Aberrant Promoter Methylation of YAP Gene and its Subsequent Downregulation in Indian Breast Cancer Patients.

BACKGROUND: YAP, a potent oncogene and major downstream effector of the mammalian Hippo tumor suppressor pathway can act as either oncogene or tumor suppressor gene based on the type of tissue involved. Despite various studies, the role and mechanism through which YAP mediates its tumor suppressor or oncogenic effects are not yet fully understood. Therefore in the present study we aimed to investigate YAP at DNA, mRNA and protein level and also attempted to correlate our molecular findings with various clinicopathological variables of the patients. METHODS: The study comprised of a total 137 genetically unrelated women with sporadic breast cancer cases and normal adjacent tissues not infiltrated with tumor. Mutation of YAP gene was analyzed by automated DNA sequencing. YAP promoter methylation was studied using MS-PCR. Expression at mRNA and protein level was studied using qPCR and IHC respectively. RESULTS: In our study YAP mRNA expression was found to be 8.65 ± 6.17 fold downregulated in 67.15% cases. The expression of YAP when analyzed at the protein level by IHC was found to be absent in 78.83% cases. Results from MS-PCR analysis showed that YAP promoter methylation plays an important role in declining the expression of YAP protein. The absence of YAP protein coincided with 86.60% methylated cases thereby showing a very strong correlation (p = 0.001). We also investigated YAP mutation at the major check point sites in the Hippo pathway and observed no mutation. A significant association was observed on correlating mRNA expression with clinical stages (p = 0.038) and protein expression with ER status (p = 0.018) among Indian breast cancer patients. CONCLUSION: The expression of YAP was found to be downregulated in response to aberrant promoter methylation. The downregulation of YAP are consistent with previous studies suggesting it to have a tumor suppressive role in breast cancer. We did not observe any mutation at the major check point sites in the Hippo pathway.

Glutathione-S-transferase polymorphism and acute lymphoblastic leukemia (ALL) in north Indian children: a case-control study and meta-analysis.

Various studies on association of glutathione S-transferase (GST) polymorphisms and childhood acute lymphoblastic leukemia (ALL) have yielded conflicting results. We examined this association among north Indian children and conducted an updated meta-analysis to overcome sample size-related limitations. GSTM1, GSTP1 and GSTT1 genotypes in 100 children with ALL and 300 healthy controls were compared. GSTT1 null mutation (odds ratio (OR) 2.54, 95% confidence interval (CI) 1.50-4.32) and GSTP1 homozygous mutation (OR 3.13, 95%CI 1.48-6.59) were found to increase the risk of childhood ALL, while GSTM1 did not alter the risk. Meta-analysis included 22, 10 and 20 studies examining the association of childhood ALL with GSTM1, GSTP1 and GSTT1 genotypes, respectively. Only GSTM1 genotype (OR 1.29, 95%CI 1.10-1.62) was associated with increased risk in the overall analysis. However, both GSTM1 (OR 1.54, 95%CI 1.12-2.10) and GSTT1 (OR 1.63, 95%CI 1.32-1.99) null genotypes were associated with increased risk in Asian subjects. The risk of developing childhood ALL was not associated with GSTP1 genotype.

MTHFR gene polymorphism in acute lymphoblastic leukemia among North Indian children: a case-control study and meta-analysis updated from 2011.

Studies on the association of methylenetetrahydrofolate reductase (MTHFR) genotype in childhood acute lymphoblastic leukemia (ALL) have yielded conflicting results. The present study examines this association in north Indian children with ALL and includes an updated meta-analysis. MTHFR (677 and 1298) genotype of children with ALL and healthy adult controls were done by the PCR-restriction fragment length polymorphism (PCR-RFLP) method and were compared using various models of inheritance. A total of 150 patients and 300 controls were included. The 677T allele was found protective (odds ratio (OR) 0.21, 95% confidence interval (CI) 0.04-0.94), whereas 1298C allele led to an increase in risk (OR 4.44, 95% CI 2.19-8.99) of childhood ALL. Meta-analysis included 31 and 27 studies examining the association of 677 and 1298 genotypes, respectively. The 677 C -> T polymorphism was protective (OR 0.90, 95% CI 0.82-0.99). Protection was more pronounced in folate-sufficient populations as compared with those not covered by folate fortification guidelines. The 1298A->C polymorphism was associated with a marginal increase in risk (OR 1.19, 95% CI 1.01-1.40).

