Enrichment of target sequences for next-generation sequencing applications in research and diagnostics

2014 ◽  
Vol 395 (2) ◽  
pp. 231-237 ◽  
Author(s):  
Janine Altmüller ◽  
Birgit S. Budde ◽  
Peter Nürnberg
Keyword(s):  
Research Projects ◽  
Sequencing Technology ◽  
Sequencing Strategy ◽  
Diagnostic Applications ◽  
Technical Principles ◽  
Gene Panel Sequencing ◽  
Generation Sequencing ◽  
Panel Sequencing ◽  
Enrichment Product

Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

Next Generation Sequencing Technology in Clinical Diagnostics

2020 ◽  
Vol 2 (7) ◽  
pp. 10-17
Author(s):  
Megha Agrawal ◽  
Keyword(s):  
Next Generation Sequencing ◽  
Basic Research ◽  
Cost Effective ◽  
Clinical Diagnostics ◽  
Library Preparation ◽  
Next Generation ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Diagnostic Applications ◽  
Generation Sequencing

The promise of next generation sequencing offers hope for the current DNA sequencing technology to evolve from the applications in basic research to transition to the clinical diagnostics. This advancement in the sequencing technology is happening in part due to the introduction of high throughput and benchtop instruments that offer fully automated cost-effective sequencing along with faster assay times. This development is believed to remove the bottleneck of the complex and cumbersome library preparation that include isolation of nucleic acids and the resulting amplified and barcoded DNA with sequencing adapters. Here, we present a brief overview of the principles of next generation sequencing and automation of library preparation along with the diagnostic applications of next generation sequencing in human immunogenetics. Finally, an outlook is presented.

scholarly journals Use of dedicated gene panel sequencing using next generation sequencing to improve the personalized care of lung cancer

Oncotarget ◽  
2016 ◽  
Vol 7 (17) ◽  
pp. 24860-24870 ◽  
Author(s):  
Coureche Guillaume Kaderbhai ◽  
Romain Boidot ◽  
Françoise Beltjens ◽  
Sandy Chevrier ◽  
Laurent Arnould ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Gene Panel ◽  
Next Generation ◽  
Personalized Care ◽  
Gene Panel Sequencing ◽  
Generation Sequencing ◽  
Panel Sequencing

Use of dedicated gene panel sequencing using next generation sequencing to improve the personalized care of lung cancer.

2016 ◽  
Vol 34 (15_suppl) ◽  
pp. e20523-e20523
Author(s):  
Coureche-Guillaume Kaderbhai ◽  
Francois Ghiringhelli ◽  
Romain Boidot ◽  
Françoise Beltjens ◽  
Sandy Chevrier ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Gene Panel ◽  
Next Generation ◽  
Personalized Care ◽  
Gene Panel Sequencing ◽  
Generation Sequencing ◽  
Panel Sequencing

scholarly journals A case of hypereosinophilic syndrome with STAT5b N642H mutation

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
Feihong Ding ◽  
Chaoping Wu ◽  
Yun Li ◽  
Sudipto Mukherjee ◽  
Subha Ghosh ◽  
...  
Keyword(s):  
Complete Blood Count ◽  
Hypereosinophilic Syndrome ◽  
Organ Damage ◽  
Myeloid Neoplasm ◽  
Acute Eosinophilic Pneumonia ◽  
Myeloid Neoplasms ◽  
Somatic Signal ◽  
Generation Sequencing

ABSTRACT Hypereosinophilia is defined as persistent eosinophilia (>1.5 × 109/L). Hypereosinophilic syndrome (HES) is a term used to describe a group of disorders characterized by sustained hypereosinophilia associated with end-organ damage. Based on underlying molecular mechanism of eosinophilia, there are different subtypes of HES. Diagnosis of HES subtype can be challenging, especially in the absence of overt lymphoid/myeloid neoplasms or discernable secondary causes. Long-term outpatient follow-up with periodic complete blood count and repeated bone marrow biopsy may be needed to monitor disease activity. Somatic signal transducer and activation transcription 5b (STAT5b) N642H mutation was recently found to be associated with myeloid neoplasms with eosinophilia. We report a case of HES who presented with pulmonary embolism and acute eosinophilic pneumonia, found to have recurrent STAT5b N642H mutation by next-generation sequencing, suggesting possible underlying myeloid neoplasm.

scholarly journals Matrilineal analysis of mutations in the DMD gene in a multigenerational South Indian cohort using DMD gene panel sequencing

