Statistical analysis of Single Nucleotide Polymorphism microarrays in cancer studies

In this chapter, we focus on statistical questions raised by the identification of copy number alterations in tumor samples using genotyping microarrays, also known as Single Nucleotide Polymorphism (SNP) arrays. We define the copy number states formally, and show how they are assessed by SNP arrays. We identify and discuss general and cancer-specific challenges for SNP array data preprocessing, and how they are addressed by existing methods. We review existing statistical methods for the detection of copy number changes along the genome. We describe the influence of two biological parameters — the proportion of normal cells in the sample, and the ploidy of the tumor — on observed data. Finally, we discuss existing approaches for the detection and calling of copy number aberrations in the particular context of cancer studies, and identify statistical challenges that remain to be addressed. Pierre Neuvial Department of Statistics, University of California, Berkeley, USA e-mail: [email protected] Henrik Bengtsson Department of Statistics, University of California, Berkeley, USA and Department of Epidemiology & Biostatistics, University of California, San Francisco, USA e-mail: [email protected]