Add HCMI Cohort

[ayan-b]

No description provided.

[maryjgoldman]

Please hold off on this until I determine if it's worth getting this data in. I will update here when it is

[maryjgoldman]

Tumor (6 are primary, 1 met) - DNA and RNA
organoid - DNA and RNA
blood derived normal - only DNA
-> Only RNA is open
-> Does have clinical and biospecimen XML files

Have 7 samples now with sequencing. Have models for 28 total but no sequencing data yet, aiming to have 1k samples by the end of the project
Primary Site: Brain, Colon, Rectum

Notes from https://ocg.cancer.gov/programs/hcmi/research
The tumor-derived models, normal tissue, and parent tumor generated from the NCI-supported CMDCs are sequenced. The sequencing information, as well as patients’ clinical data, will be available to researchers.

Background
Many of the cancer lines that are commonly used in cancer research were established decades ago. These cell lines have been useful for in vitro experiments to study cancer biology, biochemistry, and drug targets. However, drawing conclusions about how in vitro observations may relate to clinical biology is challenging because cancer cell lines:

• lack the cellular complexity and architecture of human tumors, which introduces possibility that genetic drift may have occurred after the cell line was established.
  are not associated with clinical information from the patient.
• genomic relatedness to the parent tumor is unknown, and molecular characterization including assessment of genomes and transcriptomes of these cell lines, until recently, were mostly unavailable.
• from diverse racial and ethnic groups and rare cancers are seldom represented in currently available cell lines.

HCMI addresses the deficiencies in current models by collecting patients’ clinical data and assessing, as much as possible, the genomes and transcriptomes of the parent tumor, case-matched normal tissue, and the resulting next-generation cancer model. The information collected will be made available to the end-user.

[maryjgoldman]

Link to look at the organoids, etc they have already: https://hcmi-searchable-catalog.nci.nih.gov/