The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources.

The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources.

Publication date: Aug 01, 2018

 The aim is to provide a comprehensive review of state-of-the art omics approaches, including proteomics, metabolomics, cell-free DNA, and patient cohort matching algorithms in precision oncology.

 In the past several years, the cancer informatics revolution has been the beneficiary of a data explosion. Different complementary omics technologies have begun coming into their own to provide a more nuanced view of the patient-tumor interaction beyond that of DNA alterations. A combined approach is beneficial to the patient as nearly all new cancer therapeutics are designed with an omics biomarker in mind. Proteomics and metabolomics provide us with a means of assaying in real-time the response of the tumor to treatment. Circulating cell-free DNA may allow us to better understand tumor heterogeneity and interactions with the host genome.

 Integration of increasingly available omics data increases our ability to segment patients into smaller and smaller cohorts, thereby prompting a shift in our thinking about how to use these omics data. With large repositories of patient omics-outcomes data being generated, patient cohort matching algorithms have become a dominant player.

 The continued promise of precision oncology is to select patients who are most likely to benefit from treatment and to avoid toxicity for those who will not. The increased public availability of omics and outcomes data in patients, along with improved computational methods and resources, are making precision oncology a reality.

Open Access PDF

Math’e, E., Hays, J.L., Stover, D.G., and Chen, J.L. The Omics Revolution Continues: The Maturation of High-Throughput Biological Data Sources. 05534. 2018 Yearb Med Inform (27):1.

Concepts Keywords
Assaying Proteomics
Biomarker Precision medicine
DNA Evidence-based medicine
Genome Metabolism
Heterogeneity Genomics
Informatics Systems biology
Metabolomics Branches of biology
Omics Real time tumor
Oncology Tumor
Proteomics Biomarker
Throughput Metabolomics
Toxicity Metabolomics
Tumor Proteomics

