scholarly journals Molecular Characterization of a Novel Splicing Mutation Underlying Mucopolysaccharidosis (MPS) Type VI—Indirect Proof of Principle on Its Pathogenicity

Diagnostics ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 58 ◽  
Author(s):  
Maria Francisca Coutinho ◽  
Marisa Encarnação ◽  
Liliana Matos ◽  
Lisbeth Silva ◽  
Diogo Ribeiro ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Variant Calling ◽  
Turnaround Time ◽  
Compound Heterozygous ◽  
Final Report ◽  
Targeted Next Generation Sequencing ◽  
Novel Variant ◽  
Arsb Gene ◽  
The One ◽  
Proof Of Principle

Here, we present the molecular diagnosis of a patient with a general clinical suspicion of Mucopolysaccharidosis, highlighting the different tools used to perform its molecular characterization. In order to decrease the turnaround time for the final report and contribute to reduce the “diagnostic odyssey”, which frequently afflicts affected families, the proband’s sample was simultaneously screened for mutations in a number of lysosomal function-related genes with targeted next-generation sequencing (NGS) protocol. After variant calling, the most probable cause for disease was a novel ARSB intronic variant, c.1213+5G>T [IVS6+5G>T], detected in homozygosity. In general, homozygous or compound heterozygous mutations in the ARSB gene, underlie MPS type VI or Maroteaux-Lamy syndrome. Still, even though the novel c.1213+5G>T variant was easy to detect by both NGS and Sanger sequencing, only through indirect studies and functional analyses could we present proof of principle on its pathogenicity. Globally, this case reminds us that whenever a novel variant is detected, its pathogenicity must be carefully assessed before a definitive diagnosis is established, while highlighting alternative approaches that may be used to assess its effect in the absence RNA/cDNA sample(s) from the proband. This is particularly relevant for intronic variants such as the one here reported. Special attention will be given to the use of reporter minigene systems, which may be constructed/designed to dissect the effect of this sort of alterations, providing an insight into their consequences over the normal pre-mRNA splicing process of the affected gene.

scholarly journals A novel LOXHD1 variant in a Chinese couple with hearing loss

2019 ◽  
Vol 47 (12) ◽  
pp. 6082-6090 ◽  
Author(s):  
Chuan Zhang ◽  
Shengju Hao ◽  
Yali Liu ◽  
Bingbo Zhou ◽  
Furong Liu ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Molecular Diagnosis ◽  
Protein Function ◽  
Mexican American ◽  
Compound Heterozygous ◽  
Congenital Hearing Loss ◽  
Targeted Next Generation Sequencing ◽  
Novel Variants ◽  
Novel Variant ◽  
Compound Heterozygous Variants

Objective To perform molecular diagnosis and genetic counseling in a young Chinese couple with congenital hearing loss. Methods Variant screening analysis was performed by PCR and direct Sanger sequencing or targeted next-generation sequencing of all known hearing loss genes. Novel variants were evaluated by PolyPhen2 and PROVEAN software tools to evaluate possible effects on protein function. Results We identified causative variants in the young couple: c.235delC (rs80338943)/c.299-300delAT (rs111033204) compound heterozygous variants of GJB2 in the husband and c.1828G>A (p.Glu610Lys, rs535637788)/c.2825-2827delAGA compound heterozygous variants of LOXHD1 in the wife. The LOXHD1 c.1828G>A variant has only previously been reported in a Mexican-American individual in the 1000 Genomes Project database. Using PolyPhen2 and PROVEAN, we speculated that the LOXHD1 variant c.1828G>A is potentially pathogenic. Conclusion We carried out molecular diagnosis in a young couple with congenital hearing loss, and identified different disease-causing genes in the two individuals. The LOXHD1 variant c.1828G>A present in the wife had not previously been reported in individuals with congenital hearing loss. We determined this to be a potential pathogenic variant, and a novel variant associated with hearing loss in a Chinese individual.

scholarly journals Impact of an in-house emergency radiologist on report turnaround time

CJEM ◽  
2015 ◽  
Vol 17 (1) ◽  
pp. 21-26 ◽  
Author(s):  
Leslie Lamb ◽  
Paria Kashani ◽  
John Ryan ◽  
Guy Hebert ◽  
Adnan Sheikh ◽  
...  
Keyword(s):  
Patient Care ◽  
Emergency Radiology ◽  
Time Frame ◽  
Turnaround Time ◽  
Time Interval ◽  
Final Report ◽  
Radiology Resident ◽  
Cross Sectional ◽  
Patient Disposition ◽  
Report Turnaround Time

