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Background: Deep Vein Thrombosis (DVT) is a multicausal disease involving both acquired as well as genetic factors. Nitric oxide is an influential endogenous factor having its role in the development of deep vein thrombosis. It maintains the vascular integrity and any alterations in its levels may lead to a thrombotic event. It may also modulate homocysteine metabolism to cause hyperhomocysteinemia, which is a prominent risk factor for thrombosis. The objective of the study was to study if endothelial nitric oxide gene polymorphisms, 894G/T, and 2479G/A alter the plasma nitric oxide and homocysteine levels which may eventually increase the risk of deep vein thrombosis. Methods: One hundred Doppler ultrasonography and computerized tomography confirmed (for cerebral venous thrombosis), non-related DVT patients (M:F = 58:42; age range = 18 to 61 years) served as the study population. Two hundred hospital staff and their relatives or unrelated attendants of the patients served as the controls. Nitric oxide levels were determined by measuring its metabolites (NOx), and EIA was used to measure homocysteine levels. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used for detecting the eNOS polymorphisms 894G/T and 2479G/A. Results: In total, DVT subjects have 25% higher plasma levels of homocysteine and 37% lower levels of NOx in their circulation when compared to controls. In tertile analysis of nitric oxide and homocysteine levels, 894G/T and 2479G/A polymorphisms were associated with plasma nitric oxide and homocysteine levels. The increased risk of deep vein thrombosis was associated with endothelial nitric oxide gene polymorphisms and nitric oxide levels, but homocysteine levels were not a risk for deep vein thrombosis. Conclusion: The present study demonstrates that 894G/T and 2479G/A polymorphisms interact with lower levels of nitric oxide and higher levels of homocysteine that may possess the risk of deep vein thrombosis. [ABSTRACT FROM AUTHOR]

This study aimed to determine whether there is an influence of interleukin 6 (IL-6) gene promoter polymorphisms on IL-6 plasma levels and its role in the development of ischemic stroke in young Indians. One hundred young patients with ischemic stroke (age ≥ 45 years) and equal number of age- and sex-matched controls were genotyped for 174G>C, -572G>C, and -597G>A promoter polymorphisms by polymerase chain reaction-restriction fragment length polymorphism. Plasma IL-6 levels were measured by enzyme-linked immunosorbent assay. Plasma IL-6 levels were significantly higher in patients as compared to controls (patients: 28.61 + 8.61 pg/mL, controls: 7.60 + 4.10 pg/mL, P = .001). Both -174G>C (allelic χ²/P value: 4.79/.028, genotypic χ²/P value: 5.3/.021) and -572G>C (allelic χ²/P value: 9.63/.00113 Genotypic χ²/P value: 74/.0002) polymorphisms exhibited genotypic as well as allelic significant association with the disease phenotype. Comparison was made between patients and controls for all 3 polymorphisms using a recessive model with respect to plasma IL-6 levels; no polymorphism showed any significant correlative association with the increased IL-6 levels (P = .31, .51, .32). Interleukin 6 is an inflammatory marker that is considerably influenced by nongenetic factors and is not a good candidate gene for studying genetic components associated with ischemic stroke. It seems that the variability in IL-6 levels is an integrated effect of nongenetic influences and the inflammatory events that follow ischemic stroke instead of being its cause. It is suggested that there is no direct association between -174G>C, -572G>C, and -597G>A polymorphisms and elevated IL-6 levels in the development of ischemic stroke. [ABSTRACT FROM AUTHOR]

Objectives: To evaluate the association of interleukin 6 (IL-6) levels with deep vein thrombosis (DVT) and to assess the impact of IL-6 promoter polymorphisms (−174G > C, −572G > C and −597G > A) on its plasma levels and their influence in the development of DVT in India. Methods: One hundred DVT patients and 100 age and sex-matched healthy controls were study subjects. IL-6 polymorphisms were identified by polymerase chain reaction-restriction fragment length polymorphism. IL-6 levels were detected by enzyme-linked immunosorbent assay. Results: Significantly raised IL-6 levels were observed in patients as compared to controls. (Patients: 13.73 ± 6.30 pg/ml, Controls: 11.83 ± 4.47 pg/ml, p = 0.014). The prevalence of C allele of −572G > C polymorphism was significantly higher in patients than controls (Patients: 39.5%, Controls: 27.5%, p = 0.011, χ2=6.463). Subjects with GC and CC genotype had significantly higher IL-6 levels than GG genotype (p=<0.001). Patients with GC and CC genotype increased the DVT risk by 1.39 fold (ORa: 1.39, CI: 0.74-2.62) and 2.69 fold (ORa: 2.42, CI: 1.08-6.70), respectively. IL-6 −174G > C and −597G > A polymorphisms were not associated with raised IL-6 levels and nor with thrombotic risk (−174G > C: p = 0.823 χ2=0.369; −597G > A: p = 0.678 χ2=1.08). Conclusion: Our study emphasizes the importance of −572G > C polymorphism in increasing IL-6 levels, thereby showing its significant role in DVT in India. IL-6 −174G > C and −597G > A were neither associated with raised plasma IL-6 levels nor with thrombotic risk. Thus −572G > C polymorphism detection may be one of the connecting links between IL-6 and thrombotic risk in Indian DVT patients. [ABSTRACT FROM AUTHOR]

