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WG-GCP - 4) Best practice: links to common equipment used in NGS

Click on the links to access the related webpages


a. Wet Lab

DNA quantification

Liquid handling

Popular Thermal Cyclers

qPCR machines

ddPCR

Sonication


b. Bioinformatics

  • Roy S, LaFramboise WA, Nikiforov YE, et al. Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment. Arch Pathol Lab Med. 2016;140(9):958-975.
  • Haeussler M, Zweig AS, Tyner C, et al. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res. 2019;47(D1):D853-D858.

 

c. Reporting and variant interpretation

  • Chakravarty D, Gao J, Phillips SM, et al. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol. 2017
  • Johnson A, Khotskaya YB, Brusco L, et al. Clinical Use of Precision Oncology Decision Support. JCO Precis Oncol. 2017
  • Huang L, Fernandes H, Zia H, et al. The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations. J Am Med Inform Assoc. 2017;24(3):513-519.
  • Patterson SE, Statz CM, Yin T, Mockus SM. Utility of the JAX Clinical Knowledgebase in capture and assessment of complex genomic cancer data. NPJ Precis Oncol. 2019;3:2.
  • Landrum MJ, Lee JM, Benson M, et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018;46(D1):D1062-D1067.
  • Kopanos C, Tsiolkas V, Kouris A, et al. VarSome: the human genomic variant search engine. Bioinformatics. 2019;35(11):1978-1980.
  • UCSC genome browser: http://genome.ucsc.edu/cgi-bin/hgGateway
  • Catalogue of Somatic Mutations In Cancer, COSMIC: https://cancer.sanger.ac.uk/cosmic
  • Cbioportal: https://www.cbioportal.org/
  • gnomAD: https://gnomad.broadinstitute.org/

Incidental findings

  • Saelaert M, Mertes H, Moerenhout T, De Baere E, Devisch I. Criteria for reporting incidental findings in clinical exome sequencing - a focus group study on professional practices and perspectives in Belgian genetic centres. BMC Med Genomics. 2019;12(1):123.


d. Clinical treatment guidelines

The NCCN guidelines are probably the best guidelines for treatment recommendations based on molecular alterations

For more rare alterations

General information about what is coming out in targeted oncology 

American Society of Clinical Oncology guidelines

Basic websites on cancer treatment

 
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