Genetic Disease Gene Identification

It is proposed to identify and recruit individuals and/or families with specified the disorders listed above. 10-20 ml (2-4 teaspoons) of peripheral blood will be collect¬ed from all adult subjects. Smaller volumes of blood would be collected from children based on their age/size. In some cases, as an adequate alternative to collecting peripheral blood, buccal cells will be collected using cheek swabs (Epicentre Biotechnologies). All relevant living members of each pedigree will be asked to partici¬pate, free of charge, on a research basis only. Genomic DNA will be extracted by standard methods and used as template for Polymerase Chain Reac¬tion (PCR) amplification reactions. Individuals will be genotyped at markers and candidate gene sequenced.

Essentially two approaches will be used:

1. Circumstances that may provide knowledge of candidate genes include reviews of the literature, biology of the disease, understanding of biological pathways, chromosomal rearrangements, mutants in model organisms etc. When candidate genes exist, it is proposed to use linked microsatellite and/or single nucleotide polymorphism (SNP) PCR primer pairs on the DNA from families to determine if there is co-segregation of the disease and markers and thus linkage between the disease gene and previously mapped markers.

If the disease appears to be linked to the candidate gene, PCR primers flanking all coding exons will be used to amplify the exons and intron/exon boundaries followed by sequencing to detect disease-causing mutations. A web site that enables the design of primers to amplify candidate gene exons is available (http://genome.ucsc.edu/cgi-bin/hgGateway ). If a very strong candidate gene exists, candidate gene sequencing will be performed on affected individual samples without first performing a linkage study. 2. When no obvious candidate genes exist, and a family of sufficient size has been collected, it is proposed to use Affymetrix SNP microarrays to perform a human genome-wide search for linkage. We have used this approach successfully before (Shrimpton et al 2004), utilizing the whole genome linkage analysis with the Human Mapping 10K Array (Affymetrix Inc., Santa Clara, CA). The 10K Array permits the simultaneous genotyping of more than 11,200 mapped SNPs spaced throughout the human genome at 210 KB intervals. Affymetrix 100K and 500K arrays are also available. SNP genotype information will be analyzed using Varia (Silicon Genetics) and/or Merlin software. The data will be used to define a critical region. If statistically significant segregation is detected, candidate genes within the critical region will be evaluated and ranked in order of their likelihood of being the disease gene. Candidate genes will then be sequenced as detailed above.

Summary.