A new method for autozygosity mapping using single nucleotide polymorphisms (SNPs) and EXCLUDEAR.

T he development of a silicon chip, such as the Affymetrix 10K Xba 131, bearing sufficient oligonucleotides to analyse 10 913 single nucleotide polymorphisms (SNPs) presents a new method for seeking autosomal recessive loci. This letter describes a practical strategy to analyse the data output of such an ‘‘SNP-chip’’ for this purpose. Autozygosity mapping, first suggest by Lander and Botstein, is the method of choice for the discovery of autosomal recessive gene loci. The methodology seeks homozygous regions in consanguineous families. The greater the number of affected individuals who have a shared homozygous region and the greater the size of the region, the more likely it is to harbour the mutation that causes the disease. Mueller and Bishop modelled the use of a single multi-affected family and suggested that this was the most efficient strategy to determine a disease locus, particularly given the complexities of genetic heterogeneity. Autozygosity mapping became practical with the discovery of multiple highly polymorphic microsatellite repeat markers spread throughout the genome. Most researchers currently use optimised panels of approximately 400 markers for an initial genome-wide screen for linkage, giving 10–12 cM coverage of the autosomal genome; a process that has lead to the discovery of many recessive loci. The currently available SNP-chip detects SNPs spread throughout the genome (with the exception of the Y chromosome) and is analysed following a single hybridisation reaction with one individual’s genomic DNA. The results are produced as a simple spreadsheet of the SNP allele calls. Whilst each SNP has far less power to detect a homozygous chromosomal segment than a microsatellite marker, it is both their number (10 913 SNPs are equivalent to a 3–4 cM microsatellite marker map) and their ability to detect a heterozygous region, and hence exclude linkage, that suggested their potential use in autozygosity mapping. An average microsatellite marker has a 70% chance of detecting a heterozygous region, but the approximately 30 SNPs within the same region have a .99% chance of detecting heterozygosity. (The chance that one of the 30 SNPs will be heterozygous is 1–0.7, which is .0.999, and on average nine of the 30 SNPs will be heterozygous.) We have designed the following method to adapt Affymetrix SNP-chip output for autozygosity mapping.