Linkage disequilibrium and haplotype tagging polymorphisms in the Tau H1 haplotype.
We and others have previously detected association of the Tau H1 haplotype on chromosome 17 with risk of idiopathic Parkinson disease (PD). The H1 haplotype appears to have a fundamental importance in neurodegeneration, as multiple studies have shown it is also associated with an increased risk for progressive supranuclear palsy, corticobasal degeneration, frontotemporal lobar degeneration syndromes, and primary progressive aphasia. Therefore, to divide the H1 haplotype into sub-haplotypes that could be more significantly associated with the risk of developing PD, and to delimit the genes lying in the H1 haplotype, we analyzed 34 single nucleotide polymorphisms (SNPs) spanning over 3.15 megabases in the region containing Tau. These SNPs are located in or flank the corticotropin-releasing hormone receptor 1, presenilin homolog 2, Tau, Saitohin, and KIAA1267 genes. Analysis of linkage disequilibrium (LD) using these 34 SNPs suggests that the H1 haplotype extends over about 1.3 megabases, making it the largest region of LD reported to date. Of the 29 SNPs lying in this region of LD, 5 were identified as "haplotype tagging" SNPs (htSNPs), capturing 96% of the sample's haplotype diversity. Association analysis with these htSNPs revealed a new H1 sub-haplotype that is significantly associated with PD ( P<0.02). These results define the genes and regulatory regions included in this region of LD, containing an important susceptibility allele contributing to increased risk of neurodegeneration.
Oliveira
Sofia A
SA
Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
Scott
William K
WK
Zhang
Fengyu
F
Stajich
Jeffrey M
JM
Fujiwara
Kenichiro
K
Hauser
Michael
M
Scott
Burton L
BL
Pericak-Vance
Margaret A
MA
Vance
Jeffery M
JM
Martin
Eden R
ER
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000483:Alleles; D002874:Chromosome Mapping; D002886:Chromosomes, Human, Pair 17; D005192:Family Health; D005260:Female; D020022:Genetic Predisposition to Disease; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D008565:Membrane Proteins / Q000235:genetics; D008875:Middle Aged; D008957:Models, Genetic; D019636:Neurodegenerative Diseases / Q000235:genetics; D010300:Parkinson Disease / Q000235:genetics; D010375:Pedigree; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D053766:Presenilin-2; D018019:Receptors, Corticotropin-Releasing Hormone / Q000235:genetics; D016875:tau Proteins / Q000235:genetics*
D008565:Membrane Proteins; C508861:PSEN2 protein, human; D053766:Presenilin-2; D018019:Receptors, Corticotropin-Releasing Hormone; C458340:STH protein, human; D016875:tau Proteins