A survey of haplotype variants at several disease candidate genes: the importance of rare variants for complex diseases. J Med Genet 2005 Mar;42(3):221-7
Date
03/04/2005Pubmed ID
15744035Pubmed Central ID
PMC1736011DOI
10.1136/jmg.2004.024752Scopus ID
2-s2.0-20144371261 42 CitationsAbstract
BACKGROUND: The haplotype based association method offers a powerful approach to complex disease gene mapping. In this method, a few common haplotypes that account for the vast majority of chromosomes in the populations are usually examined for association with disease phenotypes. This brings us to a critical question of whether rare haplotypes play an important role in influencing disease susceptibility and thus should not be ignored in the design and execution of association studies.
METHODS: To address this question we surveyed, in a large sample of 1873 white subjects, six candidate genes for osteoporosis (a common late onset bone disorder), which had 29 SNPs, an average marker density of 13 kb, and covered a total of 377 kb of the DNA sequence.
RESULTS: Our empirical data demonstrated that two rare haplotypes of the parathyroid hormone (PTH)/PTH related peptide receptor type 1 and vitamin D receptor genes (PTHR1 and VDR) with frequencies of 1.1% and 2.9%, respectively, had significant effects on osteoporosis phenotypes (p = 4.2 x 10(-6) and p = 1.6 x 10(-4), respectively). Large phenotypic differences (4.0 approximately 5.0%) were observed between carriers of these rare haplotypes and non-carriers. Carriers of the two rare haplotypes showed quantitatively continuous variation in the population and were derived from a wide spectrum rather than from one extreme tail of the population phenotype distribution.
CONCLUSIONS: These findings indicate that rare haplotypes/variants are important for disease susceptibility and cannot be ignored in genetics studies of complex diseases. The study has profound implications for association studies and applications of the HapMap project.
Author List
Liu PY, Zhang YY, Lu Y, Long JR, Shen H, Zhao LJ, Xu FH, Xiao P, Xiong DH, Liu YJ, Recker RR, Deng HWAuthors
Pengyuan Liu PhD Adjunct Professor in the Physiology department at Medical College of WisconsinDonghai Xiong PhD Associate Professor in the Pharmacology and Toxicology department at Medical College of Wisconsin
MESH terms used to index this publication - Major topics in bold
Apolipoproteins EBone Density
Collagen Type I
Estrogen Receptor alpha
Female
Genetic Testing
Haplotypes
Humans
Male
Middle Aged
Osteoporosis
Parathyroid Hormone
Phenotype
Polymorphism, Single Nucleotide
Receptor, Parathyroid Hormone, Type 1
Receptors, Calcitriol
