ABSTRACT
This chapter deals with genetic variants other than single nucleotide polymorphisms (SNPs). It explains how SNP array data can be used to detect other structural variants such as copy number (CNV), genetic mosaicisms and polymorphic inversions. The chapter discusses how CNVs, and mosaicisms, can be called using the log R ratio and B-allele frequencies of raw microarray data, and how polymorphic inversions can be called using SNP genotypes. It demonstrates how to detect regions with copy-number alterations, such as gains or losses of genetic material, using quantitative data obtained from aCGH or SNP arrays. The chapter illustrates how to incorporate the uncertainty derived from the calling of the copy-number status of individuals in association studies. Microarrays measure the fluorescence light of tagged DNA segments that hybridize with the probes in the chip array. One of the signals that inversions leave on SNP data is the singular changes in the linkage disequilibrium across their breakpoints.
