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1.  MBL2 Variations and Malaria Susceptibility in Indian Populations 
Infection and Immunity  2014;82(1):52-61.
Human mannose-binding lectin (MBL) encoded by the MBL2 gene is a pattern recognition protein and has been associated with many infectious diseases, including malaria. We sought to investigate the contribution of functional MBL2 gene variations to Plasmodium falciparum malaria in well-defined cases and in matched controls. We resequenced the 8.7 kb of the entire MBL2 gene in 434 individuals clinically classified with malaria from regions of India where malaria is endemic. The study cohort included 176 patients with severe malaria, 101 patients with mild malaria, and 157 ethnically matched asymptomatic individuals. In addition, 830 individuals from 32 socially, linguistically, and geographically diverse endogamous populations of India were investigated for the distribution of functional MBL2 variants. The MBL2 −221C (X) allelic variant is associated with increased risk of malaria (mild malaria odds ratio [OR] = 1.9, corrected P value [PCorr] = 0.0036; severe malaria OR = 1.6, PCorr = 0.02). The exon1 variants MBL2*B (severe malaria OR = 2.1, PCorr = 0.036; mild versus severe malaria OR = 2.5, PCorr = 0.039) and MBL2*C (mild versus severe malaria OR = 5.4, PCorr = 0.045) increased the odds of having malaria. The exon1 MBL2*D/*B/*C variant increased the risk for severe malaria (OR = 3.4, PCorr = 0.000045). The frequencies of low MBL haplotypes were significantly higher in severe malaria (14.2%) compared to mild malaria (7.9%) and asymptomatic (3.8%). The MBL2*LYPA haplotypes confer protection, whereas MBL2*LXPA increases the malaria risk. Our findings in Indian populations demonstrate that MBL2 functional variants are strongly associated with malaria and infection severity.
doi:10.1128/IAI.01041-13
PMCID: PMC3911836  PMID: 24126531
2.  Investigation of Host Candidate Malaria-Associated Risk/Protective SNPs in a Brazilian Amazonian Population 
PLoS ONE  2012;7(5):e36692.
The Brazilian Amazon is a hypo-endemic malaria region with nearly 300,000 cases each year. A variety of genetic polymorphisms, particularly in erythrocyte receptors and immune response related genes, have been described to be associated with susceptibility and resistance to malaria. In order to identify polymorphisms that might be associated with malaria clinical outcomes in a Brazilian Amazonian population, sixty-four human single nucleotide polymorphisms in 37 genes were analyzed using a Sequenom massARRAY iPLEX platform. A total of 648 individuals from two malaria endemic areas were studied, including 535 malaria cases (113 individuals with clinical mild malaria, 122 individuals with asymptomatic infection and 300 individuals with history of previous mild malaria) and 113 health controls with no history of malaria. The data revealed significant associations (p<0.003) between one SNP in the IL10 gene (rs1800896) and one SNP in the TLR4 gene (rs4986790) with reduced risk for clinical malaria, one SNP in the IRF1 gene (rs2706384) with increased risk for clinical malaria, one SNP in the LTA gene (rs909253) with protection from clinical malaria and one SNP in the TNF gene (RS1800750) associated with susceptibility to clinical malaria. Also, a new association was found between a SNP in the CTL4 gene (rs2242665), located at the major histocompatibility complex III region, and reduced risk for clinical malaria. This study represents the first association study from an Amazonian population involving a large number of host genetic polymorphisms with susceptibility or resistance to Plasmodium infection and malaria outcomes. Further studies should include a larger number of individuals, refined parameters and a fine-scale map obtained through DNA sequencing to increase the knowledge of the Amazonian population genetic diversity.
doi:10.1371/journal.pone.0036692
PMCID: PMC3353949  PMID: 22615793
3.  A globally occurring indel polymorphism in the promoter of the IFNA2 gene is not associated with severity of malaria but with the positivity rate of HCV 
BMC Genetics  2008;9:80.
Background
Type I Interferons (IFNs) are well known cytokines which exert antiviral activity, antitumor activity and immunomodulatory effects. Single-nucleotide polymorphisms (SNP) and deletions in the gene coding for IFNA2 have been shown to influence the level of expression in vitro. The indel polymorphism -305_-300delAACTTT showed the strongest effect in vitro. To analyse the worldwide distribution of this polymorphism we analyzed five different populations (586 Vietnamese, 199 Central Africans, 265 Brazilians, 108 Kaingang and 98 Guarani). To investigate a possible association with susceptibility to infectious diseases we determined the polymorphism in malaria patients suffering either mild or severe malaria and in a cohort of hepatitis C virus infected individuals.
