Genome-wide linkage analysis of a Parkinsonian-pyramidal syndrome pedigree by 500 K SNP arrays

Abstract

Robust SNP genotyping technologies and data analysis programs have encouraged researchers in recent years to use SNPs for linkage studies. Platforms used to date have been 10 K chip arrays, but the possible value of interrogating SNPs at higher densities has been considered. Here, we present a genome-wide linkage analysis by means of a 500 K SNP platform. The analysis was done on a large pedigree affected with Parkinsonian-pyramidal syndrome (PPS), and the results showed linkage to chromosome 22. Sequencing of candidate genes revealed a disease-associated homozygous variation (R378G) in FBXO7. FBXO7 codes for a member of the F-box family of proteins, all of which may have a role in the ubiquitin-proteosome protein-degradation pathway. This pathway has been implicated in various neurodegenerative diseases, and identification of FBXO7 as the causative gene of PPS is expected to shed new light on its role. The performance of the array was assessed and systematic analysis of effects of SNP density reduction was performed with the real experimental data. Our results suggest that linkage in our pedigree may have been missed had we used chips containing less than 100,000 SNPs across the genome.

Figure 1

Parkinsonian-Pyramidal Syndrome Pedigree Affected individuals are shown by shading. All individuals with number ID were included in pedigree file imported into MERLIN. Only living individuals whose ID numbers start with 5 were genotyped on the chips. Individuals 5042 and 5043 and individuals 5049 and 4106 were each reported to be distally related, but consanguinity between the individuals is not indicated because the exact relationship between the individuals could not be ascertained. The dashed line delineates the margin between the two minimized pedigrees.

Figure 2

LOD Plots and Information Content for Chromosome 22 (A) The LOD plots under NPL, autosomal-dominant, and autosomal-recessive models of disease inheritance are shown. (B) Information content for chromosome 22.

Figure 3

Prioritization of Linkage to Region of 0.9 cM on Chromosome 22 Regions on chromosome 22 showing maximum linkage to disease phenotype under NPL (34.40–41.93 cM), autosomal-dominant (34.40–35.97 cM), and autosomal-recessive (34.49–36.88 cM) models are shown as overlapping regions. The solid gray bar (36.00–36.88 cM) indicates region prioritized for selection of candidate genes.

Figure 4

Schematic View of F-Box Only Protein 7, Isoform 1 Numbers on top indicate amino acid residue positions of left and right borders of F-box and proline-rich regions. The position of putative disease associated variation is shown below.

Figure 5

Effects of Reduction of Chromosome 22 SNP Numbers (A) Effect on maximum LOD scores under NPL and recessive models of inheritance. (B and C) Effect on position and length of linked area with cut offs of 0.1, 0.3, 0.4, and 0.5 below maximum LOD scores under NPL (B) and recessive (C) models. The y axis shows cM along chromosome 22. The horizontal grid shows the 36.00–36.88 cM region.

Figure 6

Effects of Change In-Frame of SNP Reductions (A) Effect on maximum LOD score. Bars indicate ± 1 standard deviation. (B) Effect on length of linked region. The linked region is defined by cut off of 0.1 below maximum LOD score. The y axis shows cM along chromosome 22. The horizontal grid shows the 36.00–36.88 cM region.