A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.

ABSTRACT:

Motivation

DNA sequencing of multiple bulk samples from a tumor provides the opportunity to investigate tumor heterogeneity and reconstruct a phylogeny of a patient's cancer. However, since bulk DNA sequencing of tumor tissue measures thousands of cells from a heterogeneous mixture of distinct sub-populations, accurate reconstruction of the tumor phylogeny requires simultaneous deconvolution of cancer clones and inference of ancestral relationships, leading to a challenging computational problem. Many existing methods for phylogenetic reconstruction from bulk sequencing data do not scale to large datasets, such as recent datasets containing upwards of ninety samples with dozens of distinct sub-populations.

Results

We develop an approach to reconstruct phylogenetic trees from

SUBMITTER: Schmidt H 

PROVIDER: S-EPMC11661639 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature