Campaign: Analysis Priorities

Re-normalize/re-smooth raw data

Re-normalize or in other ways re-smooth raw data

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Campaign: Analysis Priorities

Comparative genome analysis of private data to public data

Perform comparative genome analysis involving a direct comparison of in-house generated research or clinical data to public datasets (for example, clustering of patient tumor genomes with TCGA tumor genomes)

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Campaign: Analysis Priorities

CANCER whole genomes codon populations analysis

In this main open access article

http://fr.scribd.com/doc/169323556/7401586of18september2013

published in october 2013 by APPLIED MATHEMATICS (BIOMATHEMATICS issue http://www.scirp.org/journal/am/ ) we show how our human genome MUST be considedred as a NUMERICAL WHOLE. The idea is now to run this kind of analysis on complete genomes DNA from CANCER CELLS (LOH) at individual chromosomes and whole genome scales.

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Campaign: Data Priorities

Patient Access

Allow patients and their doctors to access data about them securely

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Campaign: Data Priorities

Longitudinal sequencing

Longitudinal sequencing: obtain the samples from patients at different time points. For examples, biopsy at diagnosis, pretreatment, post-treatment, and relaps

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Campaign: Analysis Priorities

dissect tumors into clones and store the information for reuse

each tumor contains multiple clones, genomic alterations are linked to these clones. clinical factors such as survival, drug response should be correlated with patients at the clonal level but not whole tumor level

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Campaign: Analysis Priorities

Construct background mutation rate

Construct background mutation rate (noise) based on the correlation of mutation frequency and expression levels or replication time. It has been shown that longer replication time and lower expression levels imply higher mutation rates among the genome (http://www.nature.com/nature/journal/v499/n7457/full/nature12213.html). Transcription-coupled DNA repair results in high expression levels and low mutation rate. So I ...more »

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Campaign: Data Priorities

Images & dilution curves for TCGA expression protein arrays

Provide access to high resolution images and dilution curves for TCGA expression protein arrays for analysis

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Campaign: Data Priorities

Access to TCGA microsatellite instability data

Provide access to TCGA microsatellite instability data for analysis

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Campaign: Analysis Priorities

Common framework for all kind of analysis

One backend framework for custom analysis tools that can be developed by the community.

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Campaign: Analysis Priorities

large scale computation time

Provide CPU time for the community with allocations set by NCI to users AND on a pay per node model.

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Campaign: Analysis Priorities

Deployment of databases and web applications

Please provide a process for the deployment of databases and web applications such as MSKCC cBio, or ISB's Regulome Explorer or GeneSpot.

 

(You could use Github as a platform for accepting contributions.)

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