Cellular Oncology

, Volume 36, Issue 1, pp 27–36

Detection limits of DNA copy number alterations in heterogeneous cell populations

  • Oscar Krijgsman
  • Daniëlle Israeli
  • Hendrik F. van Essen
  • Paul P. Eijk
  • Michel L. M. Berens
  • Clemens H. M. Mellink
  • Aggie W. Nieuwint
  • Marjan M. Weiss
  • Renske D. M. Steenbergen
  • Gerrit A. Meijer
  • Bauke Ylstra
Original Paper

DOI: 10.1007/s13402-012-0108-2

Cite this article as:
Krijgsman, O., Israeli, D., van Essen, H.F. et al. Cell Oncol. (2013) 36: 27. doi:10.1007/s13402-012-0108-2

Abstract

Background

Array Comparative Genomic Hybridization (aCGH) is a widely used technique to assess chromosomal copy number alterations. Chromosomal content, however, is often not uniform throughout cell populations. Here we evaluated to what extent aCGH can detect DNA copy number alterations in heterogeneous cell populations. A systematic evaluation is currently lacking, despite its importance in diagnostics and research. The detection limits reported are a compound of analytical software and laboratory techniques and do not account for the number of probes in relation to sample homogeneity.

Methods

Detection limits were explored with DNA isolated from a patient with intellectual disability (ID) and from tumor cell line BT474. Both were diluted with increasing amounts of normal DNA to simulate different levels of cellularity. Samples were hybridized on microarrays containing 180,880 oligonucleotides evenly distributed over the genome (spacing ~17 kb).

Results

Single copy number alterations, represented by down to 249 probes (4 Mb) and present in 10 % of a cell population, could be detected. Alterations encompassing as few as 14 probes (~238 Kb) could also be detected, but for this a 35 % mosaic level was required.

Conclusions

DNA copy number alterations can be detected in cell populations containing 10 % abnormal cells. Detection of sub-megabase alterations requires a higher percentage of abnormal cells or microarrays with a higher probe density.

Keywords

aCGH Microarray Clinical genetics Tumor heterogeneity Mosaicism 

Abbreviations

aCGH

Array comparative genome hybridization

WCP

Whole chromosome paint

CEP

Centromere probe

FISH

Fluorescence in situ hybridization

GEO

Gene expression omnibus

CNV

Copy number variation

ID

Intellectual disability

Supplementary material

13402_2012_108_Fig6_ESM.jpg (95 kb)
Supplementary_Figure 1

Chromosome 5 profile of BT474. aCGH profiles of a gain at the p-arm of chromosome 5 in BT474 with 100 %, 30 % and 20 % tumor DNA. (JPEG 95 kb)

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High resolution image (TIFF 273 kb)
13402_2012_108_MOESM2_ESM.png (203 kb)
Supplementary_Figure 2Dilution range of BT474 DNA on the NimbleGen platform. Profiles of all dilutions of BT474 DNA were performed on the NimbleGen platform. (PNG 203 kb)
13402_2012_108_Fig7_ESM.jpg (95 kb)
Supplementary_Figure 3

aCGH profiles for CNVR3771/2 on chromosome 8 in a patient with ID. Panel A shows an overview of chromosome 8 in the undiluted sample. Panels BD show the detection of CNVR3771/2 (DNA loss) in dilutions to 35 %, 30 % and 25 % patient DNA. CNVR3771/2 (21 probes, ~1 Mb) could be detected with dilutions down to 35 % and 30 %, but not with 25 % patient DNA. The genomic locations of both CNVs are indicated in B. The X-axis represents the genomic locations (in Mb), and the Y-axis represents the log2 ratios for each probe. Grey lines represent the CBS segments [17]. (JPEG 94 kb)

13402_2012_108_MOESM3_ESM.tif (254 kb)
High resolution image (TIFF 253 kb)
13402_2012_108_Fig8_ESM.jpg (120 kb)
Supplementary_Figure 4

HER2/neu amplification in BT474. aCGH profiles of an amplification at 17q12 (30 probes, ~0.3 Mb), which includes HER2/neu. Hybrizations were performed with 100 %, 20 % and 10 % tumor DNA. The X-axis represents the chromosomal locations, and the Y-axis the log2 ratios. Grey lines represent the CBS segments [17]. (JPEG 120 kb)

13402_2012_108_MOESM4_ESM.tif (329 kb)
High resolution image (TIFF 329 kb)

Copyright information

© International Society for Cellular Oncology 2012

Authors and Affiliations

  • Oscar Krijgsman
    • 1
  • Daniëlle Israeli
    • 1
  • Hendrik F. van Essen
    • 1
  • Paul P. Eijk
    • 1
  • Michel L. M. Berens
    • 3
  • Clemens H. M. Mellink
    • 3
  • Aggie W. Nieuwint
    • 2
  • Marjan M. Weiss
    • 2
  • Renske D. M. Steenbergen
    • 1
  • Gerrit A. Meijer
    • 1
  • Bauke Ylstra
    • 1
  1. 1.Department of PathologyVU University Medical CenterAmsterdamThe Netherlands
  2. 2.Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
  3. 3.Department of Clinical GeneticsAcademic Medical CenterAmsterdamThe Netherlands

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