Candidate Cancer Allele cDNA Collection

CTD2 researchers at the Broad Institute/DFCI have developed a collection of plasmids including mutant alleles found in sequencing studies of cancer. It includes somatic variants found in lung adenocarcinoma and across other cancer types. The clones enable researchers to characterize the function of the cancer variants in a high throughput experiments. These plasmids are collectively called the “Broad Target Accelerator Plasmid Collections”. The design and construction of these plasmids is described in the manuscripts listed below and are available through a distributor.

Kim E, et al. Systematic functional interrogation of rare cancer variants identifies oncogenic alleles. Cancer Discovery. 2016 Jul;6(7):714-26. (PMID: 27147599)
Berger AH, Brooks AN, Wu X, et al. High-throughput phenotyping of lung cancer somatic mutations. Cancer Cell. 2016 Aug 8;30(2):214-28. (PMID: 27478040)

cDNA Clones with Rare and Recurrent Mutations Found in Cancers

The CTD2 Center at UT-MD Anderson Cancer Center has developed a High-Throughput Mutagenesis and Molecular Barcoding (HiTMMoB) pipeline to construct mutant alleles open reading frame expression clones that are either recurrent or rare in cancers. These barcoded genes can be used for context-specific functional validation, detection of novel biomarkers (pathway activation) and targets (drug sensitivity). The list of available gene expression clones can be accessed here: FileMDACC ORF Clones.xlsx

Contact: Gordon B. Mills

Dogruluk T, et al. Identification of variant-specific functions of PIK3CA by rapid phenotyping of rare mutations. Cancer Research. 2015 Dec 15;75(24):5341-54. (PMID: 26627007)

Tsang YH, et al. Functional annotation of rare gene aberration drivers of pancreatic cancer. Nature Communications. 2016 Jan 25;7:10500. (PMID: 26806015)

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRi) Plasmids

CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes. The CRISPR/dCas9 system has several advantages: i) enables robust gene repression (CRISPRi) or activation (CRISPRa) in human cells, ii) allows specific knockdown with minimal off-target effects in human cells, iii) works efficiently in human and yeast cells, and iv) does not cause double-strand breaks. Plasmid design and construction for CRISPRi (human and yeast cells) are described in the manuscript listed below and are available through a distributor.

Gilbert LA, et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell. 2013 Jul 18;154(2):442-51. (PMID: 23849981)

Online Bioinformatics Tutorials

Bioinformatics is a scientific discipline that applies computer science and information technology to help understand biological processes. The NIH provides a list of free online bioinformatics tutorials, either generated by the NIH Library or other institutes, which includes introductory lectures and "how to" videos on using various tools.

Open versus Controlled-Access Data

OCG employs stringent human subjects’ protection and data access policies to protect the privacy and confidentiality of the research participants. Depending on the risk of patient identification, OCG programs data are available to the scientific community in two tiers: open or controlled-access. Both types of data can be accessed through its corresponding OCG program-specific data matrix or portal.

Open-access Data

Data within this category presents minimal risk of participant identification. Much of OCG program data, excluding patient identifiers, are open-access. OCG provides the scientific community the maximum amount of open-access data allowable under HIPAA guidelines. Access to these data does not require user certification, and researchers may explore data content without restriction.

Controlled-access Data

Data within this category present a higher risk of patient identification. While stripped of direct patient identifiers as defined by HIPAA, controlled-access data contain specific demographic, clinical, and genotypic information that are excluded in open-access data. Controlled-access data are unique and valuable to research projects for which open-access data are insufficient. Access to protected data requires user certification which can be obtained through NCBI’s dbGaP (National Center for Biotechnology Information’s database of Genotypes and Phenotypes). 

To learn more and understand which data each OCG program provides, visit How to Access Multiple Datasets

Protein-Protein Interaction (PPI) Reagents

A large number of gene mutations give proteins new capabilities to bind cellular proteins and create new signaling pathways that drive tumor growth. To discover and validate mutation-created protein-protein interactions (PPI) as therapeutic targets for cancer, the CTD2 Center at Emory University has created PPI expression vector libraries. A list of available cancer-associated genes can be accessed here: FileEmory_CTD^2_PPI_Reagents.xlsx

Contact: Haian Fu 

Li Z, et al. The OncoPPi network of cancer-focused protein-protein interactions to inform biological insights and therapeutic strategies. Nature Communications. 2017 Feb 16;8:14356. (PMID: 28205554)

What is Cancer?

A brief explanation of how cancer forms, basic statistics, and links to additional resources.