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, and 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

Submit the following via email to moltarget@mail.nih.gov:

Name, Institution, and Contact Info
Molecular target(s) to be measured
Proposed method and scientific rationale
Requested materials and quantities
Funding source and estimated timeline
Agreement to return results and publish data per MTA

All applicants must complete a standard Material Transfer Agreement (MTA) and agree to share finalized data for public release following publication.

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.