scholarly journals Next-Generation Sequencing-Based Molecular Diagnosis of Choroideremia

2015 ◽  
Vol 6 (2) ◽  
pp. 246-250 ◽  
Author(s):  
Kayo Shimizu ◽  
Akio Oishi ◽  
Maho Oishi ◽  
Ken Ogino ◽  
Satoshi Morooka ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Retinal Detachment ◽  
Macular Hole ◽  
Molecular Diagnosis ◽  
Novel Mutation ◽  
Case Series ◽  
Next Generation ◽  
Macular Hole Retinal Detachment ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

We screened patients with choroideremia using next-generation sequencing (NGS) and identified a novel mutation and a known mutation in the CHM gene. One patient presented an atypical fundus appearance for choroideremia. Another patient presented macular hole retinal detachment in the left eye. The present case series shows the utility of NGS-based screening in patients with choroideremia. In addition, the presence of macular hole in 1 of the 2 patients, together with a previous report, indicated the susceptibility of patients with choroideremia to macular hole.

scholarly journals Utility of Whole-Genome Next-Generation Sequencing of Plasma in Identifying Opportunistic Infections in HIV/AIDS

2019 ◽  
Vol 13 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Yang Zhou ◽  
Vagish Hemmige ◽  
Sudeb C. Dalai ◽  
David K. Hong ◽  
Kenneth Muldrew ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Opportunistic Infections ◽  
Case Series ◽  
Whole Genome ◽  
Next Generation ◽  
Invasive Procedures ◽  
First Case ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Hiv Aids

Background:AIDS-associated Opportunistic Infections (OIs) have significant morbidity and mortality and can be diagnostically challenging, requiring invasive procedures as well as a combination of culture and targeted molecular approaches.Objective:We aimed to demonstrate the clinical utility of Next-generation Sequencing (NGS) in pathogen identification; NGS is a maturing technology enabling the detection of miniscule amounts of cell-free microbial DNA from the bloodstream.Methods:We utilized a novel Next-generation Sequencing (NGS) test on plasma samples to diagnose a series of HIV-associated OIs that were diagnostically confirmed through conventional microbial testing.Results:In all cases, NGS test results were available sooner than conventional testing. This is the first case series demonstrating the utility of whole-genome NGS testing to identify OIs from plasma in HIV/AIDS patients.Conclusion:NGS approaches present a clinically-actionable, comprehensive means of diagnosing OIs and other systemic infections while avoiding the labor, expense, and delays of multiple tests and invasive procedures.

scholarly journals Next-generation sequencing approach to hyperCKemia

2019 ◽  
Vol 5 (5) ◽  
pp. e352 ◽  
Author(s):  
Anna Rubegni ◽  
Alessandro Malandrini ◽  
Claudia Dosi ◽  
Guja Astrea ◽  
Jacopo Baldacci ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnosis ◽  
Diagnostic Yield ◽  
Clinical Neurology ◽  
Next Generation ◽  
Variants Of Unknown Significance ◽  
Unknown Significance ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ObjectiveNext-generation sequencing (NGS) was applied in molecularly undiagnosed asymptomatic or paucisymptomatic hyperCKemia to investigate whether this technique might allow detection of the genetic basis of the condition.MethodsSixty-six patients with undiagnosed asymptomatic or paucisymptomatic hyperCKemia, referred to tertiary neuromuscular centers over an approximately 2-year period, were analyzed using a customized, targeted sequencing panel able to investigate the coding exons and flanking intronic regions of 78 genes associated with limb-girdle muscular dystrophies, rhabdomyolysis, and metabolic and distal myopathies.ResultsA molecular diagnosis was reached in 33 cases, corresponding to a positive diagnostic yield of 50%. Variants of unknown significance were found in 17 patients (26%), whereas 16 cases (24%) remained molecularly undefined. The major features of the diagnosed cases were mild proximal muscle weakness (found in 27%) and myalgia (in 24%). Fourteen patients with a molecular diagnosis and mild myopathic features on muscle biopsy remained asymptomatic at a 24-month follow-up.ConclusionsThis study of patients with undiagnosed hyperCKemia, highlighting the advantages of NGS used as a first-tier diagnostic approach in genetically heterogeneous conditions, illustrates the ongoing evolution of molecular diagnosis in the field of clinical neurology. Isolated hyperCKemia can be the sole feature alerting to a progressive muscular disorder requiring careful surveillance.