Should factor V Leiden mutation and prothrombin gene polymorphism testing be done in women with recurrent miscarriage from North India?

PURPOSE: Role of thrombophilic factor (FV) in the etiology of recurrent miscarriages is not confirmed till date. It has been hypothesized that thrombophilic G1691A factor V Leiden (FVL), if detected well ahead in time among recurrent miscarriages may be a treatable. The role of FVL mutation in the pathogenesis of sporadic and recurrent miscarriages among North Indian women was studied to construct the frequency data in this part of the country. Further, we have evaluated the cost-benefit factor. METHODS: This is a case-control study, women with recurrent miscarriages (n = 1,000) as cases and healthy parous women (n = 500) as controls were enrolled in the study between January 2003 and January 2012. DNA was extracted from peripheral blood and analyzed for the presence of FVL mutation and prothrombin gene polymorphism (G20210A). We have carried out the meta-analysis taking into consideration 20 other world populations. RESULTS: In total, 50 (5.0 %) cases and 12 (2.4 %) controls were heterozygous for the FVL mutation. The incidence of FVL was higher in recurrent miscarriage cases as compared to the control group (OR 2.14; 95 % CI 1.12-4.05). CONCLUSION: Our results revealed the absence of FVL mutation in a homozygous state among patients and controls. Although the heterozygous mutation is almost double in cases as compared to controls, we still suggest that looking at the cost-benefit analysis this test may not be included in the battery of tests performed on recurrent miscarriages among North Indians from this part of the country.

Polymorphisms in MTHFR, MTHFD, and PAI-1 and recurrent miscarriage among North Indian women.

PURPOSE: The aim of this study was to investigate the association between MTHFR C677T, A1298C, MTHFD G1958A and plasminogen activator inhibitor type 1 (PAI-1) 4G/5G polymorphism among first trimester recurrent miscarriages. MATERIALS AND METHODS: DNA was extracted from peripheral blood samples from 200 patients and 300 controls. Polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequencing were used to identify the polymorphisms. We have analyzed the frequencies, odds ratio, Hardy-Weinberg equilibrium. RESULTS: MTHFR C677T, A1298C, and MTHFD G1958A variant alleles were found to be significantly more prevalent in patients than control. However, variant genotype of MTHFR C677T (OR = 2.54; 95 % CI = 1.23-5.24; p value = 0.014), 1298C (OR = 2.23; 95 % CI = 1.09-4.52; p value = 0.028), and MTHFD-1958 showed significant association with pregnancy loss (OR = 2.36; 95 % CI = 1.39-4.02; p value = 0.002). Both MTHFR 677 and MTHFD 1958 showed susceptible effect under recessive model of inheritance. PAI-1 mutations showed no significance. CONCLUSION: We observed significant susceptible effects of MTHFR C677T, A1298C, and MTHFD G1958A among RM cases. Our data points toward the multifactorial nature of the recurrent miscarriage as relative contribution of variant genotype of MTHFR C677T is only twofold and further decreased to only onefold, and MTHFD-1958 lost its significance upon meta-analysis.

Association of CTLA-4 and TNF-α polymorphism with recurrent miscarriage among North Indian women.

CONTEXT: CTLA-4 is engaged on effector cells that may alter signal transduction and subsequently cytokine production. The transmission of longer repeats of (AT)(n) alleles of CTLA-4 is also associated with women undergoing recurrent miscarriage. The TNF-α known as an embryo-toxic cytokine is reported to be greater in placentas of abortion prone pregnancies. OBJECTIVES: The present study investigated the role of CTLA-4+49 A/G, CTLA-4 (AT)(n) 3'UTR, TNF-α-308G/A and TNF-α-238G/A polymorphisms as a susceptibility marker for recurrent miscarriage (RM). PARTICIPANTS AND METHODS: We genotyped CTLA4+49 A/G, TNF-α-308 and TNF-α-238 gene polymorphisms in 300 patients with RM and 500 age and ethnically matched negative controls using PCR-RFLP method. While gene sequencing method was adopted for studying the CTLA-4 (AT)(n) 3'UTR polymorphism. RESULTS: The mutant homozygous genotype GG of CTLA4+49A/G, AA genotype and A allele of TNF-α-308, G allele of TNF-α-238 were observed to be predisposing among RM cases along with the 104 bp, 106 bp, 110 bp and 116 bp alleles of CTLA-4 (AT)(n) microsatellite repeat. GA and AG haplotypes of TNF-α were low risk associated haplotypes among recurrent miscarriage women. CONCLUSIONS: Roles of CTLA-4 A49G, CTLA-4 (AT)(n) 3'UTR, TNF-α-308 and TNF-α-238 polymorphisms in RM cases from North India is reflected through this study.

