MDA231

<p>Pre-stored dataset for project MDA231. A transplantable metastasis model
system was derived from a heterogeneous human breast cancer cell line 
MDA-MB-231. Cancer cells from the parental line MDA-MB-231 were engrafted into
mouse hosts leading to organ-specific metastasis. Mixed cell populations (MCPs)
were in vivo selected from either bone or lung metastasis and grew into 
phenotypically stable and metastatically competent cancer cell lines. The
parental line as well as the MCP sublines were whole-exome sequenced with 
somatic SNAs and CNAs profiled.</p>

datasets

A statistical framework and computational procedure for identifying
the sub-populations within a tumor, determining the mutation profiles of each
subpopulation, and inferring the tumor's phylogenetic history. The input are
variant allele frequencies (VAFs) of somatic single nucleotide alterations
(SNAs) along with allele-specific coverage ratios between the tumor and matched
normal sample for somatic copy number alterations (CNAs). These quantities can
be directly taken from the output of existing software. Canopy provides a
general mathematical framework for pooling data across samples and sites to
infer the underlying parameters. For SNAs that fall within CNA regions, Canopy
infers their temporal ordering and resolves their phase.  When there are
multiple evolutionary configurations consistent with the data, Canopy outputs
all configurations along with their confidence assessment.

Yuchao Jiang

MDA231: Dataset for project MDA231

Description

Usage

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Examples