The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

Journal of the American Medical Informatics Association

Volumn 24, Issue 3, 2017, Pages 513-519

  Huang, Linda ^a,b   Fernandes, Helen ^a,c   Zia, Hamid ^a,c   Tavassoli, Peyman ^a,c   Rennert, Hanna ^c   Pisapia, David ^a,c   Imielinski, Marcin ^a,c   Sboner, Andrea ^a,b,c   Rubin, Mark A ^a,c   Kluk, Michael ^a,c   Elemento, Olivier ^a,b  

^a Weill Cornell Medicine   (United States)

^b Institute for Computational Biomedicine   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

Application programming interface; Cancer genomics; Clinical reporting; Database; Pathology; Precision medicine

Indexed keywords

ANTINEOPLASTIC AGENT; B RAF KINASE; EPIDERMAL GROWTH FACTOR RECEPTOR; K RAS PROTEIN;

ARTICLE; CODON; COPY NUMBER VARIATION; EXON; GENE; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; KIT GENE; KNOWLEDGE BASE; MALIGNANT NEOPLASM; MISSENSE MUTATION; PERSONALIZED MEDICINE; POINT MUTATION; TISSUE SPECIFICITY; WHOLE EXOME SEQUENCING; COMPUTER INTERFACE; GENETIC DATABASE; GENETICS; GENOMICS; NEOPLASM; ONLINE SYSTEM;

DATABASES, GENETIC; GENOMICS; HUMANS; KNOWLEDGE BASES; NEOPLASMS; ONLINE SYSTEMS; PRECISION MEDICINE; USER-COMPUTER INTERFACE;

EID: 85019771721     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1093/jamia/ocw148     Document Type: Article

References (11)

1. Roychowdhury S, Iyer MK, Robinson DR, et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Trans Med. 2011;3(111):111ra21.
2. Van Allen EM, Wagle N, et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med. 2014;20(6):682-8.
3. Beltran H, Eng K, Mosquera JM, et al. Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response. JAMA Onco.l 2015;1(4):466-74.
4. McLaren W, Gil L, Hunt SE, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122.
5. Cingolani P, Platts A, Wang le L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80-92.
6. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
7. Landrum MJ, Lee JM, Riley GR, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(Database issue):D980-85.
8. den Dunnen JT, Dalgleish R, Maglott DR, et al. HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum Mutat. 2016;37(6):564-69.
9. Yates A, Beal K, Keenan S, et al. The Ensembl REST API: Ensembl Data for Any Language. Bioinformatics. 2015;31(1):143-45.
10. Forbes SA, Beare D, Gunasekaran P, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43(Database issue):D805-11.
11. Gray KA, Yates B, Seal RL, Wright MW, Bruford EA. Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015;43(Database issue):D1079-85.