Results
We could detect the indel polymorphism in all populations analysed. There was no association with this polymorphism and the outcome of malaria but we found an increase of this indel polymorphism in hepatitis C virus positive individuals compared to healthy controls (p = 0.014).
Conclusion
Polymorphisms in genes involved in the interferon pathway have been implicated in the resistance or susceptibility against cerebral malaria and HBV. Here we show that an indel polymorphism, which mediates a disadvantageous effect in HBV patients, may also play a disadvantageous role in HCV infections stressing the importance of a fully functional interferon pathway.
doi:10.1186/1471-2156-9-80
PMCID: PMC2612697  PMID: 19055755
4.  Population Structure of Aggarwals of North India as Revealed by Molecular Markers 
Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.
doi:10.1089/gtmb.2010.0095
PMCID: PMC3490109  PMID: 20979565
5.  Tracking the genetic imprints of lost Jewish tribes among the gene pool of Kuki-Chin-Mizo population of India 
Genome Biology  2004;6(1):P1.
DNA markers from the Kuki-Chin-Mizo population of Mizoram, India, who claim their descent from the ten lost tribes of Israel that were exiled by the Assyrians, show no evidence of Cohanim origin but some genetic relatedness to Near Eastern lineages.
Background
The Kuki-Chin-Mizo population comprising traditionally endogamous tribal groups residing in the state of Mizoram, India claim their descent from the ten lost tribes of Israel that were exiled by the Assyrians. To ascertain their oral history, we analysed DNA markers comprising 15 autosomal microsatellite markers, 5 biallelic and 20 microsatellite markers on Y-chromosome and the maternally inherited mitochondrial DNA sequence variations on 414 individuals belonging to 5 tribal communities from Mizoram (Hmar, Kuki, Mara, Lai and Lusei). The genetic profiles obtained were compared either with populations sharing Jewish ancestry or with local populations along the probable route of migration of the Jewish ancestry claimant Mizoram tribes.
Results
Y-STR analyses showed absence of the Cohen Modal Haplotype, the genetic signature of Cohanim origin. Y-chromosomal biallelic marker analyses revealed the presence of East and Southeast Asian-specific lineages and absence of haplogroup J predominant among Jewish populations. The mitochondrial DNA sequence analyses however revealed traces of genetic relatedness between the Jewish ancestry claimant Mizoram tribes and Near Eastern lineages. Autosomal analyses showed moderate degree of genetic differentiation among the different Mizoram tribes.
Conclusions
Migration of the lost tribes through China resulting in subsequent genetic admixture over a long period of time has probably diluted the extant gene pool of the Kuki-Chin-Mizo population. Although their paternal lineages do not exhibit any trace of Jewish ancestry, incidence of maternal Near Eastern lineages among the Mizoram tribals suggests their claim to Jewish ancestry cannot be excluded.
doi:10.1186/gb-2004-6-1-p1
PMCID: PMC4071260
6.  IL4 gene polymorphism and previous malaria experiences manipulate anti-Plasmodium falciparum antibody isotype profiles in complicated and uncomplicated malaria 
Malaria Journal  2009;8:286.
Background
The IL4-590 gene polymorphism has been shown to be associated with elevated levels of anti-Plasmodium falciparum IgG antibodies and parasite intensity in the malaria protected Fulani of West Africa. This study aimed to investigate the possible impact of IL4-590C/T polymorphism on anti-P. falciparum IgG subclasses and IgE antibodies levels and the alteration of malaria severity in complicated and uncomplicated malaria patients with or without previous malaria experiences.
Methods
Anti-P.falciparum IgG subclasses and IgE antibodies in plasma of complicated and uncomplicated malaria patients with or without previous malaria experiences were analysed using ELISA. IL4-590 polymorphisms were genotyped using RFLP-PCR. Statistical analyses of the IgG subclass levels were done by Oneway ANOVA. Genotype differences were tested by Chi-squared test.