2021 ◽  
Author(s):  
Arun Shastry ◽  
Sankaramoorthy Aravind ◽  
Meeta Sunil ◽  
Keerthi Ramesh ◽  
Berty Ashley ◽  
...  
Keyword(s):  
Gene Panel ◽  
South Indian ◽  
Dmd Gene ◽  
Gene Panel Sequencing ◽  
Panel Sequencing

scholarly journals Chances and challenges of a long-term data repository in multiple sclerosis: 20th birthday of the German MS registry

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lisa-Marie Ohle ◽  
David Ellenberger ◽  
Peter Flachenecker ◽  
Tim Friede ◽  
Judith Haas ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Sociodemographic Factors ◽  
Healthcare Research ◽  
Structure Design ◽  
Data Repository ◽  
Research Projects ◽  
Real World Data ◽  
Data Repositories ◽  
Term Data

AbstractIn 2001, the German Multiple Sclerosis Society, facing lack of data, founded the German MS Registry (GMSR) as a long-term data repository for MS healthcare research. By the establishment of a network of participating neurological centres of different healthcare sectors across Germany, GMSR provides observational real-world data on long-term disease progression, sociodemographic factors, treatment and the healthcare status of people with MS. This paper aims to illustrate the framework of the GMSR. Structure, design and data quality processes as well as collaborations of the GMSR are presented. The registry’s dataset, status and results are discussed. As of 08 January 2021, 187 centres from different healthcare sectors participate in the GMSR. Following its infrastructure and dataset specification upgrades in 2014, more than 196,000 visits have been recorded relating to more than 33,000 persons with MS (PwMS). The GMSR enables monitoring of PwMS in Germany, supports scientific research projects, and collaborates with national and international MS data repositories and initiatives. With its recent pharmacovigilance extension, it aligns with EMA recommendations and helps to ensure early detection of therapy-related safety signals.

scholarly journals Identification of a Novel Papillomavirus Type (MfoiPV1) Associated with Acrochordon in a Stone Marten (Martes foina)

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 539
Author(s):  
Urška Kuhar ◽  
Diana Žele Vengušt ◽  
Urška Jamnikar-Ciglenečki ◽  
Gorazd Vengušt
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Manifestation ◽  
Skin Tumor ◽  
Wild Animals ◽  
Stone Marten ◽  
Sequencing Technology ◽  
Martes Foina ◽  
Tumor Sample ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Papillomaviruses (PVs) are an extremely large group of viruses that cause skin and mucosal infections in humans and various domestic and wild animals. Nevertheless, there is limited knowledge about PVs in wildlife hosts, including mustelid species. This study describes a case in stone marten (Martes foina) with a clinical manifestation of skin tumor, which is rather atypical for infections with PVs. The result of the papillomavirus PCR performed on the skin tumor sample was positive, and the complete PV genome was determined in the studied sample using next-generation sequencing technology. The analysis of the PV genome revealed infection of the stone marten with a putative new PV type belonging to the Dyonupapillomavirus genus. The proposed new stone marten PV type was named MfoiPV1.

scholarly journals A Comprehensive Analysis of Hungarian MODY Patients—Part I: Gene Panel Sequencing Reveals Pathogenic Mutations in HNF1A, HNF1B, HNF4A, ABCC8 and INS Genes

Life ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 755
Author(s):  
Zsolt Gaál ◽  
Zsuzsanna Szűcs ◽  
Irén Kántor ◽  
Andrea Luczay ◽  
Péter Tóth-Heyn ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Low Dose ◽  
Comprehensive Analysis ◽  
First Line ◽  
Pathogenic Mutations ◽  
Appropriate Treatment ◽  
Causal Genes ◽  
Hnf1a Gene ◽  
Gene Panel Sequencing ◽  
Generation Sequencing

Maturity-onset diabetes of the young (MODY) has about a dozen known causal genes to date, the most common ones being HNF1A, HNF4A, HNF1B and GCK. The phenotype of this clinically and genetically heterogeneous form of diabetes depends on the gene in which the patient has the mutation. We have tested 450 Hungarian index patients with suspected MODY diagnosis with Sanger sequencing and next-generation sequencing and found a roughly 30% positivity rate. More than 70% of disease-causing mutations were found in the GCK gene, about 20% in the HNF1A gene and less than 10% in other MODY-causing genes. We found 8 pathogenic and 9 likely pathogenic mutations in the HNF1A gene in a total of 48 patients and family members. In the case of HNF1A-MODY, the recommended first-line treatment is low dose sulfonylurea but according to our data, the majority of our patients had been on unnecessary insulin therapy at the time of requesting their genetic testing. Our data highlights the importance of genetic testing in the diagnosis of MODY and the establishment of the MODY subtype in order to choose the most appropriate treatment.

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