The Clinical Utility Of Next-Generation Sequencing In The Diagnosis Of Hereditary Hemolytic Anemias

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3421-3421
Author(s):  
Roberto H Nussenzveig ◽  
Nikhil Sangle ◽  
Robert D. Christensen ◽  
Mohamed E Salama ◽  
Josef Prchal ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Family History ◽  
Hemolytic Anemia ◽  
Molecular Diagnosis ◽  
Clinical Utility ◽  
Novel Mutation ◽  
Red Cell ◽  
The Novel ◽  
Next Generation ◽  
Generation Sequencing

Abstract Hereditary hemolytic anemia encompasses a diverse group of genetically and phenotypically heterogeneous disorders that are characterized by increased red cell destruction, with consequences ranging from relatively harmless to severe life-threatening anemia. Moreover, red cell hemolysis leads to increased production of bilirubin, a breakdown product of hemoglobin, which in neonates places them at risk for extreme jaundice and its consequences. Two of the more common genetic causes of hereditary hemolytic anemia, excluding hemoglobinopathies, can be attributed to defects in either the red cell cytoskeleton or enzyme deficiency (e.g. G6PD, PKLR). Morphological and biochemical diagnosis of hereditary hemolytic anemia due to defects in RBC cytoskeleton or enzyme deficiency is routinely performed in many laboratories. However, routine studies can be challenging, particularly in transfusion-dependent infants and children since these patients have mostly transfused RBCs. Molecular diagnosis has also been challenging not only due to molecular heterogeneity but also due to the number and size of the genes involved. We developed a novel, high-throughput, sensitive sequencing assay for diagnosis of the molecular causes of the two major types of hereditary hemolytic anemia described above. Our diagnostic panel includes 25 genes encoding cytoskeletal proteins and enzymes, and covers the complete coding region, splice site junctions, and, where appropriate, deep intronic or regulatory regions. Targeted gene capture and library construction for next-generation sequencing (NGS) was performed using HaloPlex as described by the manufacturer (Agilent Technologies, Santa Clara, CA). One hundred base-pair paired-end sequencing was done on a HiSeq 2000 system (Illumina, San Diego, CA). Bioinformatic analysis was based on an “in house” pipeline using standard open-source software. A total of 19 patients with unexplained hemolytic anemia, and 30 normal controls were tested in our assay. Mutations in the appropriate genes were identified in 17/19 patients, many of these being novel. All identified mutations were confirmed by Sanger sequencing. In silico prediction of the impact resulting from the novel mutations was performed using two web-based software packages, Sift and Polyphen. Where possible, inheritance of pathogenic mutations was determined in immediate relatives. One of the cases we investigated involved a neonate with unexplained jaundice and subsequent, significantly compensated, anemia without family history of a hemolytic disorder. Routine studies were suggestive for hereditary spherocytosis due to the presence of microspherocytes on the proband’s blood film, increased osmotic fragility, and decreased eosin-5-maleimide stained red cells. Two pathogenic mutations, in compound heterozygosity, were identified in the SPTA1 gene (α-spectrin). A previously reported mutation αLEPRA, known to be associated with recessive spectrin-deficient HS, and a novel mutation in intron 45 +1 (c.6530+1G>A) disrupting the consensus splice site. Screening of other relevant genes failed to reveal additional mutations. Studies of his parents revealed both to be heterozygous carriers with the asymptomatic mother harboring the αLEPRA mutation and the asymptomatic father harboring the novel mutation. Our results demonstrate the clinical utility of this assay for molecular diagnosis and genetic counseling for parents at risk of having affected children. Next-generation sequencing provides a cost-effective and rapid approach to molecular diagnosis, especially in cases where traditional testing has failed. We have used this technology successfully to determine the molecular causes of hemolytic anemia in several cases with no family history. Furthermore, we have validated its clinical utility in neonates risk for hyperbillirubinemia, as well as, in patients with transfusion dependent hemolytic anemia. Disclosures: No relevant conflicts of interest to declare.

