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