E-64 in European ancestry, validated in African ancestry, p = 0.006). Interestingly, these novel variants are not associated with other biomarkers of hyperglycemia or diabetes (p > 0.2). The large effect sizes and protein-altering, multiple independent signals suggest SLC5A10 may code for an important transporter of 1,5-AG in the kidney, with a potential nonglucose-related effect on 1,5-AG, impacting its clinical utility as a diabetes biomarker in this subpopulation.

Prevalence of spinocerebellar ataxia 36 in a US population

OBJECTIVE

To assess the prevalence and clinical features of individuals affected by spinocerebellar ataxia 36 (SCA36) at a large tertiary referral center in the United States.

METHODS

A total of 577 patients with undiagnosed sporadic or familial cerebellar ataxia comprehensively evaluated at a tertiary referral ataxia center were molecularly evaluated for SCA36. Repeat primed PCR and fragment analysis were used to screen for the presence of a repeat expansion in the NOP56 gene.

RESULTS

Fragment analysis of triplet repeat primed PCR products identified a GGCCTG hexanucleotide repeat expansion in intron 1 of NOP56 in 4 index cases. These 4 SCA36-positive families comprised 2 distinct ethnic groups: white (European) (2) and Asian (Japanese [1] and Vietnamese [1]). Individuals affected by SCA36 exhibited typical clinical features with gait ataxia and age at onset ranging between 35 and 50 years. Patients also suffered from ataxic or spastic limbs, altered reflexes, abnormal ocular movement, and cognitive impairment.

CONCLUSIONS

In a US population, SCA36 was observed to be a rare disorder, accounting for 0.7% (4/577 index cases) of disease in a large undiagnosed ataxia cohort.

Primary lung carcinoid metastatic to the breast

Lung carcinoid tumors account for approximately 2% of lung cancers, with 10% of the tumors represented by the atypical type. While atypical carcinoids are metastatic to intrathoracic lymph nodes in approximately half of the cases on the initial presentation, distant metastases are seen in only 20% of the patients and are found most frequently in bones, liver, adrenal glands, and brain. We present a case of an unusual metastatic disease to the breast in 51-year-old female who developed a new breast mass 2 years after left lower lobectomy due to atypical carcinoid tumor. Atypical pulmonary carcinoid metastases to the breast are exceptionally uncommon, yet they are important considerations for appropriate management, especially with an anamnesis of this neoplasm.

SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data

Background

Targeted next-generation sequencing (NGS) has been widely used as a cost-effective way to identify the genetic basis of human disorders. Copy number variations (CNVs) contribute significantly to human genomic variability, some of which can lead to disease. However, effective detection of CNVs from targeted capture sequencing data remains challenging.

Results

Here we present SeqCNV, a novel CNV calling method designed to use capture NGS data. SeqCNV extracts the read depth information and utilizes the maximum penalized likelihood estimation (MPLE) model to identify the copy number ratio and CNV boundary. We applied SeqCNV to both bacterial artificial clone (BAC) and human patient NGS data to identify CNVs. These CNVs were validated by array comparative genomic hybridization (aCGH).

Conclusions

SeqCNV is able to robustly identify CNVs of different size using capture NGS data. Compared with other CNV-calling methods, SeqCNV shows a significant improvement in both sensitivity and specificity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1566-3) contains supplementary material, which is available to authorized users.

Practical Approaches for Whole-Genome Sequence Analysis of Heart- and Blood-Related Traits

Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes. These tests were performed treating all variants equally as well as with individual variants weighted by a measure of predicted functional consequence. Significant findings were assessed in 1,705 individuals of European ancestry. After these steps, we identified and replicated components of the genomic landscape significantly associated with heart- and blood-related traits. For two traits, lipoprotein(a) levels and neutrophil count, aggregate tests of low-frequency and rare variation were significantly associated across multiple motifs. For a third trait, cardiac troponin T, investigation of regulatory domains identified a locus on chromosome 9. These practical approaches for WGS analysis led to the identification of informative genomic regions and also showed that defined non-coding regions, such as first introns of genes and regulatory domains, are associated with important risk factor phenotypes. This study illustrates the tractable nature of WGS data and outlines an approach for characterizing the genetic architecture of complex traits.

