Allele and haplotype frequency distribution in PTPN22 gene across variable ethnic groups: Implications for genetic association studies for autoimmune diseases.

Abstract	The rs2476601-T allele at the protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene has been consistently associated with several autoimmune diseases in European-derived populations. However, little is known about the allele and haplotype frequency distributions in PTPN22 among populations derived from other ethnic groups. In the present study, the allele and haplotype frequency distributions of six single nucleotide polymorphisms (SNPs) in the PTPN22 gene were compared among Brazilian populations and HapMap phase 3 dataset. A total of 10 different population samples were evaluated. Additionally, in admixed populations, individual genetic ancestries were estimated for Native American, African, and European contributions. Estimated individual ancestries were used as quantitative traits in a conditional approach for single-marker and haplotype-specific regression analyses. It was shown that several SNPs and haplotypes have different frequencies among different ethnic populations. Individual genetic ancestries were not associated with the rs2476601-T allele, but were associated with PTPN22 haplotypes in Brazilian, Mexican, and African-American admixed populations. Our results suggest caution in the interpretation of results found in association studies involving PTPN22 polymorphisms in admixed populations. Correction for stratification generated by admixture should be mandatory to minimize or avoid chances of spurious association.
Authors	Tulio C Lins, Rodrigo G Vieira, Dario Grattapaglia, Rinaldo W Pereira
Journal	Autoimmunity (Autoimmunity) Vol. 43 Issue 4 Pg. 308-16 (Jun 2010) ISSN: 1607-842X [Electronic] England
PMID	20166877 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
Chemical References	PTPN22 protein, human Protein Tyrosine Phosphatase, Non-Receptor Type 22
Topics	Autoimmune Diseases (ethnology, genetics) Black People Brazil Ethnicity (genetics) Gene Frequency Genetic Association Studies Genetic Predisposition to Disease Genotype Haplotypes Humans Indians, North American (genetics) Polymorphism, Single Nucleotide Protein Tyrosine Phosphatase, Non-Receptor Type 22 (genetics) White People

Join CureHunter, for free Research Interface BASIC access!

Take advantage of free CureHunter research engine access to explore the best drug and treatment options for any disease. Find out why thousands of doctors, pharma researchers and patient activists around the world use CureHunter every day.

Realize the full power of the drug-disease research graph!