Objective: Cell-free DNA from maternal plasma can be used for non-invasive prenatal testing for aneuploidies and single gene disorders, and also has applications as a biomarker for monitoring high-risk pregnancies, such as those at risk of pre-eclampsia. On average, the fractional cell-free fetal DNA concentration in plasma is approximately 15%, but can vary from less than 4% to greater than 30%. Although quantification of cell-free fetal DNA is straightforward in the case of a male fetus, there is no universal fetal marker; in a female fetus measurement is more challenging. We have developed a panel of multiplexed insertion/deletion polymorphisms that can measure fetal fraction in all pregnancies in a simple, targeted sequencing reaction. Methods: A multiplex panel of primers was designed for 35 indels plus a ZFX/ZFY amplicon. cfDNA was extracted from plasma from 157 pregnant women, and maternal genomic DNA was extracted for 20 of these samples for panel validation. Sixty-one samples from pregnancies with a male fetus were subjected to whole genome sequencing on the Ion Proton sequencing platform, and fetal fraction derived from Y chromosome counts was compared to fetal fraction measured using the indel panel. A total of 157 cell-free DNA samples were sequenced using the indel panel, and informativity was assessed, along with the proportion of fetal DNA. Results: Using gDNA we optimised the indel panel, removing amplicons giving rise to PCR bias. Good correlation was found between fetal fraction using indels and using whole genome sequencing of the Y chromosome (Spearmans r = 0.69). A median of 12 indels were informative per sample. The indel panel was informative in 157/157 cases (mean fetal fraction 14.4% (±0.58%)). Conclusions: Using our targeted next generation sequencing panel we can readily assess the fetal DNA percentage in male and female pregnancies. [ABSTRACT FROM AUTHOR]

Mild factor XIII deficiency is an underdiagnosed coagulation disorder. Considering the large number of coding and non-coding polymorphisms identified in the F13A1 gene, there is a possibility that some of these might result in alterations of plasma FXIII levels and cause mild FXIII deficiency. Recently, a homozygous F13A1 gene intron 1 variant (IVS1+12C>A) was found in a patient with FXIII deficiency. In vitro expression studies for this variant demonstrated its lowering effect on FXIII levels. In order to determine the impact of this variant on a population level, we analysed the prevalence of this variant in three clinically and genetically defined population cohorts: an apparently healthy control cohort C1 ( n = 102), a mild FXIII deficiency cohort C2 with no detectable F13A1 or F13B gene mutations ( n = 183) and a mild FXIII-A deficiency cohort C3 exhibiting heterozygous F13A1 mutations ( n = 37). FXIII activity was determined using photometric assay on plasma samples. The F13A1 gene intron 1 variant was analysed by direct sequencing. The C1 cohort showed a normal distribution of FXIII activity (mean 114.1 ± 20.86 %). Mean FXIII activity levels for the C2 and C3 cohorts were 54.45 ± 11.12 % and 44.21 ± 10.16 %, respectively. The frequencies of minor allele (A) were 0.07 in C1 cohort, 0.19 in C2 cohort and 0.11 in C3 cohort. The difference in minor allele frequencies for the C1 and C2 cohorts were highly significant ( p < 0.001). The greater frequency of the IVS1+12(A) variant among C2 cohort patients suggests that this polymorphism is associated with mild FXIII deficiency. [ABSTRACT FROM AUTHOR]

Abstract: Background: Endothelium derived nitric oxide is formed from l-arginine by endothelial nitric oxide synthase encoded by the nitric oxide synthase 3 (NOS3) gene. Nitric oxide possesses a variety of protective effects on endothelial cells and therefore NOS3 is a logical candidate gene to be investigated for the susceptibility of deep vein thrombosis (DVT). Methods: One hundred consecutive patients (M: F=56:44) with idiopathic deep vein thrombosis and an equal number of age and sex matched healthy controls were the study subjects. All study subjects were typed for five NOS3 polymorphisms (−786C/T, −922A/G, 894G/T, Intron 4 VNTR, and Intron 23 G10T). Results: Two polymorphisms (−922A/G and 894G/T) are showing their association with DVT. −922A/G shows both genotypic (P =0.0218; χ 2 =5.25; O.R=1.94) as well as allelic association (P =0.0014; χ 2 =10.19; O.R=2.0) while 894G/T shows only allelic (P =0.04; χ 2 =3.93; O.R=3.93) association with DVT. Conclusion: Susceptibility to DVT in North Indian Asian patients may be associated with some variants of NOS3 gene. [Copyright &y& Elsevier]

