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Genetic variation and haplotype structure of the gene Vitamin K epoxide reductase complex, subunit 1 in the Tamilian population.

Kumar DK, Shewade DG, Surendiran A, Adithan C - J Pharmacol Pharmacother (2013)

Bottom Line: To study the genetic variation and haplotype structure of Vitamin K epoxide reductase complex, subunit 1 (VKORC1) gene in the Tamilian population.The major alleles of VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), and rs23596121 (C), were found to be at frequencies of 90.0%, 89.2%, 90.9%, 94.1%, 90.7%, 89.5% and 91.2%, respectively.The frequencies of haplotypes HAP1 (GTTCCGCA), HAP2 (ACGCTCTG), HAP3 (GTTTCGCG), HAP4 (GTTCCGCG) and HAP5 (GCTCCCCG) were found to be 80.0%, 7.4%, 4.7%, 1.5% and 1.1%, respectively.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India.

ABSTRACT

Objective: To study the genetic variation and haplotype structure of Vitamin K epoxide reductase complex, subunit 1 (VKORC1) gene in the Tamilian population.

Materials and methods: The study was performed on 210 unrelated, healthy volunteers of the Tamilian population, of either sex between the age group of 18-60 years. Five ml of venous blood sample was collected using sodium ethylene diamine tetra acetic acid (EDTA) as anticoagulant. DNA was extracted using phenol-chloroform extraction method. Eight single nucleotide polymorphisms (SNPs) VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), rs23596121 (C), and rs7294 (A) were studied using real-time quantitative Polymerase Chain Reaction (qPCR) method and they were included for constructing five-major haplotype blocks of VKORC1 gene.

Results: The major alleles of VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), and rs23596121 (C), were found to be at frequencies of 90.0%, 89.2%, 90.9%, 94.1%, 90.7%, 89.5% and 91.2%, respectively. The variant allele of VKORC1 rs7294 (A) was more frequent (83.6%) in the Tamilian population. The frequencies of haplotypes HAP1 (GTTCCGCA), HAP2 (ACGCTCTG), HAP3 (GTTTCGCG), HAP4 (GTTCCGCG) and HAP5 (GCTCCCCG) were found to be 80.0%, 7.4%, 4.7%, 1.5% and 1.1%, respectively.

Conclusion: In the present study the allele- frequency distributions, genotype and haplotype frequencies of the VKORC1 gene was considered. The findings of this study provide the genetic information required for learning the association of VKORC1 genetic variation and oral anticoagulant dose variability among patients receiving oral anticoagulants in the Tamilian population.

No MeSH data available.


Related in: MedlinePlus

Linkage disequilibrium pattern of VKORC1 genetic variants in the Tamilian population. The single nucleotide polymorphisms (SNPs) in Chromosome 16 were positioned according to the order and orientation. Each of the variant is given with its specific chromosomal position and the rsID. LD pattern of the rs9923231, rs7196161, rs2884737, rs1770847, rs9934438, rs8050894, rs23596121and rs7294 in the Tamilian population. Red and pink colors represent a very strong LD pattern (D′>0.8) and white color represents moderate to low LD (D′ <0.8 to > 0.5)
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Figure 1: Linkage disequilibrium pattern of VKORC1 genetic variants in the Tamilian population. The single nucleotide polymorphisms (SNPs) in Chromosome 16 were positioned according to the order and orientation. Each of the variant is given with its specific chromosomal position and the rsID. LD pattern of the rs9923231, rs7196161, rs2884737, rs1770847, rs9934438, rs8050894, rs23596121and rs7294 in the Tamilian population. Red and pink colors represent a very strong LD pattern (D′>0.8) and white color represents moderate to low LD (D′ <0.8 to > 0.5)

Mentions: The allele frequency of VKORC1 in Tamilians was compared with other ethnic populations [Table 3]. The most studied SNPs (rs9923231, rs9934438, rs2359612 and rs7294) were compared with other ethnic populations. The results reveal that the frequency distribution of Han Chinese, Caucasians and African Americans were significantly different from the Tamilian population (P < 0.001). The frequency distributions of rs9923231 and rs9934438 among North Indians were not significantly different from the Tamilian population which is in south India (P > 0.05). The haplotype structure and pair-wise LD pattern of the eight VKORC1 SNPs were identified [Figure 1] and their frequencies in the Tamilian population were established [Table 4] by accelerated expectation-maximization (EM) algorithm. A strong LD pattern (D′>0.8) was observed between all the SNPs except between rs7294 and other SNPs, where only a moderate LD (D′ <0.8) was observed. But the LD between rs17708472 and rs7294 was found to be strong (D′>0.8).


Genetic variation and haplotype structure of the gene Vitamin K epoxide reductase complex, subunit 1 in the Tamilian population.

