scholarly journals Improved molecular diagnosis by the detection of exonic deletions with target gene capture and deep sequencing

2014 ◽  
Vol 17 (2) ◽  
pp. 99-107 ◽  
Author(s):  
Yanming Feng ◽  
David Chen ◽  
Guo-Li Wang ◽  
Victor Wei Zhang ◽  
Lee-Jun C. Wong
Keyword(s):  
Molecular Diagnosis ◽  
Deep Sequencing ◽  
Target Gene ◽  
Gene Capture ◽  
Target Gene Capture

scholarly journals Target Gene Capture Sequencing in Chinese Population of Sporadic Parkinson Disease

Medicine ◽  
2015 ◽  
Vol 94 (20) ◽  
pp. e836 ◽  
Author(s):  
Zhiming Li ◽  
Qing Lin ◽  
Wenqing Huang ◽  
Chi-Meng Tzeng
Keyword(s):  
Parkinson Disease ◽  
Chinese Population ◽  
Target Gene ◽  
Gene Capture ◽  
Capture Sequencing ◽  
Target Gene Capture

scholarly journals Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Pierpaolo Maisano Delser ◽  
Shannon Corrigan ◽  
Matthew Hale ◽  
Chenhong Li ◽  
Michel Veuille ◽  
...  
Keyword(s):  
Target Gene ◽  
Population Genomics ◽  
Gene Capture ◽  
Target Gene Capture

scholarly journals Population genomics ofC. melanopterususing target gene capture data: demographic inferences and conservation perspectives

2016 ◽  
Author(s):  
Pierpaolo Maisano Delser ◽  
Shannon Corrigan ◽  
Matthew Hale ◽  
Chenhong Li ◽  
Michel Veuille ◽  
...  
Keyword(s):  
Target Gene ◽  
Population Genomics ◽  
Model Organism ◽  
Sampling Scheme ◽  
Model Organisms ◽  
Gene Capture ◽  
Sampling Schemes ◽  
History Of ◽  
Carcharhinus Melanopterus ◽  
Target Gene Capture

AbstractPopulation genetics studies on non-model organisms typically involve sampling few markers from multiple individuals. Next-generation sequencing approaches open up the possibility of sampling many more markers from fewer individuals to address the same questions. Here, we applied a target gene capture method to deep sequence ∼1000 independent autosomal regions of a non-model organism, the blacktip reef shark (Carcharhinus melanopterus). We devised a sampling scheme based on the predictions of theoretical studies of metapopulations to show that sampling few individuals, but many loci, can be extremely informative to reconstruct the evolutionary history of species. We collected data from a single deme (SID) from Northern Australia and from a scattered sampling representing various locations throughout the Indian Ocean (SCD). We explored the genealogical signature of population dynamics detected from both sampling schemes using an ABC algorithm. We then contrasted these results with those obtained by fitting the data to a non-equilibrium finite island model. Both approaches supported anNmvalue ∼40, consistent with philopatry in this species. Finally, we demonstrate through simulation that metapopulations exhibit greater resilience to recent changes in effective size compared to unstructured populations. We propose an empirical approach to detect recent bottlenecks based on our sampling scheme.

Dependable and Efficient Clinical Utility of Target Capture-Based Deep Sequencing in Molecular Diagnosis of Retinitis Pigmentosa

2014 ◽  
Vol 55 (10) ◽  
pp. 6213 ◽  
Author(s):  
Jing Wang ◽  
Victor W. Zhang ◽  
Yanming Feng ◽  
Xia Tian ◽  
Fang-Yuan Li ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Molecular Diagnosis ◽  
Deep Sequencing ◽  
Clinical Utility ◽  
Target Capture

scholarly journals Molecular Diagnosis of Actinomadura madurae Infection by 16S rRNA Deep Sequencing

2013 ◽  
Vol 51 (12) ◽  
pp. 4262-4265 ◽  
Author(s):  
S. J. Salipante ◽  
D. J. SenGupta ◽  
D. R. Hoogestraat ◽  
L. A. Cummings ◽  
B. H. Bryant ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Diagnosis ◽  
Deep Sequencing ◽  
Actinomadura Madurae

scholarly journals Identification of a Novel ACTN4 Gene Mutation Which Is Resistant to Primary Nephrotic Syndrome Therapy

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Lingzhang Meng ◽  
Shan Cao ◽  
Na Lin ◽  
Jingjie Zhao ◽  
Xulong Cai ◽  
...  
Keyword(s):  
Nephrotic Syndrome ◽  
Target Gene ◽  
Minimal Change ◽  
Cleavage Sites ◽  
Primary Nephrotic Syndrome ◽  
Minimal Change Nephropathy ◽  
Filtration Barrier ◽  
Capture Method ◽  
Generation Sequencing ◽  
Target Gene Capture