Semantics

Type Source Name
gene UNIPROT NFKBIZ
gene UNIPROT CTSB
gene UNIPROT ZBTB8OS
drug DRUGBANK Ilex paraguariensis leaf
gene UNIPROT ALPK3
gene UNIPROT MAK
disease DOID squamous carcinoma
disease MESH squamous carcinoma
disease MESH postoperative complications
gene UNIPROT TNFRSF11A
gene UNIPROT CES2
gene UNIPROT CASP1
pathway BSID Release
gene UNIPROT PACC1
gene UNIPROT SON
disease DOID neuroblastoma
disease MESH neuroblastoma
gene UNIPROT TNIP1
gene UNIPROT RENBP
disease DOID blood cancer
gene UNIPROT TNIP3
gene UNIPROT MS4A2
disease DOID colon cancer
disease MESH colon cancer
gene UNIPROT TIE1
pathway BSID Colorectal cancer
disease DOID colorectal cancer
disease MESH colorectal cancer
disease MESH carcinomas
pathway BSID Prostate cancer
disease DOID prostate cancer
disease MESH prostate cancer
gene UNIPROT AR
gene UNIPROT KRAS
disease MESH Clonal evolution
gene UNIPROT GALE
gene UNIPROT CASP8
gene UNIPROT ESR1
gene UNIPROT PIK3CA
disease MESH aneuploidy
disease DOID myelodysplastic syndrome
disease MESH myelodysplastic syndrome
drug DRUGBANK Rasagiline
disease MESH Point mutations
gene UNIPROT UBXN11
pathway BSID Pancreatic cancer
disease DOID pancreatic cancer
disease MESH pancreatic cancer
gene UNIPROT IDO1
gene UNIPROT ADCY10
gene UNIPROT KCNJ5
gene UNIPROT CIR1
gene UNIPROT PDCD6IP
drug DRUGBANK (S)-Des-Me-Ampa
gene UNIPROT FUT2
gene UNIPROT EXOG
disease DOID coronary heart disease
disease MESH coronary heart disease
disease DOID metabolic disease
disease MESH metabolic disease
disease MESH inflammation
gene UNIPROT GEM
drug DRUGBANK Carboxyamidotriazole
gene UNIPROT PAMR1
gene UNIPROT DTL
gene UNIPROT ZMYM2
disease MESH RaMP
disease MESH rheumatic diseases
pathway BSID Dilated cardiomyopathy
disease DOID dilated cardiomyopathy
disease MESH dilated cardiomyopathy
pathway BSID Metabolism
drug DRUGBANK Guanosine
gene UNIPROT MYC
drug DRUGBANK Myricetin
gene UNIPROT TBPL1
disease DOID renal carcinoma
disease DOID ductal adenocarcinoma
gene UNIPROT BRCA2
gene UNIPROT BRCA1
drug DRUGBANK Carboplatin
drug DRUGBANK Olaparib
gene UNIPROT NUCB1
gene UNIPROT ENG
disease DOID leukemia
disease MESH leukemia
disease DOID ovarian cancer
disease MESH ovarian cancer
gene UNIPROT MAP2K4
gene UNIPROT NEK9
pathway BSID Breast cancer
disease DOID breast cancer
gene UNIPROT FAM168B
gene UNIPROT APOBEC3A
disease MESH breast tumors
gene UNIPROT ACTA1
disease DOID lung cancer
disease MESH lung cancer
gene UNIPROT NSMAF
disease DOID ovarian carcinoma
drug DRUGBANK Isosorbide Mononitrate
gene UNIPROT PDF
gene UNIPROT GDF15
gene UNIPROT SYNC
disease MESH rare diseases
gene UNIPROT LITAF
gene UNIPROT INPP5D
gene UNIPROT SET
disease MESH recurrence
disease MESH carcinogenesis
gene UNIPROT WLS
disease MESH minimal residual disease
gene UNIPROT STUB1
gene UNIPROT RXFP2
gene UNIPROT MET
gene UNIPROT SLTM
drug DRUGBANK Methionine
drug DRUGBANK Erlotinib
gene UNIPROT EGFR
disease DOID anxiety
disease MESH anxiety
disease MESH complications
disease MESH metastases
drug DRUGBANK Nonoxynol-9
gene UNIPROT CCAR1
gene UNIPROT PTPRF
disease MESH cardiovascular diseases
disease DOID obesity
disease MESH obesity
disease MESH dysbiosis
gene UNIPROT PATE1
gene UNIPROT PSD4
disease MESH tic
gene UNIPROT TFPI
gene UNIPROT ITGBL1
disease MESH dif
pathway BSID Translation
gene UNIPROT DYNLL1
drug DRUGBANK Pirenzepine
drug DRUGBANK Naproxen
gene UNIPROT PDGFB
gene UNIPROT SERPINB6
gene UNIPROT SORBS1
gene UNIPROT HACD1
gene UNIPROT CAP1
drug DRUGBANK Gold
gene UNIPROT GAST
gene UNIPROT PAGR1
disease MESH separation
gene UNIPROT TNFSF13
gene UNIPROT ANP32B
gene UNIPROT ENDOG
disease MESH lifestyle
pathway BSID Metabolic pathways
gene UNIPROT RNF128
disease MESH multi
drug DRUGBANK Hexocyclium
gene UNIPROT RELA
disease MESH community
gene UNIPROT TBATA
gene UNIPROT SRM
gene UNIPROT TALDO1
gene UNIPROT LRSAM1
gene UNIPROT TPSG1
gene UNIPROT SGSM3
gene UNIPROT DEPP1
gene UNIPROT GOPC
gene UNIPROT MEA1
drug DRUGBANK Cysteamine
gene UNIPROT GKN2
disease MESH diagnosis
gene UNIPROT EMD
gene UNIPROT SLC35G1
gene UNIPROT DESI1
disease MESH abnormalities
disease MESH Typ
drug DRUGBANK Coenzyme M
drug DRUGBANK Methotrexate
gene UNIPROT TRA
disease MESH circulating tumor cell
disease MESH growth
disease MESH treatment failure
drug DRUGBANK Spinosad
gene UNIPROT MENT
drug DRUGBANK Trestolone
gene UNIPROT SCN8A
gene UNIPROT LARGE1
drug DRUGBANK Tropicamide
disease DOID cancer
disease MESH cancer
gene UNIPROT EHD1
gene UNIPROT AGRP
gene UNIPROT DNMT1
gene UNIPROT CD69

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