Improved molecular diagnosis of patients with neonatal diabetes using a combined next-generation sequencing and MS-MLPA approach

2016 ◽  
Vol 29 (5) ◽  
Author(s):  
Gorka Alkorta-Aranburu ◽  
Madina Sukhanova ◽  
David Carmody ◽  
Trevor Hoffman ◽  
Latrice Wysinger ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnosis ◽  
Neonatal Diabetes ◽  
Unknown Etiology ◽  
Chromosome 6 ◽  
Next Generation ◽  
Transient Neonatal Diabetes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Parental Inheritance

Abstract: We evaluated a methylation-specific multiplex-ligation-dependent probe amplification (MS-MLPA) assay for the molecular diagnosis of transient neonatal diabetes mellitus (TNDM) caused by 6q24 abnormalities and assessed the clinical utility of using this assay in combination with next generation sequencing (NGS) analysis for diagnosing patients with neonatal diabetes (NDM).: We performed MS-MLPA in 18 control samples and 42 retrospective NDM cases with normal bi-parental inheritance of chromosome 6. Next, we evaluated 22 prospective patients by combining NGS analysis of 11 NDM genes and the MS-MLPA assay.: 6q24 aberrations were identified in all controls and in 19% of patients with normal bi-parental inheritance of chromosome 6. The MS-MLPA/NGS combined approach identified a genetic cause in ~64% of patients with NDM of unknown etiology.MS-MLPA is a reliable method to identify all known 6q24 abnormalities and comprehensive testing of all causes reveals a causal mutation in ~64% of patients.

scholarly journals Unravelling the Complexity of Inherited Retinal Dystrophies Molecular Testing: Added Value of Targeted Next-Generation Sequencing

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Isabella Bernardis ◽  
Laura Chiesi ◽  
Elena Tenedini ◽  
Lucia Artuso ◽  
Antonio Percesepe ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnosis ◽  
Genetic Alterations ◽  
Macular Dystrophy ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Inherited Retinal Dystrophies ◽  
Retinal Dystrophies ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

To assess the clinical utility of targeted Next-Generation Sequencing (NGS) for the diagnosis of Inherited Retinal Dystrophies (IRDs), a total of 109 subjects were enrolled in the study, including 88 IRD affected probands and 21 healthy relatives. Clinical diagnoses included Retinitis Pigmentosa (RP), Leber Congenital Amaurosis (LCA), Stargardt Disease (STGD), Best Macular Dystrophy (BMD), Usher Syndrome (USH), and other IRDs with undefined clinical diagnosis. Participants underwent a complete ophthalmologic examination followed by genetic counseling. A custom AmpliSeq™ panel of 72 IRD-related genes was designed for the analysis and tested using Ion semiconductor Next-Generation Sequencing (NGS). Potential disease-causing mutations were identified in 59.1% of probands, comprising mutations in 16 genes. The highest diagnostic yields were achieved for BMD, LCA, USH, and STGD patients, whereas RP confirmed its high genetic heterogeneity. Causative mutations were identified in 17.6% of probands with undefined diagnosis. Revision of the initial diagnosis was performed for 9.6% of genetically diagnosed patients. This study demonstrates that NGS represents a comprehensive cost-effective approach for IRDs molecular diagnosis. The identification of the genetic alterations underlying the phenotype enabled the clinicians to achieve a more accurate diagnosis. The results emphasize the importance of molecular diagnosis coupled with clinic information to unravel the extensive phenotypic heterogeneity of these diseases.

#40: Next-generation Sequencing Improves the Diagnosis of Uncommon Infection in children with Hematologic Malignancies: A Case Series Study

2021 ◽  
Vol 10 (Supplement_1) ◽  
pp. S2-S2
Author(s):  
Mi Zhou ◽  
Peifang Xiao ◽  
Hailong He ◽  
Jun Lu ◽  
Jie Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Symptoms ◽  
Case Series ◽  
Hematologic Malignancies ◽  
Next Generation ◽  
Promising Tool ◽  
Case Series Study ◽  
Next Generation Sequencing Ngs ◽  
Series Study ◽  
Generation Sequencing

Abstract Background Children with hematological malignancies are at high risk of infection. Various kinds of pathogens may cause infection in these patients. The effect of traditional methods on these patients is not ideal. Methods This was a case series study. The cases of five patients with clinical symptoms of pulmonary infection. Next-generation sequencing (NGS) was used to identify pathogens in these 5 patients. Results Uncommon pathogens were detected in five patients. Case information are shown in Table 1. Conclusion NGS may serve as a promising tool for rapid and accurate etiological diagnosis, which could greatly improve the diagnosis of uncommon infection in children with hematologic malignancies.

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