Genetic association of adipokine and UCP2 polymorphism with recurrent miscarriage among non-obese women.

The adipokines produced from adipose tissues influence energy homeostasis, resulting in alterations of the adipokine concentrations. This process may be associated with fertility impairment, resulting in recurrent miscarriage. The present study investigated whether there was any association between the UCP2 45-bp indel polymorphism and the adipokine gene polymorphisms, namely leptin 2549 (C/A), adeponectin 276 (G/T) and 45 (T/G) and resistin 420 (C/G) in 200 non-obese recurrent miscarriage patients and 300 ethnically matched negative controls. These markers were studied using gene-specific PCR single specific primer and restriction fragment length polymorphism. For leptin 2549 and adeponectin 276, the A allele and G allele showed 3.42-fold (P=0.0001) and 1.36-fold (P=0.036) increased risk of recurrent miscarriage, respectively. Combined analysis of UCP2 45-bp indel and leptin 2549 showed U0-L0 and U1-L0 variants to be at 2- and 3-fold increased associative risk, respectively. Combined analysis of leptin 2549 and adeponectin 276 showed L0-D0 and L0-D1 variants to be at 2- and 4-fold increased associative risk, respectively. The combination U1-L0-D1-A1-R1 was 4.39-fold higher (P=0.0007) among recurrent miscarriage patients. In conclusion, the results highlight the role of the studied adipokine and UCP2 polymorphisms in recurrent miscarriage among the North Indian non-obese population. Pregnancy invokes a large shift in maternal metabolism. The normal concentrations of adipokines, which maintain the integrity of the hypothalamus-pituitary-gonadal axis, regular ovulatory processes and successful embryo implantation, are altered because of the influence of energy homeostasis, which in turn leads to fertility impairment and recurrent miscarriage of unknown aetiology. Recurrent miscarriage is reported in higher frequency among obese women. The UCP2 45-bp indel polymorphism and the adipokine gene polymorphisms namely leptin 2549 (C/A), adeponectin 276 (G/T), adeponectin 45 (T/G) and resistin 420 (C/G) have been shown to be associated with obesity. Most of the adipokine-related studies done previously have taken into consideration the metabolic function and obesity. However, there exist very few studies to evaluate the role of adipokines in non-obese recurrent miscarriage with no cause of repeated pregnancy losses. The present study focused at evaluating the independent effect of these single-nucleotide polymorphisms in non-obese women undergoing recurrent miscarriage.

Vascular endothelial growth factor gene polymorphisms in North Indian patients with recurrent miscarriages.

The association of four common polymorphisms of vascular endothelial growth factors (VEGF) with recurrent miscarriages(RM) was evaluated in North Indian women for 200 patients with RM and 200 controls. The subjects were genotyped for the polymorphisms 2578C/A, 2549 18-bp I/D, 1154G/A and +936C/T. Association of VEGF genotypes, alleles and haplotypes with recurrent miscarriage were evaluated by Fisher's exact test. 1154G/A and +936C/T modified the risk of RM. The 1154A allel and +936T allel significantly increased the risk of RM (OR = 1.485, P = 0.0210, 95% CI 1.072­2.057 and OR = 1.869, P = 0.0054, 95% CI 1.214­2.876 respectively). Risk was further increased when ­1154A/A genotype and +936C/T genotype were considered (OR = 2.0, P = 0.0310,95% CI 1.068­3.747 and OR = 1.716, P = 0.0293, 95% CI 1.058­2.784 respectively). However, no association was found between 2578C/A or 2549 18-bp I/D and RM. Four haplotypes, AIAC, ADAC, CIAT and ADGT, were found to predispose to RM while the haplotypes CIAC, CDGT and ADGC were found to show protective effect. In conclusion, two common polymorphisms of the VEGF gene,1154G/A and +936C/T, increase the risk of RM in North Indian women. RM is also predisposed in the presence of haplotypes AIAC,ADAC, CIAT and ADGT.

Prevalence, human leukocyte antigen typing and strategy for screening among Asian first-degree relatives of children with celiac disease.