Corner fracture type spondylometaphyseal dysplasia: Overlap with type II collagenopathies

Spondylometaphyseal dysplasia (SMD) corner fracture type (also known as SMD "Sutcliffe" type, MIM 184255) is a rare skeletal dysplasia that presents with mild to moderate short stature, developmental coxa vara, mild platyspondyly, corner fracture-like lesions, and metaphyseal abnormalities with sparing of the epiphyses. The molecular basis for this disorder has yet to be clarified. We describe two patients with SMD corner fracture type and heterozygous pathogenic variants in COL2A1. These two cases together with a third case of SMD corner fracture type with a heterozygous COL2A1 pathogenic variant previously described suggest that this disorder overlaps with type II collagenopathies. The finding of one of the pathogenic variants in a previously reported case of spondyloepimetaphyseal dysplasia (SEMD) Strudwick type and the significant clinical similarity suggest an overlap between SMD corner fracture and SEMD Strudwick types. © 2016 Wiley Periodicals, Inc.

A hybrid computational strategy to address WGS variant analysis in >5000 samples

Background

The decreasing costs of sequencing are driving the need for cost effective and real time variant calling of whole genome sequencing data. The scale of these projects are far beyond the capacity of typical computing resources available with most research labs. Other infrastructures like the cloud AWS environment and supercomputers also have limitations due to which large scale joint variant calling becomes infeasible, and infrastructure specific variant calling strategies either fail to scale up to large datasets or abandon joint calling strategies.

Results

We present a high throughput framework including multiple variant callers for single nucleotide variant (SNV) calling, which leverages hybrid computing infrastructure consisting of cloud AWS, supercomputers and local high performance computing infrastructures. We present a novel binning approach for large scale joint variant calling and imputation which can scale up to over 10,000 samples while producing SNV callsets with high sensitivity and specificity. As a proof of principle, we present results of analysis on Cohorts for Heart And Aging Research in Genomic Epidemiology (CHARGE) WGS freeze 3 dataset in which joint calling, imputation and phasing of over 5300 whole genome samples was produced in under 6 weeks using four state-of-the-art callers. The callers used were SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud. We used Amazon AWS, a 4000-core in-house cluster at Baylor College of Medicine, IBM power PC Blue BioU at Rice and Rhea at Oak Ridge National Laboratory (ORNL) for the computation. AWS was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for the imputation and phasing step. All other steps were carried out on the local compute cluster. The entire operation used 5.2 million core hours and only transferred a total of 6 TB of data across the platforms.

Conclusions

Even with increasing sizes of whole genome datasets, ensemble joint calling of SNVs for low coverage data can be accomplished in a scalable, cost effective and fast manner by using heterogeneous computing platforms without compromising on the quality of variants.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-1211-6) contains supplementary material, which is available to authorized users.

Short- and Long-term Results of Hybrid Arch and Proximal Descending Thoracic Aortic Repair

Purpose: To evaluate the short- and long-term outcomes of hybrid repair of the arch and proximal descending aorta in a single tertiary center for aortic disease. Methods: A retrospective analysis was performed of 55 patients (median age 67 years; 36 men) who underwent hybrid repair of thoracic aortic pathology with involvement of the arch between January 2005 and May 2015 at a single tertiary center. The pathologies included 40 (73%) with aneurysmal disease, 10 (18%) acute type B aortic dissections, 2 with acute aortic syndrome, an acute type A dissection, and left and aberrant right subclavian artery aneurysms. Seven (13%) procedures were performed as an emergency. Demographics and procedure characteristics were collected for analysis of survival and reinterventions. Results: Complete aortic debranching was performed in 14 (25%) to facilitate endograft placement in zone 0; debranching was partial in 20 (36%) patients for zone 1 deployments and 21 (38%) for zone 2. Primary technical success was achieved in 51 (93%) cases. One patient died in-hospital from aneurysm rupture following aortic debranching prior to stent-graft repair. In another, the stent-graft procedure proved infeasible and was abandoned. The other 2 technical failures were due to type Ia endoleaks. Five (9%) patients died in-hospital (4 of 48 elective and 1 of 7 emergency cases); 2 of these patients died within 30 days (4%). Eight (14%) patients had a stroke, 6 of 48 elective and 2 of the 7 emergency patients. Spinal cord ischemia was reported in 3 (6%) patients. Mean follow-up was 74.6 months. Overall cumulative survival was 70% at 1 year, 68% at 2 years, and 57% at 5 years. Reintervention to the proximal landing zone for type Ia endoleak was required in 6% of cases. The overall rate of aortic reintervention was 18% at 1 year, 21% at 2 years, and 36% at 5 years. Overall extra-anatomic graft patency was 99%. Conclusion: Hybrid repair of the aortic arch and proximal descending thoracic aorta is technically feasible, with acceptable short-term mortality. There is a low rate of proximal landing zone reintervention when hybrid techniques are used to create an adequate proximal landing zone. Extra-anatomic bypass grafts have good long-term patency. Ongoing disease progression means that further distal aortic interventions are often necessary in patients with extensive disease.