On-Boarding at CMO

This contains has all the onboarding information for people joining Center for Molecular Oncology

View the Project on GitHub mskcc/on-boarding

Useful papers to read

Note: URL last checked 19th March 2020

Institutional Resources/Methods

OncoKB: https://www.ncbi.nlm.nih.gov/pubmed/28890946
Hotspots:
- https://www.nature.com/articles/nbt.3391
- https://www.ncbi.nlm.nih.gov/pubmed/29247016
FACETS: https://www.ncbi.nlm.nih.gov/pubmed/27270079
MSK-IMPACT: https://www.ncbi.nlm.nih.gov/pubmed/25801821
MSK-ACCESS: https://www.nature.com/articles/s41467-021-24109-5
Duplex Sequencing: https://www.pnas.org/content/109/36/14508

Landscape

MSK-IMPACT: https://www.ncbi.nlm.nih.gov/pubmed/28481359
Clonal Hematopoiesis:
- https://www.ncbi.nlm.nih.gov/pubmed/29872864
- https://www.biorxiv.org/content/10.1101/848739v1
Gene specific: https://www.ncbi.nlm.nih.gov/pubmed/31292550
Germline: https://www.sciencedirect.com/science/article/pii/S0092867418303635?via%3Dihub

Scientific

Mutational Signatures: http://www.nature.com/nature/journal/v500/n7463/full/nature12477.html
WGD: https://www.ncbi.nlm.nih.gov/pubmed/30013179
Allelic Imbalance: https://www.ncbi.nlm.nih.gov/pubmed/30393068
Neoantigen: https://www.nature.com/articles/nrc.2016.154
Aneuploidy: http://www.ncbi.nlm.nih.gov/pubmed/22269907
Epigenetics: https://www.ncbi.nlm.nih.gov/pubmed/22770212

Translational

RECIST 1.1: https://ctep.cancer.gov/protocolDevelopment/docs/recist_guideline.pdf
Basket trials:
- https://www.ncbi.nlm.nih.gov/pubmed/28489509
- https://www.ncbi.nlm.nih.gov/pubmed/29420467

Clinical Genomics

Clinical genomics: https://www.ncbi.nlm.nih.gov/pubmed/29599476
Best practices for variant calling in clinical sequencing : https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00791-w
NGS-based cancer genomes: https://www.nature.com/articles/nrg2841
Genome-driven oncology: https://www.sciencedirect.com/science/article/pii/S0092867416317299?via%3Dihub
Immunotherapy:
- https://science.sciencemag.org/content/359/6382/1350
- https://www.nature.com/articles/s41591-019-0382-x
Oldies but goodies:
- https://www.cell.com/fulltext/S0092-8674(11)00127-9
- https://www.cell.com/fulltext/S0092-8674(13)00288-2

Common Genomic Terms

Genetics Glossary: https://www.genome.gov/genetics-glossary
JAMA: https://jamanetwork.com/journals/jama/fullarticle/1677346