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Series GSE58951 Query DataSets for GSE58951
Status Public on Jul 28, 2014
Title Single Nucleotide Polymorphisms Other Than Factor V Leiden are Associated with Coagulopathy and Osteonecrosis of the Femoral Head in Chinese Patients
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Single nucleotide polymorphisms (SNPs) of factor V Leiden have been associated with osteonecrosis of the femoral head (ONFH) in Caucasians but remains controversial in Asians. We used an SNP microarray to screen 55 loci of factor V gene in patients with ONFH of Chinese. Significantly different candidate SNPs at 14 loci were analyzed in 146 patients and 116 healthy controls using MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry and gene sequencing. The factor V Leiden (rs6025) was not found in all participants. Six SNP loci (rs9332595, rs6020, rs9332647, rs3766110, rs10919186, and rs12040141) were confirmed with significant differences in patients but not in controls. The rs6020 G-to-A polymorphism was found in 88.9% of the patients. In addition, a high percentage (84.7%) of the patients had an abnormal coagulation profile that included hyperfibrinogen, elevated fibrinogen degradation products, elevated D-dimer, abnormal protein S, abnormal protein C, or a decrease in anti-thrombin III. Patients with the rs6020 G-to-A polymorphism (mutation) had a higher risk (odds ratio: 4.33; 95% confidence interval: 1.36-13.76) of having coagulation abnormalities than did those without the mutation (wild-type) (p = 0.008). Our findings suggested that the rs6020 polymorphism might be the genetic trait that accounts for the higher prevalence of ONFH in the Chinese population than in Westerners. Exposure to risk factors such as alcohol and steroids in patients with the rs6020 polymorphism causes coagulation abnormalities and, subsequently, thromboembolisms in the femoral head.
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.
SNP genotype analysis of Affymetrix 6.0 Chip. SNP arrays was performed for 22 Chinese patients with Osteonecrosis of the Femoral Head.
Contributor(s) Peng K, Hwang K, Hwang T, Lee Y, Hsu W, Hsu RW, Ueng SW, Lee MS
Citation(s) 25119470
Submission date Jun 30, 2014
Last update date Nov 27, 2018
Contact name Yun-Shien Lee
Organization name Ming Chuan Univ
Department Dept. Biotechnology
Street address TauYau
City TauYau
State/province Taiwan
ZIP/Postal code 115
Country Taiwan
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (22)
GSM1422871 ONFH Patient 3
GSM1422872 ONFH Patient 13
GSM1422873 ONFH Patient 46
BioProject PRJNA253963

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE58951_RAW.tar 653.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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