Inferring Phenotypes of Copy Number Clones in Cancer Populations Using TreeAlign Journal Article

  


Authors: Shi, H.; Zatzman, M.; Shah, S.; McPherson, A.
Article Title: Inferring Phenotypes of Copy Number Clones in Cancer Populations Using TreeAlign
Abstract: Somatic copy number changes modify gene expression and drive cancer development and progression. Single-cell techniques now allow for the profiling of both gene expression and copy number, opening the possibility of linking expression changes with copy number changes at a single-cell level. However, joint measurement of both expression and copy number from the same cell is not commonplace, and thus joint analysis of expression and copy number requires computational integration of the two modalities. TreeAlign is a method for matching cells in single-cell RNA (scRNA) data to clones inferred from single-cell whole genome sequence (scWGS) data. TreeAlign is phylogeny aware and capable of robustly modeling the effect of gene dosage on gene expression. In this chapter, we provide a practical guide for using TreeAlign to jointly analyze copy number and gene expression from single-cell whole genome sequencing and single-cell RNA sequencing datasets. This record is sourced from MEDLINE/PubMed, a database of the U.S. National Library of Medicine
Keywords: genetics; neoplasm; neoplasms; phenotype; gene expression profiling; computational biology; algorithms; gene expression regulation; gene expression regulation, neoplastic; algorithm; gene dosage; bioinformatics; software; dna copy number variations; cancer genomics; tumor microenvironment; copy number variation; single cell analysis; single-cell analysis; procedures; humans; human; whole genome sequencing; tumor evolution; single-cell rna sequencing; probabilistic modeling; single-cell whole genome sequencing
Journal Title: Methods in Molecular Biology
Volume: 2932
ISSN: 1064-3745
Publisher: Humana Press Inc  
Date Published: 2025-01-01
Start Page: 137
End Page: 152
Language: English
DOI: 10.1007/978-1-0716-4566-6_7
PUBMED: 40779108
PROVIDER: scopus
DOI/URL:

https://www.scopus.com/inward/record.uri?eid=2-s2.0-105013174049&doi=10.1007%2F978-1-0716-4566-6_7&partnerID=40&md5=0242a6468406588d506c081fff7f8563
Notes: Book Chapter 7 -- This chapter is part of the book "Cancer Bioinformatics, 2nd edition" (ISBN: 978-1-0716-4565-9) -- Source: Scopus
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MSK Authors
  1. Sohrab Prakash Shah
    95 Shah
  2. Andrew William Mcpherson
    42 Mcpherson
  3. Hongyu Shi
    15 Shi
  4. Matthew Zatzman
    8 Zatzman
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