A systematic evaluation of hybridization-based mouse exome capture system

BACKGROUND: Exome sequencing is increasingly used to search for phenotypically-relevant sequence variants in the mouse genome. All of the current hybridization-based mouse exome capture systems are designed based on the genome reference sequences of the C57BL/6 J strain. Given that the substantial sequence divergence exists between C57BL/6 J and other distantly-related strains, the impact of sequence divergence on the efficiency of such capture systems needs to be systematically evaluated before they can be widely applied to the study of those strains. RESULTS: Using the Agilent SureSelect mouse exome capture system, we performed exome sequencing on F1 generation hybrid mice that were derived by crossing two divergent strains, C57BL/6 J and SPRET/EiJ. Our results showed that the C57BL/6 J-based probes captured the sequences derived from C57BL/6 J alleles more efficiently and that the bias was higher for the target regions with greater sequence divergence. At low sequencing depths, the bias also affected the efficiency of variant detection. However, the effects became negligible when sufficient sequencing depth was achieved. CONCLUSION: Sufficient sequence depth needs to be planned to match the sequence divergence between C57BL/6 J and the strain to be studied, when the C57BL/6 J --based Agilent SureSelect exome capture system is to be used

Exome sequencing helped the fine diagnosis of two siblings afflicted with atypical Timothy syndrome (TS2)

BACKGROUND: Long-QT syndrome (LQTS) causes a prolongation of the QT-interval in the ECG leading to life threatening tachyarrhythmia and ventricular fibrillation. One atypical form of LQTS, Timothy syndrome (TS), is associated with syndactyly, immune deficiency, cognitive and neurological abnormalities as well as distinct cranio-facial abnormalities. CASE PRESENTATION: On a family with both children diagnosed with clinical LQTS, we performed whole exome sequencing to comprehensively screen for causative mutations after a targeted candidate gene panel screen for Long-QT syndrome target genes failed to identify any underlying genetic defect. Using exome sequencing, we identified in both affected children, a p.402G > S mutation in exon 8 of the CACNA1C gene, a voltage-dependent Ca2+ channel. The mutation was inherited from their father, a mosaic mutation carrier. Based on this molecular finding and further more careful clinical examination, we refined the diagnosis to be Timothy syndrome (TS2) and thereby were able to present new therapeutic approaches. CONCLUSIONS: Our study highlights the difficulties in accurate diagnosis of patients with rare diseases, especially those with atypical clinical manifestation. Such challenge could be addressed with the help of comprehensive and unbiased mutation screening, such as exome sequencing

Combined immunodeficiency develops with age in immunodeficiency-centromeric instability-facial anomalies syndrome 2 (ICF2)

The autosomal recessive immunodeficiency-centromeric instability-facial anomalies syndrome (ICF) is characterized by immunodeficiency, developmental delay, and facial anomalies. ICF2, caused by biallelic ZBTB24 gene mutations, is acknowledged primarily as an isolated B-cell defect. Here, we extend the phenotype spectrum by describing, in particular, for the first time the development of a combined immune defect throughout the disease course as well as putative autoimmune phenomena such as granulomatous hepatitis and nephritis. We also demonstrate impaired cell-proliferation and increased cell death of immune and non-immune cells as well as data suggesting a chromosome separation defect in addition to the known chromosome condensation defect

Interhospital Transfer Before Thrombectomy Is Associated With Delayed Treatment and Worse Outcome in the STRATIS Registry (Systematic Evaluation of Patients Treated With Neurothrombectomy Devices for Acute Ischemic Stroke).

