Genomewide linkage searches for Mendelian disease loci can be efficiently conducted using high-density SNP genotyping arrays

Abstract

Genomewide linkage searches aimed at identifying disease susceptibility loci are generally conducted using 300-400 microsatellite markers. Genotyping bi-allelic single nucleotide polymorphisms (SNPs) provides an alternative strategy. The availability of dense SNP maps coupled with recent technological developments in highly paralleled SNP genotyping makes it practical to now consider the use of these markers for whole-genome genetic linkage analyses. Here, we report the findings from three successful genomewide linkage analyses of families segregating autosomal recessively inherited neonatal diabetes, craniosynostosis and dominantly inherited renal dysplasia using the Affymetrix 10K SNP array. A single locus was identified for each disease state, two of which are novel. The performance of the SNP array, both in terms of efficiency and precision, indicates that such platforms will become the dominant technology for performing genomewide linkage searches.

Figure 1

Pedigrees of the three families showing microsatellite marker genotypes and the segregating disease-causing haplotype. Blackened symbols indicate affected individuals. Individuals with asterisk were subject to whole-genome SNP genotyping. (A) Neonatal diabetes pedigree (Family 1). Symbols with internal black squares indicate individuals affected with non-insulin dependent diabetes mellitus. Stripped symbols denote individuals affected with gestational diabetes. Black rectangles denote the shared disease haplotype on chromosome 10p13-p12.1. The marker order is telomere, D10S548, D10S586, centromere. (B) Craniosynostosis pedigree (Family 2). Black rectangles denote the shared disease haplotype on chromosome 2p16.3-p14. The marker order is telomere, D2S1352, D2S166, centromere. (C) Renal dysplasia pedigree (Family 3). Black rectangles denote the shared disease haplotype on chromosome 10q23.31-q25.1. The marker order is telomere, D10S185, D10S1239, telomere.

Figure 1

Pedigrees of the three families showing microsatellite marker genotypes and the segregating disease-causing haplotype. Blackened symbols indicate affected individuals. Individuals with asterisk were subject to whole-genome SNP genotyping. (A) Neonatal diabetes pedigree (Family 1). Symbols with internal black squares indicate individuals affected with non-insulin dependent diabetes mellitus. Stripped symbols denote individuals affected with gestational diabetes. Black rectangles denote the shared disease haplotype on chromosome 10p13-p12.1. The marker order is telomere, D10S548, D10S586, centromere. (B) Craniosynostosis pedigree (Family 2). Black rectangles denote the shared disease haplotype on chromosome 2p16.3-p14. The marker order is telomere, D2S1352, D2S166, centromere. (C) Renal dysplasia pedigree (Family 3). Black rectangles denote the shared disease haplotype on chromosome 10q23.31-q25.1. The marker order is telomere, D10S185, D10S1239, telomere.

Figure 2

Partial multiple protein alignment of human PAX2 with orthologs of mouse, zebrafish, Japanese madaka and sea lamprey showing the disease-associated A111T mutation segregating in Family 3. The human protein sequence was used as the basis for amino acid numbering beginning from the initiating methionine. Black shading of residues shows fully conserved amino acids. Above sequences, the Paired-box functional domain is shown as a horizontal bar, while the octapeptide functional domain is indicated by a double horizontal bar. The A111T mutation found in individuals with renal dysplasia is indicated by a blacked triangle.

Figure 3

Comparison of the chromosome location and heterozygosity of SNPs within the Affymetrix 10K XbaI SNP array and microsatellites within the ABI medium density (MD10) marker set. Marker locations were taken from the UCSC database (http://genome.ucsc.edu, July 2003 release).

Figure 3

Comparison of the chromosome location and heterozygosity of SNPs within the Affymetrix 10K XbaI SNP array and microsatellites within the ABI medium density (MD10) marker set. Marker locations were taken from the UCSC database (http://genome.ucsc.edu, July 2003 release).