Human genetic variation is most frequently seen as single-nucleotide polymorphism (SNP). Many of these have been discovered more or less by chance when comparing sequence trace files of overlapping contigs from different individuals. A more systematic approach by comparative sequencing in a defined group of individuals by the SNP consortium has now greatly improved our understanding of genetic variation. SNP coverage across the human genome is not random and may be completely absent in highly conserved regions or highly abundant in other regions where genetic diversity is biologically important. Large-scale association studies by genotyping many individuals by many single SNPs are considered to be the most promising method to identify the cause of complex diseases. In addition, it will also improve the understanding of the individual response to drugs, also termed pharmacogenetics.

The technical possibilities to genotype SNPs in individuals has exploded in the past few years with more than 20 different methods available today. Although traditional sequencing by the Sanger method is still the standard for assessing smaller insertions and deletions in DNA sequence, numerous new methods have been developed during the past 10 years for scoring SNPs (1). With an estimated count of more than 5 million SNPs in the human genome, SNP genotyping requires high-throughput (HT) methods. Only a few methods are suitable for HT cutting-edge genotyping (>5.000 genotypes/ day/lab) or ultra HT (>100.000 genotypes/day/lab) requirements, which is caused by the recent shift from monogenic to complex diseases. Due to much weaker genetic effects in these traits, much higher sample numbers are required. An average case-control study will comprise more than 2000 samples. Genotyping of a single gene with 50 SNPs alone will result in 100,000 single-plex genotyping reactions, which is a daunting task for a traditional laboratory.

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