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 here.