Through customized genotyping, the coverage can be specifically increased for the candidate genes/regions. In addition, the investigator has the opportunity to customise SNP selection, ensuring the inclusion of known functional or rare variants that might have been removed from other commercial panels. Therefore, the first step in SNP selection for a candidate gene or region is to find out relevant genomic information: identify all known SNPs, identify those known to be located in functional regions, and characterise the LD structure, using publicly available online databases such as Ensembl (http://www.ensembl.org), UCSC Genome Browser (http://genome.ucsc.edu) 11, and HapMap (http://www.hapmap.org).