ACTN4, a gene which codes for the protein α-actinin-4, is critical for the maintenance of the renal filtration barrier. It is well known that ACTN4 mutations can lead to kidney dysfunction, such as familial focal segmental glomerulosclerosis (FSGS), a common cause of primary nephrotic syndrome (PNS). To elucidate whether other mutations of ACTN4 exist in PNS patients, we sequenced the ACTN4 gene in biopsies collected from 155 young PNS patients (≤16 years old). The patients were classified into five groups: FSGS, minimal change nephropathy, IgA nephropathy, membranous nephropathy, and those without renal puncture. Ninety-eight healthy people served as controls. Samples were subjected to Illumina’s next generation sequencing protocols using FastTarget target gene capture method. We identified 5 ACTN4 mutations which occurred only in PNS patients: c.1516G > A (p.G506S) on exon 13 identified in two PNS patients, one with minimal change nephropathy and another without renal puncture; c.1442 + 10G > A at the splice site in a minimal change nephropathy patient; c.2191-4G > A at the cleavage site, identified from two FSGS patients; and c.1649A > G (p.D550G) on exon 14 together with c.2191-4G > A at the cleavage sites, identified from two FSGS patients. Among these, c.1649A > G (p.D550G) is a novel ACTN4 mutation. Patients bearing the last two mutations exhibited resistance to clinical therapies.

scholarly journals Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa

PLoS ONE ◽  
2018 ◽  
Vol 13 (4) ◽  
pp. e0185237 ◽  
Author(s):  
Hui Huang ◽  
Yanhua Chen ◽  
Huishuang Chen ◽  
Yuanyuan Ma ◽  
Pei-Wen Chiang ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Molecular Diagnosis ◽  
Systematic Evaluation ◽  
Gene Capture ◽  
Capture Sequencing

Rapid Molecular Diagnosis Of JAK2V617F Negative MPN By Targeted Deep Sequencing Using The Ion Torrent PGM

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 4093-4093
Author(s):  
Nathan Klose ◽  
Michael R Tallack ◽  
Graham Magor ◽  
Peter Mollee ◽  
Andrew C Perkins
Keyword(s):  
Molecular Diagnosis ◽  
Deep Sequencing ◽  
Cytokine Receptor ◽  
Causative Mutation ◽  
Receptor Signaling ◽  
Ion Torrent ◽  
Ion Torrent Pgm ◽  
Increased Risk ◽  
Stat Signaling ◽  
Stat Pathway

Abstract Myeloproliferative neoplasms (MPN) are a heterogeneous group of blood disorders characterized by excess production of mature blood cells, increased risk of thrombotic complications and slow progression to myelofibrosis or, less often, leukemia. Activation of the JAK-STAT signaling pathway is a common underlying feature of these diseases and JAK kinase inhibitors are efficacious in the more advanced forms of disease. Most cases of polycythemia vera (PV) and approximately 60% of essential thrombocythemia (ET) and primary myelofibrosis (MF) harbor a point mutation in JAK2 (V617F) which leads to constitutive JAK-STAT signaling and factor independent cell growth. The remaining 40% of cases of MF and ET harbor a broad range of mutations in many genes including those involved in cytokine receptor signaling, other components or the JAK-STAT pathway or epigenetic regulators. This poses a challenge for rapid molecular diagnosis. Also, since ET is essentially a diagnosis of exclusion of reactive causes of thrombocytosis, many cases of chronic ‘ET’ may not be clonal hematological neoplasms but reactive conditions. We have developed a rapid deep sequencing pipeline to detect mutations in 65 genes which have been implicated in MPN through previous reports of human mutations, mouse models of MPN, or other known components of hematopoietic cytokine receptor signaling. We used 10ng of DNA from blood to amplify and sequence all the exons of these 65 genes using Ampliseq and Ion Torrent PGM. Using 318 PGM chips and 8-fold multiplexing we achieved on average 200 fold coverage of the target exome. The bioinformatics of SNP validation and rapid generation of reports will be presented. From a pilot study of 30 cases referred for molecular diagnosis, we have detected the likely causative mutation in approximately 80% of ET and MF where JAK2 is wild type. Many of these mutations are known to be causative in MPN, including those in MPL, ASXL1, SET2, SH2B3 (LNK), EZH2, CBL, DNMT3A and other genes. We have identified a novel inherited mutation in a family with MPN and validated it in BAF3 factor-independency assays. We have identified further novel mutations in JAK3, EED, DNMT3A, APC and two phosphatases involved in silencing activated JAK-STAT pathway components. The biological significance of these is under investigation and progress will be reported. In many cases we find evidence for clonal evolution involving secondary mutations in epigenetic modifying proteins on top of driver mutations in the JAK-STAT pathway. In short, targeted exome re-sequencing using Ampliseq and Ion Torrent PGM provides a rapid and relatively cheap method for molecular diagnosis and characterization of most cases of MPN. Disclosures: Perkins: Novartis Oncology: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees.

1504: Molecular Diagnosis and Staging of Prostate Cancer Using Clusterin in Real Time Reverse Transcription Polymerase Chain Reaction (RT-PCR)

2006 ◽  
Vol 175 (4S) ◽  
pp. 485-486
Author(s):  
Sabarinath B. Nair ◽  
Christodoulos Pipinikas ◽  
Roger Kirby ◽  
Nick Carter ◽  
Christiane Fenske
Keyword(s):  
Prostate Cancer ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain
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