Results
The IL4-590T allele was significantly associated with anti-P. falciparum IgG3 antibody levels in patients with complicated (P = 0.031), but not with uncomplicated malaria (P = 0.622). Complicated malaria patients with previous malaria experiences carrying IL4-590TT genotype had significantly lower levels of anti-P. falciparum IgG3 (P = 0.0156), while uncomplicated malaria patients with previous malaria experiences carrying the same genotype had significantly higher levels (P = 0.0206) compared to their IL4-590 counterparts. The different anti-P. falciparum IgG1 and IgG3 levels among IL4 genotypes were observed. Complicated malaria patients with previous malaria experiences tended to have lower IgG3 levels in individuals carrying TT when compared to CT genotypes (P = 0.075). In contrast, complicated malaria patients without previous malaria experiences carrying CC genotype had significantly higher anti-P. falciparum IgG1 than those carrying either CT or TT genotypes (P = 0.004, P = 0.002, respectively).
Conclusion
The results suggest that IL4-590C or T alleles participated differently in the regulation of anti-malarial antibody isotype profiles in primary and secondary malaria infection and, therefore, could play an important role in alteration of malaria severity.
doi:10.1186/1475-2875-8-286
PMCID: PMC2799430  PMID: 20003246
7.  Group I introns and associated homing endonuclease genes reveals a clinal structure for Porphyra spiralis var. amplifolia (Bangiales, Rhodophyta) along the Eastern coast of South America 
Background
Group I introns are found in the nuclear small subunit ribosomal RNA gene (SSU rDNA) of some species of the genus Porphyra (Bangiales, Rhodophyta). Size polymorphisms in group I introns has been interpreted as the result of the degeneration of homing endonuclease genes (HEG) inserted in peripheral loops of intron paired elements. In this study, intron size polymorphisms were characterized for different Porphyra spiralis var. amplifolia (PSA) populations on the Southern Brazilian coast, and were used to infer genetic relationships and genetic structure of these PSA populations, in addition to cox2-3 and rbcL-S regions. Introns of different sizes were tested qualitatively for in vitro self-splicing.
Results
Five intron size polymorphisms within 17 haplotypes were obtained from 80 individuals representing eight localities along the distribution of PSA in the Eastern coast of South America. In order to infer genetic structure and genetic relationships of PSA, these polymorphisms and haplotypes were used as markers for pairwise Fst analyses, Mantel's test and median joining network. The five cox2-3 haplotypes and the unique rbcL-S haplotype were used as markers for summary statistics, neutrality tests Tajima's D and Fu's Fs and for median joining network analyses. An event of demographic expansion from a population with low effective number, followed by a pattern of isolation by distance was obtained for PSA populations with the three analyses. In vitro experiments have shown that introns of different lengths were able to self-splice from pre-RNA transcripts.
Conclusion
The findings indicated that degenerated HEGs are reminiscent of the presence of a full-length and functional HEG, once fixed for PSA populations. The cline of HEG degeneration determined the pattern of isolation by distance. Analyses with the other markers indicated an event of demographic expansion from a population with low effective number. The different degrees of degeneration of the HEG do not refrain intron self-splicing. To our knowledge, this was the first study to address intraspecific evolutionary history of a nuclear group I intron; to use nuclear, mitochondrial and chloroplast DNA for population level analyses of Porphyra; and intron size polymorphism as a marker for population genetics.
doi:10.1186/1471-2148-8-308
PMCID: PMC2585584  PMID: 18992156
8.  Fighting malaria in Madhya Pradesh (Central India): Are we loosing the battle? 
Malaria Journal  2009;8:93.
Malaria control in Madhya Pradesh is complex because of vast tracts of forest with tribal settlement. Fifty four million individuals of various ethnic origins, accounting for 8% of the total population of India, contributed 30% of total malaria cases, 60% of total falciparum cases and 50% of malaria deaths in the country. Ambitious goals to control tribal malaria by launching "Enhanced Malaria Control Project" (EMCP) by the National Vector Borne Disease Control Programme (NVBDCP), with the World Bank assistance, became effective in September 1997 in eight north Indian states. Under EMCP, the programme used a broader mix of new interventions, i.e. insecticide-treated bed nets, spraying houses with effective residual insecticides, use of larvivorous fishes, rapid diagnostic tests for prompt diagnosis, treatment of the sick with effective radical treatment and increased public awareness and IEC. However, the challenge is to scale up these services.
A retrospective analysis of data on malaria morbidity and associated mortality reported under the existing surveillance system of the Madhya Pradesh (Central India) for the years 1996–2007 was carried out to determine the impact of EMCP on malaria morbidity and associated mortality. Analysis revealed that despite the availability of effective intervention tools for the prevention and control of malaria, falciparum malaria remains uncontrolled and deaths due to malaria have increased. Precisely, the aim of this epidemiological analysis is to draw lessons applicable to all international aid efforts, bureaucracy, policy makers and programme managers in assessing its project performance as a new Global Malaria Action Plan is launched with ambitious goal of reducing malaria and its elimination by scaling up the use of existing tools.
doi:10.1186/1475-2875-8-93
PMCID: PMC2687456  PMID: 19419588
9.  Association of endothelial nitric oxide synthase gene polymorphisms with endometrial carcinoma: a preliminary study 
Objective
To investigate the relationship between specific endothelial nitric oxide synthase (eNOS) gene polymorphisms and endometrial cancer (ECa).