BACKGROUND AND AIM: Data on prevalence, human leukocyte antigen (HLA) typing and small bowel histology among first-degree relatives of subjects with celiac disease (CD) is scarce. This prospective study evaluated the prevalence and role of HLA DQ2/8 testing in screening of first-degree relatives of children with CD. METHODS: Thirty confirmed children with CD and 91/94 first-degree relatives (parents and siblings) were enrolled. HLA DQ2/8 testing was carried out in all index CD cases. Clinical evaluation with a questionnaire, total serum immunoglobulin A (IgA), human IgA-tissue transglutaminase (IgA-tTGA) and HLA DQ2/8 testing was carried out in all first-degree relatives. Subjects who were positive for IgA-tTGA were recommended endoscopic duodenal biopsy to document histological changes of CD. RESULTS: Nine first-degree relatives were positive for IgA-tTGA, seven underwent duodenal biopsy and four subjects had Marsh IIIa changes suggestive of CD. The prevalence of histologically confirmed CD in first-degree relatives was 4.4%. The prevalence of potential CD was 9.8%. IgA-tTGA-positive subjects (4/9) were significantly more often symptomatic than IgA-tTGA-negative first-degree relatives (2/82). Twenty-nine (96.6%) index cases of CD and all IgA-tTGA-positive first-degree relatives were positive for HLA DQ2. None of the index CD cases or first-degree relatives were HLA DQ8-positive. A total of 85% of the first-degree relatives were positive for HLA DQ2 and thus at risk of developing CD. CONCLUSIONS: In this first Asian study on a limited number of families of children with CD, 4.4% of the first-degree relatives had CD. Only 15% of the first-degree relatives were negative for HLA DQ2/DQ8. Initial evaluation with HLA and serology followed by only serial serology in HLA-positive relatives is recommended.

Genetic Polymorphism in TNF-α-308 G/A and TNF-ß +252 A/G, as Prognostic Biomarker in Breast Cancer Patients among Indian Population.

BACKGROUND: Cytokines are the key regulator molecules that modulate immune response. Tumor necrosis factor (TNF- α-308 G/A and TNF-ß +252 A/G ) are inflammatory cytokine that control the progression of several types of cancer. They play a vital role in both tumor progression and destruction based on their concentrations. The role of TNF-α-308 G/A and TNF-ß +252 A/G gene polymorphism in the etiology of breast cancer (BC) is not clearly understood. Therefore, present study investigates the association of TNF-α -308 G/A and TNF-ß +252 A/G and the clinical features with Breast cancer patients. METHODS: In a case- control study, we have investigated 150 breast cancer patients and 300 age and ethnically matched healthy controls for duration of 3 years from North India. Promoter polymorphisms of tumor necrosis factor gene (TNF-α -308 G/A and TNF-ß +252 A/G) were genotyped using allele specific oligonucleotide polymerase chain reaction ASO and restriction fragment length polymorphism (PCR-RFLP). The associations were evaluated by calculating the pooled odds ratio (OR) with 95% confidence interval (95% CI) using SPSS. RESULTS: Patients with different clinico-pathological variables and healthy controls were analyzed. Significant association was observed in A allele of TNF-α -308 G/A in breast cancer patients as compared to healthy controls (p<0.0001). However, no association was seen in TNF-ß +252 A/G both at genotypic and allelic level. The GG genotype of TNF-ß +252A/G is higher in grades III (p<0.01) patients. CONCLUSION: Our results suggest that TNF-α-308G/A polymorphism showed significant association with breast cancer patients.

Association of chemokines receptor (CCR5 Delta32) in idiopathic recurrent miscarriages among north Indians.

PURPOSE: Human reproduction is a complex process involving multiple factors for the success of pregnancy. Chemokines are one of the immunomodulators which may determine pregnancy outcome. In the present study, we have tested genetic association between CCR5 Delta32 polymorphism and idiopathic recurrent miscarriages (IRM) among north Indians. METHODS: Two hundred patients and 300 age, sex and ethnically matched controls were genotyped for CCR5 Delta32 polymorphism, genotype and allele frequencies were compared in both the groups. RESULTS: IRM patients had a three times higher (5.5 vs. 1.7%) frequency of heterozygote genotype (P = 0.0335, OR = 3.43; 95% CI = 1.17-10.04). Allele frequency in IRM patients was 3.7 and 0.83% among controls and the differences were statistically significant (P = 0.0349, OR = 3.37; 95% CI = 1.16-9.76). CONCLUSIONS: Our results demonstrated that it had a higher frequency of CCR5 Delta32 at allelic level suggesting a possible susceptibility trend (OR = 3.43) and CCR5 Delta32 may be a potential genetic risk factor for IRM.