BACKGROUND: Endovascular treatment with mechanical thrombectomy (MT) is beneficial for patients with acute stroke suffering a large-vessel occlusion, although treatment efficacy is highly time-dependent. We hypothesized that interhospital transfer to endovascular-capable centers would result in treatment delays and worse clinical outcomes compared with direct presentation. METHODS: STRATIS (Systematic Evaluation of Patients Treated With Neurothrombectomy Devices for Acute Ischemic Stroke) was a prospective, multicenter, observational, single-arm study of real-world MT for acute stroke because of anterior-circulation large-vessel occlusion performed at 55 sites over 2 years, including 1000 patients with severe stroke and treated within 8 hours. Patients underwent MT with or without intravenous tissue plasminogen activator and were admitted to endovascular-capable centers via either interhospital transfer or direct presentation. The primary clinical outcome was functional independence (modified Rankin Score 0-2) at 90 days. We assessed (1) real-world time metrics of stroke care delivery, (2) outcome differences between direct and transfer patients undergoing MT, and (3) the potential impact of local hospital bypass. RESULTS: A total of 984 patients were analyzed. Median onset-to-revascularization time was 202.0 minutes for direct versus 311.5 minutes for transfer patients ( CONCLUSIONS: In this large, real-world study, interhospital transfer was associated with significant treatment delays and lower chance of good outcome. Strategies to facilitate more rapid identification of large-vessel occlusion and direct routing to endovascular-capable centers for patients with severe stroke may improve outcomes. CLINICAL TRIAL REGISTRATION: URL: https://www.clinicaltrials.gov. Unique identifier: NCT02239640

ACCUSA: accurate SNP calling on draft genomes

Next generation sequencing technologies facilitate genome-wide analysis of several biological processes. We are interested in whole-genome genotyping. To our knowledge, none of the existing SNP callers consider the quality of the reference genome, which is not necessary for high quality assemblies of well-studied model organisms. However, most genome projects will remain in draft status with little to no genome assembly improvement due to time and financial constraints. Here we present a simple yet elegant solution ('ACCUSA'), which considers both, the read qualities as well as the reference genome's quality using a Bayesian framework. We demonstrate that ACCUSA is as good as current SNP calling software in detecting true SNPs. More important, ACCUSA does not call spurious SNPs, which originate from a poor reference sequence. AVAILABILITY: ACCUSA is available free of charge to academic users and may be obtained from ftp://bbc.mdc-berlin.de/software. ACCUSA is programmed in JAVA 6 and runs on any platform with JAVA support. CONTACT: [email protected] and [email protected]

Interhospital Transfer Prior to Thrombectomy is Associated with Delayed Treatment and Worse Outcome in the STRATIS Registry

Background -Endovascular treatment with mechanical thrombectomy (MT) is beneficial for acute stroke patients suffering a large vessel occlusion, though treatment efficacy is highly time-dependent. We hypothesized that interhospital transfer to endovascular-capable centers would result in treatment delays and worse clinical outcomes compared to direct presentation. Methods -STRATIS was a prospective, multicenter, observational, single-arm study of real-world MT for acute stroke due to anterior-circulation large vessel occlusion performed at 55 sites over 2 years, including 1000 patients with severe stroke and treated within 8 hours. Patients underwent MT with or without IV-tPA, and were admitted to endovascular-capable centers via either interhospital transfer or direct presentation. The primary clinical outcome was functional independence (modified Rankin Score 0-2) at 90 days. We assessed 1) real-world time metrics of stroke care delivery, 2) outcome differences between direct and transfer patients undergoing MT, and 3) the potential impact of local hospital bypass. Results -A total of 984 patients were analyzed. Median onset-to-revascularization time was 202.0 minutes for direct vs. 311.5 minutes for transfer patients (p \u3c 0.001). Clinical outcomes were better in the direct group with 60.0% (299/498) achieving functional independence, compared to 52.2% (213/408) in the transfer group (odds ratio 1.38, 95%CI 1.06-1.79; p=0.02). Likewise, excellent outcome (modified Rankin Score 0-1) was achieved in 47.4% (236/498) of direct patients vs. 38.0% (155/408) of transfer patients (odds ratio 1.47, 95%CI 1.13-1.92; p=0.005). Mortality did not differ between the two groups (15.1% for direct, 13.7% for transfer; p=0.55). IV-tPA did not impact outcomes. Hypothetical bypass modeling for all transferred patients suggested that IV-tPA would be delayed by 12 minutes but MT would be performed 91 minutes sooner if patients were routed directly to endovascular-capable centers. If bypass is limited to a 20-mile radius from onset, then IV-tPA would be delayed by 7 minutes and MT performed 94 minutes earlier. Conclusions -In this large, real-world study, interhospital transfer was associated with significant treatment delays and lower chance of good outcome. Strategies to facilitate more rapid identification of large vessel occlusion and direct routing to endovascular-capable centers for severe stroke patients may improve outcomes. Clinical Trial Registration -URL: http://www.clinicaltrials.gov. Unique identifier: NCT02239640