Kumar DK, Shewade DG, Surendiran A, Adithan C - J Pharmacol Pharmacother (2013)

Linkage disequilibrium pattern of VKORC1 genetic variants in the Tamilian population. The single nucleotide polymorphisms (SNPs) in Chromosome 16 were positioned according to the order and orientation. Each of the variant is given with its specific chromosomal position and the rsID. LD pattern of the rs9923231, rs7196161, rs2884737, rs1770847, rs9934438, rs8050894, rs23596121and rs7294 in the Tamilian population. Red and pink colors represent a very strong LD pattern (D′>0.8) and white color represents moderate to low LD (D′ <0.8 to > 0.5)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643344&req=5

Figure 1: Linkage disequilibrium pattern of VKORC1 genetic variants in the Tamilian population. The single nucleotide polymorphisms (SNPs) in Chromosome 16 were positioned according to the order and orientation. Each of the variant is given with its specific chromosomal position and the rsID. LD pattern of the rs9923231, rs7196161, rs2884737, rs1770847, rs9934438, rs8050894, rs23596121and rs7294 in the Tamilian population. Red and pink colors represent a very strong LD pattern (D′>0.8) and white color represents moderate to low LD (D′ <0.8 to > 0.5)
Mentions: The allele frequency of VKORC1 in Tamilians was compared with other ethnic populations [Table 3]. The most studied SNPs (rs9923231, rs9934438, rs2359612 and rs7294) were compared with other ethnic populations. The results reveal that the frequency distribution of Han Chinese, Caucasians and African Americans were significantly different from the Tamilian population (P < 0.001). The frequency distributions of rs9923231 and rs9934438 among North Indians were not significantly different from the Tamilian population which is in south India (P > 0.05). The haplotype structure and pair-wise LD pattern of the eight VKORC1 SNPs were identified [Figure 1] and their frequencies in the Tamilian population were established [Table 4] by accelerated expectation-maximization (EM) algorithm. A strong LD pattern (D′>0.8) was observed between all the SNPs except between rs7294 and other SNPs, where only a moderate LD (D′ <0.8) was observed. But the LD between rs17708472 and rs7294 was found to be strong (D′>0.8).

Bottom Line: To study the genetic variation and haplotype structure of Vitamin K epoxide reductase complex, subunit 1 (VKORC1) gene in the Tamilian population.The major alleles of VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), and rs23596121 (C), were found to be at frequencies of 90.0%, 89.2%, 90.9%, 94.1%, 90.7%, 89.5% and 91.2%, respectively.The frequencies of haplotypes HAP1 (GTTCCGCA), HAP2 (ACGCTCTG), HAP3 (GTTTCGCG), HAP4 (GTTCCGCG) and HAP5 (GCTCCCCG) were found to be 80.0%, 7.4%, 4.7%, 1.5% and 1.1%, respectively.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India.

ABSTRACT

Objective: To study the genetic variation and haplotype structure of Vitamin K epoxide reductase complex, subunit 1 (VKORC1) gene in the Tamilian population.

Materials and methods: The study was performed on 210 unrelated, healthy volunteers of the Tamilian population, of either sex between the age group of 18-60 years. Five ml of venous blood sample was collected using sodium ethylene diamine tetra acetic acid (EDTA) as anticoagulant. DNA was extracted using phenol-chloroform extraction method. Eight single nucleotide polymorphisms (SNPs) VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), rs23596121 (C), and rs7294 (A) were studied using real-time quantitative Polymerase Chain Reaction (qPCR) method and they were included for constructing five-major haplotype blocks of VKORC1 gene.

Results: The major alleles of VKORC1 rs9923231 (G), rs7196161 (T), rs2884737 (T), rs17708472 (C), rs9934438 (C), rs8050894 (G), and rs23596121 (C), were found to be at frequencies of 90.0%, 89.2%, 90.9%, 94.1%, 90.7%, 89.5% and 91.2%, respectively. The variant allele of VKORC1 rs7294 (A) was more frequent (83.6%) in the Tamilian population. The frequencies of haplotypes HAP1 (GTTCCGCA), HAP2 (ACGCTCTG), HAP3 (GTTTCGCG), HAP4 (GTTCCGCG) and HAP5 (GCTCCCCG) were found to be 80.0%, 7.4%, 4.7%, 1.5% and 1.1%, respectively.

Conclusion: In the present study the allele- frequency distributions, genotype and haplotype frequencies of the VKORC1 gene was considered. The findings of this study provide the genetic information required for learning the association of VKORC1 genetic variation and oral anticoagulant dose variability among patients receiving oral anticoagulants in the Tamilian population.

No MeSH data available.


Related in: MedlinePlus