Mutation, methylation and expression analysis of LIFR gene in Indian breast cancer patients.

LIFR functions as a tumor suppressor and metastatic suppressor of breast cancer. The present study investigates the status of LIFR gene in Indian breast cancer patients. A total of 137 breast cancer tissue and 137 adjacent normal tissue which served as controls were analyzed for mutation by automated DNA sequencing, methylation through methylation-specific polymerase chain reaction and its corresponding expression at mRNA and protein level using real-time quantitative polymerase chain reaction and immunohistochemistry respectively in Indian breast cancer patients. All the molecular findings were statistically correlated with clinopathological parameters of the patients to identify its association. LIFR mRNA expression was found to be 2.534 ±â€¯3.52 fold downregulated with subsequent absence of protein in 67.15% cases (92/137). The absence of LIFR protein coincided with 80.95% (85/105) methylated cases thereby showing a very strong correlation among the LIFR promoter methylation and LIFR protein expression (p = 0.0001). We also observed G2968C nucleotide change in 6/137 cases of exon 20 of LIFR gene resulting in Glu990Gln mutation. Correlation of LIFR promoter methylation with geographic location and age at menopause and LIFR mutation with age at menarche, age at first live birth, molecular subtypes of breast cancer, and lymph node status remained significant even after bonferroni correction (p ≤ 0.0027). All these data suggests the relevance of these associations in relation to Indian breast cancer patients. The loss of LIFR protein was frequently found in Indian breast cancer patients, and aberrant promoter methylation showed a significant correlation with its downregulation.

Recurrent miscarriage and micro-RNA among north Indian women.

Micro-RNAs (miRNAs) regulate diverse cellular processes such as cell differentiation, proliferation and apoptosis. Mutation in miRNAs results in various pathological conditions such as inflammation, viral infections, neurodegeneration, autoimmunity, and so on. We have evaluated the association of miR-146aC > G (rs2910164), miR-149T > C (rs2292832), miR-196a2T > C (rs11614913), and miR-499A > G (rs3746444) among patients with recurrent miscarriage (RM) and controls from North India. All the 200 patients with RM reported to experience at least 3 unexplained miscarriages before 20th week of gestation. Three hundred fertile women with no history of RMs were taken as controls. Both patients and controls were genotyped by the polymerase chain reaction amplification followed by restriction fragment length polymorphism. Variant alleles and genotypes of miR-499 A > G (Single Nucleotide Polymorphism Database [dbSNP] ID rs3746444) were found to be significant risks associated with patients having RM (odds ratio [OR] = 1.98; 95% confidence interval [CI] = 1.40-2.81; P value = .0001) and controls (OR = 3.64; 95% CI = 1.33-9.94; P value = .0109). A significant susceptible effect was found at allelic level in miR-196aT > C (dbSNP ID rs11614913) and miR-499 A > G (dbSNP ID rs3746444).

Molecular insights of saliva in solving paternity dispute.

Everyone is born with a unique genetic blueprint i.e. its own genome. Special locations called loci on different chromosomes display predictable inheritance patterns that could be used to determine biological relationships. These locations contain specific DNA sequences, called markers, which forensic scientists use as identifying marks for individuals. Saliva is a potentially useful source of genomic DNA for genetic studies. Paternity testing is based on the premise that we inherit half our DNA from our father and half from our mother. Therefore, persons who are biologically related must share similar DNA profile. Conversely, the absence of similarities in the DNA profiles of the child and the alleged father is used as proof that no biological relationship exists. In this paper, a female complained for being raped a year back by Mr. X and accused him of being father of her 3-months-old baby girl. DNA testing was done using saliva for the child and blood sample from the mother and the suspected father. The finding presented here allows the use of saliva as an alternative source of blood.

Association of endothelial nitric oxide synthase gene polymorphisms with coronary artery disease: an updated meta-analysis and systematic review.