AbstractBackgroundOne of the many challenges facing emergency departments (EDs) across North America is timely access to emergency radiology services. Academic institutions, which are typically also regional referral centres, frequently require cross-sectional studies to be performed 24 hours a day with expedited final reports to accelerate patient care and ED flow.ObjectiveThe purpose of this study was to determine if the presence of an in-house radiologist, in addition to a radiology resident dedicated to the ED, had a significant impact on report turnaround time.MethodsPreliminary and final report turnaround times, provided by the radiology resident and staff, respectively, for patients undergoing computed tomography or ultrasonography of their abdomen/pelvis in 2008 (before the implementation of emergency radiology in-house staff service) were compared to those performed during the same time frame in 2009 and 2010 (after staffing protocols were changed).ResultsA total of 1,624 reports were reviewed. Overall, there was no statistically significant decrease in the preliminary report turnaround times between 2008 and 2009 (p = 0.1102), 2009 and 2010 (p = 0.6232), or 2008 and 2010 (p = 0.0890), although times consistently decreased from a median of 2.40 hours to 2.08 hours to 2.05 hours (2008 to 2009 to 2010). There was a statistically significant decrease in final report turnaround times between 2008 and 2009 (p < 0.0001), 2009 and 2010 (p < 0.0011), and 2008 and 2010 (p < 0.0001). Median final report times decreased from 5.00 hours to 3.08 hours to 2.75 hours in 2008, 2009, and 2010, respectively. There was also a significant decrease in the time interval between preliminary and final reports between 2008 and 2009 (p < 0.0001) and 2008 and 2010 (p < 0.0001) but no significant change between 2009 and 2010 (p = 0.4144).ConclusionOur results indicate that the presence of a dedicated ED radiologist significantly reduces final report turnaround time and thus may positively impact the time to ED patient disposition. Patient care is improved when attending radiologists are immediately available to read complex films, both in terms of health care outcomes and regarding the need for repeat testing. Providing emergency physicians with accurate imaging findings as rapidly as possible facilitates effective and timely management and thus optimizes patient care.

scholarly journals PrimerPooler: automated primer pooling to prepare library for targeted sequencing

2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Silas S. Brown ◽  
Yun-Wen Chen ◽  
Ming Wang ◽  
Alexandra Clipson ◽  
Eguzkine Ochoa ◽  
...  
Keyword(s):  
Variant Calling ◽  
Pcr Amplification ◽  
Illumina Miseq ◽  
Degenerate Primers ◽  
Cross Hybridization ◽  
Targeted Next Generation Sequencing ◽  
Target Sequencing ◽  
A Genome ◽  
Experimental Protocols ◽  
Minimal Depth

Abstract Targeted next-generation sequencing based on PCR amplification involves pooling of hundreds to thousands of primers, for preamplification and subsequent parallel single/multiplex PCR. It is often necessary to allocate the set of primers into subpools, a common issue being potential cross-hybridization. For smaller numbers of primers, pool division can be done manually using trial and error to minimize potential hybridization, but this becomes inefficient and time consuming with increasing numbers of primer pairs. We developed PrimerPooler that automates swapping of primer pairs between any user-defined number of subpools to obtain combinations with low-potential interactions. PrimerPooler performs inter-/intra-primer hybridization analysis to identify the adverse interactions, as well as simultaneous mapping of all primers onto a genome sequence in a single run without requiring a prior index of the genome. This allows detection of overlapping primer pairs and allocation of these primer pairs into separate subpools where tiling approaches are used. Using PrimerPooler, 1153 primer pairs were assigned to three preamplification pools (388, 389 and 376 primer pairs each), then 144 subpools of six- to nine-plex PCR for Fluidigm Access Array PCR, followed by Illumina MiSeq sequencing. With optimized experimental protocols, an average of 3269 reads was achieved for the targeted regions, with 95% of targets covered by at least 50 reads, the minimal depth of reads for confident variant calling. PrimerPooler provides a fast and highly efficient stratification of primer pairs for targeted enrichment, thus ensuring representative amplification of the targeted sequences. PrimerPooler is also able to analyse degenerate primers, and is thus also useful for microbiological identification and related target sequencing.

scholarly journals A fuzzy energy and security aware scheduling in cloud

2017 ◽  
Vol 7 (1.2) ◽  
pp. 117
Author(s):  
Sirisati Ranga Swamy ◽  
Sridhar Mandapati
Keyword(s):  
Cloud Computing ◽  
Job Scheduling ◽  
Fuzzy Inference ◽  
Turnaround Time ◽  
Time Cost ◽  
Inference System ◽  
Np Hard Problem ◽  
Fuzzy Energy ◽  
The One ◽  
The Membership Function