Genes involved in the hemostatic mechanism are logical candidate genes for association studies in prothrombotic conditions such as stroke. Since the underlying etiology in pediatric strokes is different than adults, looking for genetic causes would be the logical thing to do in the pediatric stroke population. Fifty-eight Asian-Indian stroke patients below 15 years of age and equal number of age- and sex-matched healthy controls were the subjects for the study. The subjects were screened for 13 polymorphisms and three mutations spread across seven different candidate genes involved in the hemostatic system. Of the 13 polymorphisms and three mutations studied, four polymorphisms, HPA-I, TAFI 147Ala>Thr, methylene tetrahydrofolate reductase (MTHFR) 677 C>T, and MTHFR 1298 A>C, showed significant association with the disease phenotype. MTHFR 677 C>T showed the strongest association and therefore may have a strong predisposing role for pediatric strokes. Gene–gene interaction studies showed a strong interaction between HPA-I and MTHFR 677 C>T polymorphism. The wild type of both these polymorphisms synergistically showed a strong protective effect [ p < 0.0001, O.R: 10.06(4.26–23.71)]. Polymorphisms in HPA-I and MTHFR may have important predisposing roles in the development of pediatric stroke. [ABSTRACT FROM AUTHOR]

von Willebrand factor (VWF) is a complex multimeric plasma glycoprotein encoded by an approximately 178-kb large VWF gene located on the short arm of chromosome 12 (12p13.2). VWF plays an important role in hemostasis through binding with platelet GpIbα receptors. We made an attempt to correlate the 789Ala/Ala genotype of the VWF with VWF:Ag level in different types of unrelated von Willebrand disease (VWD) patients and healthy controls. VWF assays and other coagulation screening tests have been done for all 103 (50 male, 53 female) different types of index VWD patients including 19 type 1, 55 type 2, and 29 type 3 VWD patients. Genotypes were detected by polymerase chain reactions followed by restriction fragment length polymorphism. The genotype 789Ala/Ala was found in 26.3% type 1 and in 31.0% type 3 patients. This genotype was not found in any of type 2 patient or healthy controls. Overall, 789Ala/Ala genotype was found significantly higher ( P < 0.001) in quantitative type (type 1 and type 3) VWD that is occurred due to low VWF:Ag level. These results demonstrate that mutant homozygous 789Ala/Ala genotype of this polymorphism probably have their functional implications for low plasma VWF:Ag level in quantitative type of VWD. [ABSTRACT FROM AUTHOR]

Thrombin activatable fibrinolysis inhibitor [carboxypeptidase B2 (plasma), CPB2] is a basic carboxypeptidase, which inhibits fibrinolysis by cleaving the C-terminal lysine residues on plasmin-modified partially degraded fibrin. Plasma CPB2 concentrations have been reported to be under the control of numerous single nucleotide polymorphisms located in the regulatory and coding regions of the gene encoding CPB2 ( CPB2). High functional CPB2 levels have been found to be associated with an increased risk for ischemic stroke. The present study investigated CPB2 antigen levels and associated CPB2 polymorphisms in an acute onset non-cardioembolic stroke population compared with an age- and sex-matched healthy control population. This is, to the best of our knowledge, the first such study done in an Asian Indian population. CPB2 antigen levels were significantly associated with the disease phenotype ( P < 0·001) and with CPB2 polymorphisms ( P < 0·001). The haplotypes generated on analysis of the genotypic data accounted for 21% of the natural variation in the CPB2 antigenic levels. However none of the haplotype combinations generated showed any association with disease phenotype and therefore could not explain for the difference in CPB2 antigen levels between cases and controls. [ABSTRACT FROM AUTHOR]

Background: Homozygosity for MTHFR C677T polymorphism can lead to significantly high homocysteine levels and hyperhomocysteinemia is an important risk factor for thrombotic events.Aims: The aim was to determine role of MTHFR C677T polymorphism in North Indians with ischemic stroke.Settings and Design: In a prospective study, the subjects of stroke were recruited from the neurology clinic of the hospital. Controls were healthy individuals from the Hematology clinic without any history of stroke.Materials and Methods: Plasma homocysteine levels were measured by enzyme immuno assay method after 3 months of acute episode. Serum folate and Vitamin B12 levels were estimated by competitive inhibition radioassay. MTHFR polymorphism was detected by PCR-RFLP using Hinf I enzyme.Statistical Analysis: The analysis of significance of results was done using SPSS software package. A p-value.Results: Thirty-two acute ischemic stroke patients (aged 1-44 years) were studied. Fourteen (43.8%) had recurrent stroke. Nine (28%) had multiple infarcts. Four of 32 patients (12.5%) had high homocysteine levels. Three out of these 4 hyper-homocysteinemia patients were homozygous ( TT ) for MTHFR polymorphism (2 with recurrent stroke). Two of three homozygous cases with TT genotype had low serum folate. Five of 32 stroke cases (18.8%) were heterozygous ( CT ) genotype.Conclusions: Primary hyper-homocysteinemia appears to be an important risk factor for ischemic stroke in North Indians, most due to MTHFR C677T homozygosity. Folate levels may modify the presentation of the MTHFR TT genotype. [ABSTRACT FROM AUTHOR]