Several association studies of endothelial nitric oxide synthase (NOS3) gene polymorphisms with respect to coronary artery disease (CAD) have been published in the past two decades. However, their association with the disease, especially among different ethnic subgroups, still remains controversial. This prompted us to conduct a systematic review and an updated structured meta-analysis, which is the largest so far (89 articles, 132 separate studies, and a sample size of 69,235), examining association of three polymorphic forms of the NOS3 gene (i.e. Glu298Asp, T786-C and 27 bp VNTR b/a) with CAD. In a subgroup analysis, we tested their association separately among published studies originating predominantly from European, Middle Eastern, Asian, Asian-Indian and African ancestries. The pooled analysis confirmed the association of all the three selected SNP with CAD in three different genetic models transcending all ancestries worldwide. The Glu298Asp polymorphism showed strongest association (OR range = 1.28-1.52, and P<0.00001 for all comparisons), followed by T786-C (OR range = 1.34-1.42, and P<0.00001 for all comparisons) and 4b/a, (OR range = 1.19-1.41, and P ≤ 0.002 for all comparisons) in our pooled analysis. Subgroup analysis revealed that Glu298Asp (OR range = 1.54-1.87, and P<0.004 for all comparisons) and 4b/a (OR range = 1.71-3.02, and P<0.00001 for all comparisons) have highest degree of association amongst the Middle Easterners. On the other hand, T786-C and its minor allele seem to carry a highest risk for CAD among subjects of Asian ancestry (OR range = 1.61-1.90, and P ≤ 0.01 for all comparisons).

Study of Polymorphisms in CX3CR1, PLEKHA1 and VEGF genes as risk factors for age-related macular degeneration in Indian patients.

BACKGROUND AND AIMS: Age-related macular degeneration (AMD) is an important cause of visual impairment in elderly persons. AMD is a multifactorial disease in which both environmental and genetic factors have been implicated. Various single nucleotide polymorphisms (SNPs) have been found to be associated with AMD. This study aimed to investigate the association of polymorphisms in CX3CR1, PLEKHA1 and VEGF genes with AMD in Indian patients. METHODS: Genotyping for the CX3CR1 T280M (C>T) and V249I (G>A), PLEKHA1 A320T (G>A) &VEGF +674 (C>T) and +936 (C>T) was performed in 121 AMD patients and 100 controls by polymerase chain reaction, restriction fragment length polymorphism (PCR-RFLP) and sequencing method. RESULTS: The genotype analysis of VEGF gene polymorphisms (+674 and +936) showed a significant association with AMD. Odds ratios for VEGF (+674) and VEGF (+936) were 2.37 and 2.50 with a p value 0.0029 and 0.0358 for the autosomal dominant model. CX3CR1 (T280M and V249I) and PLEKHA1 (A320T) polymorphisms were not found to be associated with AMD. Odds ratios for mutant alleles of T280M and V249I polymorphisms in CX3CR1 gene were 0.95 and 0.83, respectively, compared to the wild-type alleles. Odds ratio for the polymorphism in the PLEKHA1 gene was 0.63. CONCLUSIONS: The present study suggests that both polymorphisms in VEGF gene are risk factors for AMD in the Indian population. Detection of individuals at risk could lead to strategies for prevention, early diagnosis and management of AMD.

Platelet-specific collagen receptor glycoprotein VI gene variants affect recurrent pregnancy loss.

OBJECTIVE: To determine whether platelet-specific collagen receptor glycoprotein VI (GP6) gene variants are associated with recurrent miscarriages (RM). DESIGN: Genetic association study. SETTING: Tertiary care referral hospital. PATIENT(S): A total of 200 women with at least three unexplained spontaneous abortions before 20 weeks of gestation and 300 healthy parous women. INTERVENTION(S): Determination of variants of GP6 single-nucleotide polymorphisms (SNPs) namely; rs1671153, rs1654410, rs1654419, and rs1613662 was based on polymerase chain reaction-restriction fragment-length polymorphism. MAIN OUTCOME MEASURE(S): Genotypes and haplotypes frequencies were compared in RM case subjects versus control subjects. RESULT(S): We observed significantly higher occurrence of rare alleles of SNPs in GP6, namely, rs1671153, rs1654410, rs1654419, and rs1613662, among RM cases, revealing risk association for fetal losses. The synergistic effects of haplotype combinations were also evaluated and showed that four haplotypes G-T-G-G, T-C-A-A, G-C-G-A, and G-T-A-A were more prevalent among RM cases, revealing increased risk for fetal losses. In silico analysis revealed that GP6 has an impact on biologic pathways and significant influence in collagen binding. Gene-gene interaction network analysis revealed that GP6 consisted of a total of 25 interactions with 13 genes in the human genome. CONCLUSION(S): These results suggest that variants of GP6 SNPs, namely, rs1671153, rs1654410, rs1654419, and rs1613662, may be associated with risk of recurrent miscarriage. In silico analyses demonstrated the influence of GP6 in biologic pathways, molecular function, including collagen binding, and gene-gene interaction in the human genome.

