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Molecular Targets in the NCI-60 Cell Lines

The NCI-60 Molecular Targets Dataset offers extensive omics and biochemical data for the 60 human tumor cell lines used in the HTS384 screen. This resource supports target-based drug development, integrative analyses, and COMPARE-based correlations.

All datasets are freely available. Researchers may also apply to measure additional molecular targets in the NCI-60 panel using DTP-provided cell materials. 

Available data types

Over the past two decades, thousands of molecular measurements have been generated from the NCI-60 cell lines, including:

  • Transcriptomics:
    • RNA-Seq
    • DNA microarrays
  • Genomics:
    • Single Nucleotide Polymorphisms (SNPs)
    • Copy Number Variants (CGH)
  • Proteomics:
    • Protein expression
    • Enzyme activities
  • Epigenetics:
    • DNA methylation
    • miRNA profiling
  • Metabolomics and Mutation Data

These data were generated through collaborative studies via the DTP Molecular Targets Program and are continually updated. 

Access DTP Molecular Targets Data

•    Download Molecular Target Data
•    Search Molecular Target Data
•    Browse Molecular Target Data
 

View: Download & Search Molecular Target Data  

Apply to Measure New Molecular Targets 

Investigators may apply to perform additional molecular profiling on the NCI-60 panel using DTP-provided materials. This collaborative program supports the discovery of drug-target relationships, biomarkers, or mechanistic correlates.  

What's Provided

  • Frozen cell pellets (typically 1×10⁷ cells)
  • Possible access to other NCI-60 materials (pending request)
  • Data analysis support (optional)
  • Option to link results with HTS384/COMPARE data 

Application Requirements 

Please complete and submit via email to moltarget@mail.nih.gov:

An application form for material support to undertake the measurement of molecular targets.  

Applicants must also complete a standard  Material Transfer Agreement (MTA) which includes an agreement that they will return finalized data to DTP for public release, after an embargo period. 

Integrating with Screening & COMPARE

Molecular target data can be:

  • Used alongside HTS384 screening data to explore target-sensitivity correlations
  • Integrated with COMPARE analysis to uncover potential shared mechanisms
  • Mined to identify tumor subpanel-selective biomarkers (e.g., colon vs. melanoma)

Use case: Identify genes whose expression correlates with a compound’s GI50 pattern across the NCI-60. 

Cell Line Reclassifications (Based on Molecular Profiling)

Recent omics studies led to updates in lineage assignments of certain NCI-60 lines:

  • MDA-MB-435 & MDA-N → melanoma, not breast cancer
  • NCI/ADR-RES → ovarian, not breast cancer
  • SNB-19 & U251 → derived from the same CNS tumor

These changes are based on consistent evidence from:

  • Gene expression profiling
  • SNP and CGH array data
  • DNA fingerprinting and karyotype comparisons

Full details and citations are available in the Cell Line Identity Update.

Tools & Resources

If you would like to reproduce some or all of this content, see Reuse of NCI Information for guidance about copyright and permissions. In the case of permitted digital reproduction, please credit the National Cancer Institute as the source and link to the original NCI product using the original product's title; e.g., “Molecular Targets in the NCI-60 Cell Lines was originally published by the National Cancer Institute.”

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