Material and Methods
The study group consisted of 89 patients histologically diagnosed with the endometrioid type of endometrial carcinoma. The control group consisted of 60 randomly selected individuals who had undergone total hysterectomy. Genomic DNA was isolated from paraffin-embedded endometrial tissues. We investigated the G894T polymorphisms (G894T) and variable number tandem repeats polymorphisms in intron 4 (VNTR intron 4) in the eNOS gene by using polymerase chain reaction (PCR) and/or restriction fragment length polymorphism (RFLP). The genotype distributions and allele frequencies of the two groups were compared.
Results
Analysis of the VNTR intron 4 polymorphisms in eNOS gene revealed that the frequency of the AA genotype was significantly higher in the control group, whereas the frequency of the BB genotype was significantly higher in the ECa group. Analysis of the G894T polymorphisms in eNOS gene revealed a significantly higher frequency of the GG genotype in the control group but a significantly higher frequency of the TT genotype in the endometrial cancer group.
Conclusion
The G894T and VNTR intron 4 polymorphisms in eNOS gene could be an intriguing susceptibility factor that modulates an individual’s risk of ECa in the Turkish population.
doi:10.5152/jtgga.2011.47
PMCID: PMC3939255  PMID: 24592000
eNOS gene polymorphisms; endometrial carcinoma
10.  Haplotype diversity and linkage disequilibrium at the DRD2 locus among the tribes of western and southern regions of India 
BACKGROUND:
Dopamine receptor D2 (DRD2) is an important gene having functional significance in the fields of neuropsychiatry and pharmacology and also has importance in evolutionary studies.
MATERIALS AND METHODS:
This study was undertaken to find out the haplotype distribution and linkage disequilibrium (LD) pattern for the three TaqI sites (TaqI ‘A’, TaqI ‘B’ and TaqI ‘D’) in the DRD2 gene in 232 unrelated individuals from five ethno-linguistically distinct endogamous tribal populations; Siddis and Gonds of Uttara Kannada district, Karnataka; Varli and Kolgha of Valsad district, Gujarat; and Dangi Konkana of Dang district, Gujarat. The genotype data obtained after molecular analysis of the three DRD2 sites was subjected to statistical analysis such as calculation of allele frequencies, haplotype frequencies among others. Subsequently, a neighbor-joining tree was also constructed from the data obtained.
RESULTS:
The three DRD2 sites were found to be polymorphic in all the populations. All the populations showed high levels of heterozygosities. Out of the eight possible haplotypes, most populations shared seven haplotypes. Of all the populations, Siddis showed the highest frequency of the ancestral haplotype B2D2A1 (11.4%). Significant LD was found to exist for TaqI ‘A’ and TaqI ‘B’ sites in both the populations.
CONCLUSION:
The findings are in concurrence with those from other Indian studies, especially from Dravidian-speaking South Indian populations. Similar pattern of diversity observed for ethnically and linguistically diverse populations in the present study is indicative of complex structure of Indian populations.
doi:10.4103/0971-6866.69327
PMCID: PMC2955952  PMID: 21031052
Ancestral haplotype; ethno-linguistic diversity; haplotype analysis; linkage disequilibrium; population structure
11.  Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups 
BMC Genetics  2004;5:23.
Background
A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations.
Results
Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe.
Conclusion
The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them from the northern groups. Our study also indicates a heterogeneous origin for Lyngayat and Iyengar owing to their genetic proximity with southern populations and northern Brahmins. The high-ranking communities, in particular, Iyengar, Lyngayat, Vanniyar and northern Brahmins might have experienced genetic admixture from East Asian and European ethnic groups.
doi:10.1186/1471-2156-5-23
PMCID: PMC515297  PMID: 15317657
12.  Combinatorial interaction between two human serotonin transporter gene variable number tandem repeats and their regulation by CTCF 
Journal of Neurochemistry  2010;112(1):296-306.
