Next-generation sequencing workflows in veterinary infection biology: towards validation and quality assurance

2016 ◽  
Vol 35 (1) ◽  
pp. 67-81 ◽  
Author(s):  
S. VAN BORM ◽  
J. WANG ◽  
F. GRANBERG ◽  
A. COLLING
Keyword(s):  
Quality Assurance ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Infection Biology ◽  
Generation Sequencing

scholarly journals The Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing  data quality assurance

2018 ◽  
Vol 3 ◽  
pp. 37 ◽  
Author(s):  
Shazia Mahamdallie ◽  
Elise Ruark ◽  
Shawn Yost ◽  
Márton Münz ◽  
Anthony Renwick ◽  
...  
Keyword(s):  
Quality Assurance ◽  
Next Generation Sequencing ◽  
Test Performance ◽  
Median Number ◽  
Genomic Region ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Clinical Genetic ◽  
Generation Sequencing

Next generation sequencing (NGS) is routinely used in clinical genetic testing. Quality management of NGS testing is essential to ensure performance is consistently and rigorously evaluated. Three primary metrics are used in NGS quality evaluation: depth of coverage, base quality and mapping quality. To provide consistency and transparency in the utilisation of these metrics we present the Quality Sequencing Minimum (QSM). The QSM defines the minimum quality requirement a laboratory has selected for depth of coverage (C), base quality (B) and mapping quality (M) and can be applied per base, exon, gene or other genomic region, as appropriate. The QSM format is CX_BY(PY)_MZ(PZ). X is the parameter threshold for C, Y the parameter threshold for B, PY the percentage of reads that must reach Y, Z the parameter threshold for M, PZ the percentage of reads that must reach Z. The data underlying the QSM is in the BAM file, so a QSM can be easily and automatically calculated in any NGS pipeline. We used the QSM to optimise cancer predisposition gene testing using the TruSight Cancer Panel (TSCP). We set the QSM as C50_B10(85)_M20(95). Test regions falling below the QSM were automatically flagged for review, with 100/1471 test regions QSM-flagged in multiple individuals. Supplementing these regions with 132 additional probes improved performance in 85/100. We also used the QSM to optimise testing of genes with pseudogenes such as PTEN and PMS2. In TSCP data from 960 individuals the median number of regions that passed QSM per sample was 1429 (97%).  Importantly, the QSM can be used at an individual report level to provide succinct, comprehensive quality assurance information about individual test performance. We believe many laboratories would find the QSM useful. Furthermore, widespread adoption of the QSM would facilitate consistent, transparent reporting of genetic test performance by different laboratories.

Quality assurance for next generation sequencing

Pathology ◽  
2017 ◽  
Vol 49 ◽  
pp. S31-S32
Author(s):  
Sze Chai ◽  
Nalishia Munusamy ◽  
Kwang Hong Tay ◽  
Martin P. Horan
Keyword(s):  
Quality Assurance ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validationand Quality Assurance Procedures

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1323
Author(s):  
Laila Sara Arroyo Mühr ◽  
Daniel Guerendiain ◽  
Kate Cuschieri ◽  
Karin Sundström
Keyword(s):  
Quality Assurance ◽  
Human Papillomavirus ◽  
Next Generation Sequencing ◽  
Point Mutations ◽  
Clinical Diagnostics ◽  
International Standards ◽  
Whole Genome ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.

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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