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Book ChapterDOI

Genotyping techniques to address diversity in tumors.

01 Jan 2011-Advances in Cancer Research (Elsevier)-Vol. 112, pp 151-182

TL;DR: This chapter presents 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, and describes how these techniques can beused to resolve tumor ploidy, normal cell admixture, and subclonality.
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.
Topics: Genotyping Techniques (62%), Genotyping (54%)

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Genotyping techniques to address diversity in tumors.
Lindgren, David; Höglund, Mattias; Vallon-Christersson, Johan
Published in:
Advances in Cancer Research
DOI:
10.1016/B978-0-12-387688-1.00006-5
2011
Link to publication
Citation for published version (APA):
Lindgren, D., Höglund, M., & Vallon-Christersson, J. (2011). Genotyping techniques to address diversity in
tumors.
Advances in Cancer Research
,
112
, 151-182. https://doi.org/10.1016/B978-0-12-387688-1.00006-5
Total number of authors:
3
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1
Genotyping techniques to address diversity in tumors
David Lindgren,
a
Mattias Höglund,
b
and Johan Vallon-Christersson
b, c
a
Center for Molecular Pathology, Department of Laboratory Medicine, Lund
University, SUS Malmö, Malmö, Sweden
b
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden
c
CREATE Health Strategic Center for Translational Cancer Research, Lund
University, Lund, Sweden
Correspondence to: David Lindgren, Center for Molecular Pathology, Department
of Laboratory Medicine, Lund University, SUS Malmö, Entrance 78, SE-205 02
Malmö, Sweden.

2
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 review, 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.

3
I. INTRODUCTION
Cancer development and tumor formation involves acquired genomic
aberrations, such as sequence mutations and copy number changes. Molecular
investigation of genomic alterations in tumors has traditionally been performed
using methods such as loss of heterozygosity (LOH) analyses and comparative
genomic hybridization (CGH). Conventional GCH, first described by Kallioniemi
and coworkers (Kallioniemi et al., 1992), use differentially fluorescently labeled
DNA from tumor sample and reference DNA to reveal regions of loss and gain by
competitive hybridization to immobilized normal metaphase chromosomes.
With the advent of array-technology (Schena et al., 1995), the analysis of cancer
genomes advanced rapidly with greatly increased resolution and sensitivity.
Array-based comparative genomic hybridization (aCGH) was first performed
using gene-centered arrays originally developed for gene expression analysis, or
using low-density arrays of large genomic segments cloned in bacterial artificial
chromosomes (BACs) (Pollack et al., 1999). Initial techniques were soon further
developed for genome-wide investigation of copy number aberrations at high-
resolution by tiling BAC arrays and subsequently by employing oligonucleotide
probe arrays. In short, aCGH utilizes the same strategy as conventional
metaphase CGH but DNA is hybridized to immobilized DNA probes mapped to
known genomic locations. Current array platforms, comprising from tens of
thousands up to millions of probes, allow for detection of breakpoints and copy
number alterations at sub-gene resolution and have been widely used to screen
for genomic alterations in cancer (Pinkel and Albertson, 2005). Such analyses
have provided a depiction of copy number gain and loss frequencies across large

4
tumor cohorts in a variety of cancers, highlighting recurrent alterations
important during oncogenesis and tumor development (Chin et al., 2006). LOH
analyses have, on the other hand, been widely used in cancer research to detect
regions of allelic imbalances indicating regions of genomic deletion or copy
number neutral LOH, and have been used to identify tumor suppressor genes
inactivated by mutation followed by loss of the wild-type allele. Traditionally,
LOH analysis use polymorphic markers, such as nucleotide repeat regions or
single nucleotide polymorphisms, to detect regions of allelic imbalance.
Whole genome genotyping (WGG) arrays based on Single Nucleotide
Polymorphisms (SNPs) (Wang et al., 1998) were developed to analyze blood
samples in association studies and have since its introduction successfully been
used in numerous studies for identification of genetic susceptibility loci in a
variety of diseases (Grant and Hakonarson, 2008). Progression of WGG arrays, or
SNP arrays, has followed the identification of SNPs in the human genome derived
from initiatives such as the international HapMap Project
(http://www.hapmap.org), and platforms currently in use allow for genotyping
of millions of SNPs simultaneously. Even though SNP arrays were not originally
designed for analysis of tumor samples, it was soon demonstrated that these
platforms are suitable for the analysis of cancer genomes (Lindblad-Toh et al.,
2000; Wang et al., 2004; LaFramboise et al., 2005; Zhao et al., 2005; Peiffer et al.,
2006). Allele specific interrogation of tumor DNA using SNP arrays provides
means to investigate the relative abundance of alleles and effectively combine
the advantages of LOH analysis and aCGH analysis. Thus, SNP arrays enable
researchers to detect copy neutral events in tumors along with copy number

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TL;DR: Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer.
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"Genotyping techniques to address di..." refers background in this paper

  • ...The interplay between cells within the tumor microenvironment has been highlighted as important hallmarks of cancer and its composition has been shown to represent an intrinsic property of tumors (Hanahan and Weinberg, 2011)....

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"Genotyping techniques to address di..." refers background in this paper

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TL;DR: Comparative genomic hybridization produces a map of DNA sequence copy number as a function of chromosomal location throughout the entire genome, which identified 16 different regions of amplification, many in loci not previously known to be amplified.
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Abstract: We identified 255 loci across the human genome that contain genomic imbalances among unrelated individuals. Twenty-four variants are present in > 10% of the individuals that we examined. Half of these regions overlap with genes, and many coincide with segmental duplications or gaps in the human genome assembly. This previously unappreciated heterogeneity may underlie certain human phenotypic variation and susceptibility to disease and argues for a more dynamic human genome structure.

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23 Jul 2004-Science
TL;DR: It is shown that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans.
Abstract: The extent to which large duplications and deletions contribute to human genetic variation and diversity is unknown. Here, we show that large-scale copy number polymorphisms (CNPs) (about 100 kilobases and greater) contribute substantially to genomic variation between normal humans. Representational oligonucleotide microarray analysis of 20 individuals revealed a total of 221 copy number differences representing 76 unique CNPs. On average, individuals differed by 11 CNPs, and the average length of a CNP interval was 465 kilobases. We observed copy number variation of 70 different genes within CNP intervals, including genes involved in neurological function, regulation of cell growth, regulation of metabolism, and several genes known to be associated with disease.

2,516 citations


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