Analyzing Cancer Samples with SNP Arrays

  • Peter Van LooEmail author
  • Gro Nilsen
  • Silje H. Nordgard
  • Hans Kristian Moen Vollan
  • Anne-Lise Børresen-Dale
  • Vessela N. Kristensen
  • Ole Christian Lingjærde
Part of the Methods in Molecular Biology book series (MIMB, volume 802)


Single nucleotide polymorphism (SNP) arrays are powerful tools to delineate genomic aberrations in cancer genomes. However, the analysis of these SNP array data of cancer samples is complicated by three phenomena: (a) aneuploidy: due to massive aberrations, the total DNA content of a cancer cell can differ significantly from its normal two copies; (b) nonaberrant cell admixture: samples from solid tumors do not exclusively contain aberrant tumor cells, but always contain some portion of nonaberrant cells; (c) intratumor heterogeneity: different cells in the tumor sample may have different aberrations. We describe here how these phenomena impact the SNP array profile, and how these can be accounted for in the analysis. In an extended practical example, we apply our recently developed and further improved ASCAT (allele-specific copy number analysis of tumors) suite of tools to analyze SNP array data using data from a series of breast carcinomas as an example. We first describe the structure of the data, how it can be plotted and interpreted, and how it can be segmented. The core ASCAT algorithm next determines the fraction of nonaberrant cells and the tumor ploidy (the average number of DNA copies), and calculates an ASCAT profile. We describe how these ASCAT profiles visualize both copy number aberrations as well as copy-number-neutral events. Finally, we touch upon regions showing intratumor heterogeneity, and how they can be detected in ASCAT profiles. All source code and data described here can be found at our ASCAT Web site (

Key words

Cancer Tumor SNP arrays ASCAT Allelic bias Aneuploidy Intratumor heterogeneity 


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Peter Van Loo
    • 1
    • 2
    • 3
    Email author
  • Gro Nilsen
    • 4
  • Silje H. Nordgard
    • 5
  • Hans Kristian Moen Vollan
    • 5
    • 6
    • 7
  • Anne-Lise Børresen-Dale
    • 5
    • 6
  • Vessela N. Kristensen
    • 5
    • 8
    • 9
  • Ole Christian Lingjærde
    • 4
  1. 1.Cancer Genome ProjectWellcome Trust Sanger InstituteCambridgeUK
  2. 2.Department of Molecular and Developmental GeneticsVIBLeuvenBelgium
  3. 3.Department of Human GeneticsUniversity of LeuvenLeuvenBelgium
  4. 4.Biomedical Research Group, Department of Informatics,Centre for Cancer BiomedicineUniversity of OsloOsloNorway
  5. 5.Department of Genetics, Institute for Cancer ResearchOslo University Hospital RadiumhospitaletOsloNorway
  6. 6.Institute for Clinical Medicine, Faculty of MedicineUniversity of OsloOsloNorway
  7. 7.Division of Surgery and Cancer, Department of Breast and Endocrine SurgeryOslo University Hospital UllevalOsloNorway
  8. 8.Institute for Clinical Medicine, Institute for Clinical Epidemiology and Molecular Biology (EpiGen)Akershus University HospitalNordbyhagenNorway
  9. 9.Faculty of MedicineUniversity of OsloNordbyhagenNorway

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