Challenges using diagnostic next-generation sequencing in the clinical environment for inherited retinal disorders

2014 ◽  
Vol 11 (1) ◽  
pp. 99-111 ◽  
Author(s):  
Wayne IL Davies
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Clinical Environment ◽  
Retinal Disorders ◽  
Inherited Retinal Disorders ◽  
Generation Sequencing

scholarly journals Targeted Next Generation Sequencing Identifies Novel Mutations inRP1as a Relatively Common Cause of Autosomal Recessive Rod-Cone Dystrophy

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Said El Shamieh ◽  
Elise Boulanger-Scemama ◽  
Marie-Elise Lancelot ◽  
Aline Antonio ◽  
Vanessa Démontant ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Autosomal Recessive ◽  
Cone Dystrophy ◽  
Next Generation ◽  
Prevalence Studies ◽  
Targeted Next Generation Sequencing ◽  
Retinal Disorders ◽  
Inherited Retinal Disorders ◽  
Generation Sequencing ◽  
Index Cases

We report ophthalmic and genetic findings in families with autosomal recessive rod-cone dystrophy (arRCD) andRP1mutations. Detailed ophthalmic examination was performed in 242 sporadic and arRCD subjects. Genomic DNA was investigated using our customized next generation sequencing panel targeting up to 123 genes implicated in inherited retinal disorders. Stringent filtering coupled with Sanger sequencing and followed by cosegregation analysis was performed to confirm biallelism and the implication of the most likely disease causing variants. Sequencing identified 9RP1mutations in 7 index cases. Eight of the mutations were novel, and all cosegregated with severe arRCD phenotype, found associated with additional macular changes. Among the identified mutations, 4 belong to a region, previously associated with arRCD, and 5 others in a region previously associated with adRCD. Our prevalence studies showed thatRP1mutations account for up to 2.5% of arRCD. These results point out for the necessity of sequencingRP1when genetically investigating sporadic and arRCD. It further highlights the interest of unbiased sequencing technique, which allows investigating the implication of the same gene in different modes of inheritance. Finally, it reports that different regions ofRP1can also lead to arRCD.

scholarly journals Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment

2016 ◽  
Vol 140 (9) ◽  
pp. 958-975 ◽  
Author(s):  
Somak Roy ◽  
William A. LaFramboise ◽  
Yuri E. Nikiforov ◽  
Marina N. Nikiforova ◽  
Mark J. Routbort ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Laboratory ◽  
Cost Effective ◽  
Small Degree ◽  
Clinical Informatics ◽  
Next Generation ◽  
Clinical Environment ◽  
Next Generation Sequencing Technology ◽  
Clinical Laboratories ◽  
Generation Sequencing

Context.—Next-generation sequencing (NGS) is revolutionizing the discipline of laboratory medicine, with a deep and direct impact on patient care. Although it empowers clinical laboratories with unprecedented genomic sequencing capability, NGS has brought along obvious and obtrusive informatics challenges. Bioinformatics and clinical informatics are separate disciplines with typically a small degree of overlap, but they have been brought together by the enthusiastic adoption of NGS in clinical laboratories. The result has been a collaborative environment for the development of novel informatics solutions. Sustaining NGS-based testing in a regulated clinical environment requires institutional support to build and maintain a practical, robust, scalable, secure, and cost-effective informatics infrastructure. Objective.—To discuss the novel NGS informatics challenges facing pathology laboratories today and offer solutions and future developments to address these obstacles. Data Sources.—The published literature pertaining to NGS informatics was reviewed. The coauthors, experts in the fields of molecular pathology, precision medicine, and pathology informatics, also contributed their experiences. Conclusions.—The boundary between bioinformatics and clinical informatics has significantly blurred with the introduction of NGS into clinical molecular laboratories. Next-generation sequencing technology and the data derived from these tests, if managed well in the clinical laboratory, will redefine the practice of medicine. In order to sustain this progress, adoption of smart computing technology will be essential. Computational pathologists will be expected to play a major role in rendering diagnostic and theranostic services by leveraging “Big Data” and modern computing tools.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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