Two distinct variable number tandem repeats (VNTRs) within the human serotonin transporter gene (SLC6A4) have been implicated as predisposing factors for CNS disorders. The linked polymorphic region in the 5′-promoter exists as short (s) and long (l) alleles of a 22 or 23 bp elements. The second within intron 2 (Stin2) exists as three variants containing 9, 10 or 12 copies of a 16 or 17 bp element. These VNTRs, individually or in combination, supported differential reporter gene expression in rat neonate prefrontal cortical cultures. The level of reporter gene activity from the dual VNTR constructs indicated combinatorial action between the two domains. Chromatin immunoprecipitation demonstrated that both these VNTR domains can bind the CCCTC-binding factor and this correlated with the ability of exogenously supplied CCCTC-binding factor to modulate the expression supported by these reporter gene constructs. We suggest that the potential for interaction between multiple polymorphic domains should be incorporated into genetic association studies.
J. Neurochem. (2010) 112, 296–306.
doi:10.1111/j.1471-4159.2009.06453.x
PMCID: PMC2848977  PMID: 19860858
behaviour; CCCTC-binding factor; human serotonin transporter; polymorphism; variable number tandem repeat
13.  Barriers to Malaria Control among Marginalized Tribal Communities: A Qualitative Study 
PLoS ONE  2013;8(12):e81966.
Background
Malaria infection accounts for over one million deaths worldwide annually. India has the highest number of malaria deaths outside Africa, with half among Indian tribal communities. Our study sought to identify barriers to malaria control within tribal populations in malaria-endemic Gadchiroli district, Maharashtra.
Methods and Findings
This qualitative study was conducted via focus groups and interviews with 84 participants, and included tribal villagers, traditional healers, community health workers (CHWs), medical officers, and district officials. Questions assessed knowledge about malaria, behavior during early stages of infection, and experiences with prevention among tribal villagers and traditional healers. CHWs, medical officers, and district officials were asked about barriers to treating and preventing malaria among tribal populations. Data were inductively analyzed and assembled into broader explanation linking barriers to geographical, cultural and social factors. Findings indicate lack of knowledge regarding malaria symptoms and transmission. Fever cases initially present to traditional healers or informal providers who have little knowledge of malaria or high-risk groups such as children and pregnant women. Tribal adherence with antimalarial medications is poor. Malaria prevention is inadequate, with low-density and inconsistent use of insecticide-treated nets (ITNs). Malaria educational materials are culturally inappropriate, relying on dominant language literacy. Remote villages and lack of transport complicate surveillance by CHWs. Costs of treating malaria outside the village are high.
Conclusions
Geographic, cultural, and social factors create barriers to malaria control among tribal communities in India. Efforts to decrease malaria burden among these populations must consider such realities. Our results suggest improving community-level knowledge about malaria using culturally-appropriate health education materials; making traditional healers partners in malaria control; promoting within-village rapid diagnosis and treatment; increasing ITN distribution and promoting their use as potential strategies to decrease infection rates in these communities. These insights may be used to shape malaria control programs among marginalized populations.
doi:10.1371/journal.pone.0081966
PMCID: PMC3869659  PMID: 24376507
14.  Genetic structure of Indian populations based on fifteen autosomal microsatellite loci 
BMC Genetics  2006;7:28.
Background
Indian populations endowed with unparalleled genetic complexity have received a great deal of attention from scientists world over. However, the fundamental question over their ancestry, whether they are all genetically similar or do exhibit differences attributable to ethnicity, language, geography or socio-cultural affiliation is still unresolved. In order to decipher their underlying genetic structure, we undertook a study on 3522 individuals belonging to 54 endogamous Indian populations representing all major ethnic, linguistic and geographic groups and assessed the genetic variation using autosomal microsatellite markers.
Results
The distribution of the most frequent allele was uniform across populations, revealing an underlying genetic similarity. Patterns of allele distribution suggestive of ethnic or geographic propinquity were discernible only in a few of the populations and was not applicable to the entire dataset while a number of the populations exhibited distinct identities evident from the occurrence of unique alleles in them. Genetic substructuring was detected among populations originating from northeastern and southern India reflective of their migrational histories and genetic isolation respectively.
Conclusion
Our analyses based on autosomal microsatellite markers detected no evidence of general clustering of population groups based on ethnic, linguistic, geographic or socio-cultural affiliations. The existence of substructuring in populations from northeastern and southern India has notable implications for population genetic studies and forensic databases where broad grouping of populations based on such affiliations are frequently employed.
doi:10.1186/1471-2156-7-28
PMCID: PMC1513393  PMID: 16707019
15.  Effects of methamphetamine abuse and serotonin transporter gene variants on aggression and emotion-processing neurocircuitry 
Translational Psychiatry  2012;2(2):e80-.
