Advanced

Genotyping techniques to address diversity in tumors.

Lindgren, David LU ; Höglund, Mattias LU and Vallon-Christersson, Johan LU (2011) In Advances in Cancer Research 112. p.151-182
Abstract
Array-based genotyping platforms have during recent years been established as a valuable tool for the characterization of genomic alterations in cancer. The analysis of tumor samples, however, presents challenges for data analysis and interpretation. For example, tumor samples are often admixed with nonaberrant cells that define the tumor microenvironment, such as infiltrating lymphocytes and fibroblasts, or vasculature. Furthermore, tumors often comprise subclones harboring divergent aberrations that are acquired subsequent to the tumor-initiating event. The combined analysis of both genotype and copy number status obtained by array-based genotyping platforms provide opportunities to address these challenges. In this chapter, we present... (More)
Array-based genotyping platforms have during recent years been established as a valuable tool for the characterization of genomic alterations in cancer. The analysis of tumor samples, however, presents challenges for data analysis and interpretation. For example, tumor samples are often admixed with nonaberrant cells that define the tumor microenvironment, such as infiltrating lymphocytes and fibroblasts, or vasculature. Furthermore, tumors often comprise subclones harboring divergent aberrations that are acquired subsequent to the tumor-initiating event. The combined analysis of both genotype and copy number status obtained by array-based genotyping platforms provide opportunities to address these challenges. In this chapter, we present the basic principles for current array-based genotyping platforms and how they can be used to infer genotype and copy number for acquired genomic alterations. We describe how these techniques can be used to resolve tumor ploidy, normal cell admixture, and subclonality. We also exemplify how genotyping techniques can be applied in tumor studies to elucidate the hierarchy among tumor clones, and thus, provide means to study clonal expansion and tumor evolution. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Advances in Cancer Research
volume
112
pages
151 - 182
publisher
Elsevier
external identifiers
  • wos:000295818600006
  • pmid:21925304
  • scopus:80053000957
ISSN
0065-230X
DOI
10.1016/B978-0-12-387688-1.00006-5
language
English
LU publication?
yes
id
2203c919-5d88-421c-b7d9-469b0157f8ad (old id 2168833)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/21925304?dopt=Abstract
date added to LUP
2011-10-03 11:18:46
date last changed
2017-07-23 04:29:23
@article{2203c919-5d88-421c-b7d9-469b0157f8ad,
  abstract     = {Array-based genotyping platforms have during recent years been established as a valuable tool for the characterization of genomic alterations in cancer. The analysis of tumor samples, however, presents challenges for data analysis and interpretation. For example, tumor samples are often admixed with nonaberrant cells that define the tumor microenvironment, such as infiltrating lymphocytes and fibroblasts, or vasculature. Furthermore, tumors often comprise subclones harboring divergent aberrations that are acquired subsequent to the tumor-initiating event. The combined analysis of both genotype and copy number status obtained by array-based genotyping platforms provide opportunities to address these challenges. In this chapter, we present the basic principles for current array-based genotyping platforms and how they can be used to infer genotype and copy number for acquired genomic alterations. We describe how these techniques can be used to resolve tumor ploidy, normal cell admixture, and subclonality. We also exemplify how genotyping techniques can be applied in tumor studies to elucidate the hierarchy among tumor clones, and thus, provide means to study clonal expansion and tumor evolution.},
  author       = {Lindgren, David and Höglund, Mattias and Vallon-Christersson, Johan},
  issn         = {0065-230X},
  language     = {eng},
  pages        = {151--182},
  publisher    = {Elsevier},
  series       = {Advances in Cancer Research},
  title        = {Genotyping techniques to address diversity in tumors.},
  url          = {http://dx.doi.org/10.1016/B978-0-12-387688-1.00006-5},
  volume       = {112},
  year         = {2011},
}