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

• Qubit
• Nanodrop
• Tapestation

Liquid handling

• Biomek Automated Liquid Handlers (Beckman)
• Automated Liquid Handling Solutions (Beckman)
• Hamilton
• Tecan

Popular Thermal Cyclers

• Veriti (Thermo Fisher)
• MiniAmp (Thermo Fisher)
• T100 (Bio-Rad)
• Mastercycler (Eppendorf)
• SureCycler (Agilent)

qPCR machines

• 7900 /7900 fast (Thermo Fisher) 
• 7500/7500 fast (Thermo Fisher)
• Light Cycler (Roche) 
• AriaMx (Agilent)

ddPCR

• QX200 (Bio-Rad)

Sonication

• Covaris systems

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

• https://www.nccn.org/professionals/physician_gls/default.aspx

For more rare alterations

• https://www.mycancergenome.org/

General information about what is coming out in targeted oncology 

• https://www.targetedonc.com/

American Society of Clinical Oncology guidelines

• https://www.asco.org/research-guidelines/quality-guidelines/guidelines/assays-and-predictive-markers

Basic websites on cancer treatment

• https://www.cancer.gov/about-cancer/treatment/types
• https://www.mayoclinic.org/tests-procedures/cancer-treatment/about/pac-20393344
• https://www.cancer.org/treatment/treatments-and-side-effects/treatment-types.html