CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction
Intratumor heterogeneity provides the fuel for the evolution and selection of subclonal tumor
cell populations. However, accurate inference of tumor subclonal architecture and …
cell populations. However, accurate inference of tumor subclonal architecture and …
The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations
A Villani, S Davidson, N Kanwar, WW Lo, Y Li… - Nature Cancer, 2023 - nature.com
We conducted integrative somatic–germline analyses by deeply sequencing 864 cancer-
associated genes, complete genomes and transcriptomes for 300 mostly previously treated …
associated genes, complete genomes and transcriptomes for 300 mostly previously treated …
Late-stage metastatic melanoma emerges through a diversity of evolutionary pathways
Understanding the evolutionary pathways to metastasis and resistance to immune-
checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here, we present …
checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here, we present …
Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis
Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with
germline TP53 pathogenic variants. Here, we perform whole-genome sequence (WGS) …
germline TP53 pathogenic variants. Here, we perform whole-genome sequence (WGS) …
Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data
B Lu - Cancer Pathogenesis and Therapy, 2024 - mednexus.org
Cancer is an evolutionary process involving the accumulation of diverse somatic mutations
and clonal evolution over time. Phylogenetic inference from samples obtained from an …
and clonal evolution over time. Phylogenetic inference from samples obtained from an …
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data
Motivation Eukaryotic cells contain organelles called mitochondria that have their own
genome. Most cells contain thousands of mitochondria which replicate, even in nondividing …
genome. Most cells contain thousands of mitochondria which replicate, even in nondividing …
A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors
H Schmidt, BJ Raphael - PLOS Computational Biology, 2024 - journals.plos.org
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 …
to investigate tumor heterogeneity and reconstruct a phylogeny of a patient's cancer …
[HTML][HTML] Inferring cancer type-specific patterns of metastatic spread
D Koyyalagunta, K Ganesh, Q Morris - bioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
The metastatic spread of a cancer can be reconstructed from DNA sequencing of primary
and metastatic tumours, but doing so requires solving a challenging combinatorial …
and metastatic tumours, but doing so requires solving a challenging combinatorial …
[HTML][HTML] Reconstructing cancer phylogenies using Pairtree, a clone tree reconstruction algorithm
Pairtree is a clone tree reconstruction algorithm that uses somatic point mutations to build
clone trees describing the evolutionary history of individual cancers. Using the Pairtree …
clone trees describing the evolutionary history of individual cancers. Using the Pairtree …
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History
CH Wu, S Joshi, W Robinson, PF Robbins… - … on Research in …, 2024 - Springer
Intratumoral heterogeneity arises as a result of genetically distinct subclones emerging
during tumor progression. These subclones are characterized by various types of somatic …
during tumor progression. These subclones are characterized by various types of somatic …