The cloud computing is the one that deals with the trading of the resources efficiently in accordance to the user’s need. A Job scheduling is the choice of an ideal resource for any job to be executed with regard to waiting time, cost or turnaround time. A cloud job scheduling will be an NP-hard problem that contains n jobs and m machines and every job is processed with each of these m machines to minimize the make span. The security here is one of the top most concerns in the cloud. In order to calculate the value of fitness the fuzzy inference system makes use of the membership function for determining the degree up to which the input parameters that belong to every fuzzy set is relevant. Here the fuzzy is used for the purpose of scheduling energy as well as security in the cloud computing.

scholarly journals Rickettsia felis Infection in a Common Household Insect Pest, Liposcelis bostrychophila (Psocoptera: Liposcelidae)

2010 ◽  
Vol 76 (7) ◽  
pp. 2280-2285 ◽  
Author(s):  
Adi Behar ◽  
Laurie J. McCormick ◽  
Steve J. Perlman
Keyword(s):  
Molecular Characterization ◽  
Insect Pest ◽  
Blood Feeding ◽  
Human Pathogen ◽  
Rickettsia Felis ◽  
Liposcelis Bostrychophila ◽  
The One

ABSTRACT Many species of Rickettsia are well-known mammalian pathogens transmitted by blood-feeding arthropods. However, molecular surveys are continually uncovering novel Rickettsia species, often in unexpected hosts, including many arthropods that do not feed on blood. This study reports a systematic molecular characterization of a Rickettsia infecting the psocid Liposcelis bostrychophila (Psocoptera: Liposcelidae), a common and cosmopolitan household pest. Surprisingly, the psocid Rickettsia is shown to be Rickettsia felis, a human pathogen transmitted by fleas that causes serious morbidity and occasional mortality. The plasmid from the psocid R. felis was sequenced and was found to be virtually identical to the one in R. felis from fleas. As Liposcelis insects are often intimately associated with humans and other vertebrates, it is speculated that they acquired R. felis from fleas. Whether the R. felis in psocids causes disease in vertebrates is not known and warrants further study.

A novel variant in PAX6 as the cause of aniridia in a Chinese family

2020 ◽  
Author(s):  
Xin Jin ◽  
Wei Liu ◽  
HouBin Huang
Keyword(s):  
Nonsense Mutation ◽  
Novel Mutation ◽  
Causative Mutation ◽  
Chinese Family ◽  
The Novel ◽  
Targeted Next Generation Sequencing ◽  
Iris Defect ◽  
The Family ◽  
Novel Variant ◽  
Pax6 Mutation

Abstract Background: Aniridia is a kind of congenital human panocular anomaly, which is related to PAX6 commonly. Methods: A Chinese Aniridia pedigree underwent ophthalmic examinations, including visual acuity, slit lamp and fundoscopy examination. The targeted next-generation sequencing of Aniridia genes was used to identify the causative mutation. Results: A novel heterozygous PAX6 nonsense mutation c.619A>T (p.K207*) was identified in the Chinese autosomal dominant family with aniridia. Phenotypes related to the novel mutation include nystagmus, iris defect, cataract and absence of macular fovea. Conclusion: The novel nonsense mutation in PAX6 was responsible for aniridia phenotype in the family. which expands the spectrum of the PAX6 mutation and its associated phenotype.

scholarly journals Nuclear ERK: Mechanism of Translocation, Substrates, and Role in Cancer

2019 ◽  
Vol 20 (5) ◽  
pp. 1194 ◽  
Author(s):  
Galia Maik-Rachline ◽  
Avital Hacohen-Lev-Ran ◽  
Rony Seger
Keyword(s):  
Nuclear Translocation ◽  
Resting Cells ◽  
Nuclear Pores ◽  
Cellular Processes ◽  
Extracellular Signal ◽  
Anti Cancer ◽  
Proliferation And Differentiation ◽  
The One ◽  
Signaling Components ◽  
Proof Of Principle

The extracellular signal-regulated kinases 1/2 (ERK) are central signaling components that regulate stimulated cellular processes such as proliferation and differentiation. When dysregulated, these kinases participate in the induction and maintenance of various pathologies, primarily cancer. While ERK is localized in the cytoplasm of resting cells, many of its substrates are nuclear, and indeed, extracellular stimulation induces a rapid and robust nuclear translocation of ERK. Similarly to other signaling components that shuttle to the nucleus upon stimulation, ERK does not use the canonical importinmechanism of nuclear translocation. Rather, it has its own unique nuclear translocation signal (NTS) that interacts with importin7 to allow stimulated shuttling via the nuclear pores. Prevention of the nuclear translocation inhibits proliferation of B-Raf- and N/K-Ras-transformed cancers. This effect is distinct from the one achieved by catalytic Raf and MEK inhibitors used clinically, as cells treated with the translocation inhibitors develop resistance much more slowly. In this review, we describe the mechanism of ERK translocation, present all its nuclear substrates, discuss its role in cancer and compare its translocation to the translocation of other signaling components. We also present proof of principle data for the use of nuclear ERK translocation as an anti-cancer target. It is likely that the prevention of nuclear ERK translocation will eventually serve as a way to combat Ras and Raf transformed cancers with less side-effects than the currently used drugs.

scholarly journals Digenic Inheritance of LAMA4 and MYH7 Mutations in Patient with Infantile Dilated Cardiomyopathy

Medicina ◽  
2019 ◽  
Vol 55 (1) ◽  
pp. 17 ◽  
Author(s):  
Atiyeh M Abdallah ◽  
S. Justin Carlus ◽  
Abdulhadi H Al-Mazroea ◽  
Mohammad Alluqmani ◽  
Yousef Almohammadi ◽  
...  
Keyword(s):  
Dilated Cardiomyopathy ◽  
Systolic Function ◽  
Left Ventricular ◽  
Dose Effect ◽  
Family Management ◽  
Ventricular Contractility ◽  
Targeted Next Generation Sequencing ◽  
Digenic Inheritance ◽  
Novel Variant ◽  
Next Generation Sequencing Ngs

Background and objectives: Dilated cardiomyopathy (DCM) is a rare cardiac disease characterised by left ventricular enlargement, reduced left ventricular contractility, and impaired systolic function. Childhood DCM is clinically and genetically heterogenous and associated with mutations in over 100 genes. The aim of this study was to identify novel variations associated with infantile DCM. Materials and Methods: Targeted next generation sequencing (NGS) of 181 cardiomyopathy-related genes was performed in three unrelated consanguineous families from Saudi Arabia. Variants were confirmed and their frequency established in 50 known DCM cases and 80 clinically annotated healthy controls. Results: The three index cases presented between 7 and 10 months of age with severe DCM. In Family A, there was digenic inheritance of two heterozygous variants: a novel variant in LAMA4 (c.3925G > A, p.Asp1309Asn) and a known DCM mutation in MYH7 (c.2770G > A; p.Glu924Lys). The LAMA4 p.Asp1309Asn variant was predicted to be likely pathogenic according to international guidelines. The other two families had no identifiable potentially deleterious variants. Conclusions: Inheritance of two genetic variants may have a synergistic or dose effect to cause severe DCM. We report of a novel p.Asp1309Asn variation associated with DCM. Targeted NGS is useful in the molecular diagnosis of DCM and to guide whole-family management and counselling.

scholarly journals Clinical characteristics and disease progression of retinitis pigmentosa associated with PDE6B mutations in Korean patients

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
You Na Kim ◽  
Joon Seon Song ◽  
Seak Hee Oh ◽  
Yoon Jeon Kim ◽  
Young Hee Yoon ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Disease Progression ◽  
Sequencing Data ◽  
Korean Patients ◽  
Targeted Next Generation Sequencing ◽  
Whole Exome ◽  
Structural Progression ◽  
Novel Variant ◽  
Whole Exome Sequencing Data ◽  
Phenotype Heterogeneity

Abstract Due to the genotype–phenotype heterogeneity in retinitis pigmentosa (RP), molecular diagnoses and prediction of disease progression is difficult. This study aimed to report ocular and genetic data from Korean patients with PDE6B-associated RP (PDE6B-RP), and establish genotype–phenotype correlations to predict the clinical course. We retrospectively reviewed targeted next-generation sequencing or whole exome sequencing data for 305 patients with RP, and identified PDE6B-RP in 15 patients (median age, 40.0 years). Amongst these patients, ten previously reported PDE6B variants (c.1280G > A, c.1488del, c.1547T > C, c.1604T > A, c.1669C > T, c.1712C > T, c.2395C > T, c.2492C > T, c.592G > A, and c.815G > A) and one novel variant (c.712del) were identified. Thirteen patients (86.7%) experienced night blindness as the first symptom at a median age of 10.0 years. Median age at diagnosis was 21.0 years and median visual acuity (VA) was 0.20 LogMAR at the time of genetic analysis. Nonlinear mixed models were developed and analysis revealed that VA exponentially decreased over time, while optical coherence tomography parameters linearly decreased, and this was related with visual field constriction. A high proportion of patients with the c.1669C > T variant (7/9, 77.8%) had cystoid macular edema; despite this, patients with this variant did not show a higher rate of functional or structural progression. This study will help clinicians predict functional and structural progression in patients with PDE6B-RP.

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