A study of forty-seven single nucleotide polymorphisms among recurrent miscarriage using classification and regression tree analysis.

PROBLEM: Successful pregnancy is the result of multiple genetic and non-genetic factors. Associations of various SNPs described in this study have not revealed any conclusive results. We have analyzed 47 SNPs using statistical tools like multidimensional regression, classification regression tree, and logistic regression. METHOD OF STUDY: Two hundred women with at least three consecutive unexplained spontaneous abortions before 20th week of gestation and 300 control women without any history of recurrent miscarriages (RM) were genotyped using PCR, RFLP and sequencing. RESULTS: Our results revealed that Leptin 2549 C/A (rs7799039) and TNF-α 238 (rs361525) may play an important role in the maintenance of pregnancy. TNF-α 238 may act as a protective SNP and Leptin 2549 C/A as a susceptible marker among women with RM cases. CONCLUSIONS: Present study demonstrated an association with Leptin 2549C/A (rs7799039) and TNF-α (rs361525) gene polymorphism among RM cases.

Cytokine gene polymorphisms in northern Indian women with recurrent miscarriages.

OBJECTIVE: To determine association of cytokine gene polymorphism with risk for recurrent miscarriages (RM). DESIGN: Retrospective case-control study on northern Indian RM cases versus control subjects. SETTING: Medical facility. PATIENT(S): A total of 200 women with at least three unexplained spontaneous abortions before 20 weeks of gestation. INTERVENTION(S): Subjects were genotyped by polymerase chain reaction amplification followed by restriction digestion and allele-specific oligonucleotides. MAIN OUTCOME MEASURE(S): Detection of pro- and antiinflammatory gene polymorphism genotypes and allele frequencies. RESULT(S): We applied dominant and recessive models of inheritance, showing no association among T(H)2 [interleukin (IL) 10 (592 C/A) and transforming growth factor ß] gene polymorphisms, while significant association was observed between T(H)2 [IL-4 (C590T), IL-6 (G174C), IL-10 (1082A/G and 819C/T)], and T(H)1 [interferon-γ (+874A/T)] with RM compared with control subjects. However, when classification and regression tree analysis was applied, this effect disappeared and demonstrated that IL-10 plays an important role in maintenance of pregnancy. CONCLUSION(S): Interleukin-10 acts as an immunosuppressive by keeping a balance of pro- and antiinflammatory signals that coordinate the satisfactory development of pregnancy, placental growth, and remodeling for favorable pregnancy outcome.

Recurrent pregnancy loss and apolipoprotein E gene polymorphisms: a case­control study from north India.

PROBLEM: the role of apolipoprotein E gene polymorphisms in the etiology of recurrent pregnancy loss (RPL) is not clearly understood. We evaluated this polymorphism in unexplained pregnancy losses among North Indian women. METHOD OF STUDY: in a retrospective case­control study, 200 well-characterized RPL cases were examined for their APO-E genotypes based on restriction fragment length polymorphism analysis of PCR-amplified fragments including amino acid positions 112 and 158. The observed genotypes were compared with those obtained from an equal number of ethnically matched negative controls. RESULTS: we found similar APO-E genotypes and E2, E3, and E4 allele frequency distribution among RPL patients and controls. The allele frequencies obtained in patients and controls respectively were as follows:E2 = 7.5% and 9.0% (P = 0.52; OR = 0.81; 95%CI = 0.49­1.35),E3 = 89.7% and 90% (P = 1.00; OR = 0.97; 95%CI = 0.61­1.54), and E4 = 2.8% and 1% (P = 0.12; OR = 2.79; 95%CI = 0.88­8.86). CONCLUSIONS: our data did not support the association of APO-E gene polymorphisms with recurrent pregnancy loss as reported by some of the previous studies.We endorse adequate characterization of RPL cases, inclusion of appropriate negative controls, and adequate sample size prior to addressing such studies.