Individuals who abuse methamphetamine (MA) exhibit heightened aggression, but the neurobiological underpinnings are poorly understood. As variability in the serotonin transporter (SERT) gene can influence aggression, this study assessed possible contributions of this gene to MA-related aggression. In all, 53 MA-dependent and 47 control participants provided self-reports of aggression, and underwent functional magnetic resonance imaging while viewing pictures of faces. Participants were genotyped at two functional polymorphic loci in the SERT gene: the SERT-linked polymorphic region (SERT-LPR) and the intron 2 variable number tandem repeat polymorphism (STin2 VNTR); participants were then classified as having high or low risk for aggression according to individual SERT risk allele combinations. Comparison of SERT risk allele loads between groups showed no difference between MA-dependent and control participants. Comparison of self-report scores showed greater aggression in MA-dependent than control participants, and in high genetic risk than low-risk participants. Signal change in the amygdala was lower in high genetic risk than low-risk participants, but showed no main effect of MA abuse; however, signal change correlated negatively with MA use measures. Whole-brain differences in activation were observed between MA-dependent and control groups in the occipital and prefrontal cortex, and between genetic high- and low-risk groups in the occipital, fusiform, supramarginal and prefrontal cortex, with effects overlapping in a small region in the right ventrolateral prefrontal cortex. The findings suggest that the investigated SERT risk allele loads are comparable between MA-dependent and healthy individuals, and that MA and genetic risk influence aggression independently, with minimal overlap in associated neural substrates.
doi:10.1038/tp.2011.73
PMCID: PMC3309557  PMID: 22832817
aggression; amygdala; methamphetamine; prefrontal cortex; SERT-LPR; STin2 VNTR
16.  DNA Methyltransferase 3B Gene Promoter and Interleukin-1 Receptor Antagonist Polymorphisms in Childhood Immune Thrombocytopenia 
Primary immune thrombocytopenia (ITP) is one of the most common blood diseases as well as the commonest acquired bleeding disorder in childhood. Although the etiology of ITP is unclear, in the pathogenesis of the disease, both environmental and genetic factors including polymorphisms of TNF-a, IL-10, and IL-4 genes have been suggested to be involved. In this study, we investigated the rs2424913 single-nucleotide polymorphism (SNP) (C46359T) in DNA methyltransferase 3B (DNMT3B) gene promoter and the VNTR polymorphism of IL-1 receptor antagonist (IL-1 Ra) intron-2 in 32 children (17 boys) with the diagnosis of ITP and 64 healthy individuals. No significant differences were found in the genotype distribution of DNMT3B polymorphism between the children with ITP and the control group, whereas the frequency of allele T appeared significantly increased in children with ITP (P = 0.03, OR = 2, 95% CI: 1.06–3.94). In case of IL-1 Ra polymorphism, children with ITP had a significantly higher frequency of genotype I/II, compared to control group (P = 0.043, OR = 2.60, 95% CI: 1.02–6.50). Moreover, genotype I/I as well as allele I was overrepresented in the control group, suggesting that allele I may have a decreased risk for development of ITP. Our findings suggest that rs2424913 DNMT3B SNP as well as IL-1 Ra VNTR polymorphism may contribute to the susceptibility to ITP.
doi:10.1155/2012/352059
PMCID: PMC3461273  PMID: 23049596
17.  Analysis of population genetic structure from Bucaramanga (Colombia) based on gene polymorphisms associated with the regulation of blood pressure  
Colombia Médica : CM  null;43(2):154-161.
Introduction:
In spite of nearly 40% of variability in blood pressure being explained by genetic factors, the identification of genes associated with essential high blood pressure is difficult to determine in populations where individuals have different genetic backgrounds. In these circumstances it is necessary to determinate whether the population is sub-structured because this can bias studies associated with this disease.
Objective:
To determine the genetic structure of the population in Bucaramanga from genetic polymorphisms associated with the regulation of blood pressure: 448G>T, 679C>T y 1711C>T from the gene kinase 4 of the dopaminergic receptor linked to the protein G and Glu298Asp, -786T>C and the VNTR of the intron 4 of the gene of endothelial nitric oxide.
Methods:
A sample of 552 unrelated individuals was studied through analysis of restriction fragment length polymorphism. The allelic, haplotypic and genotypic frequencies were calculated, the Hardy-Weinberg equilibrium was determined and a molecular analysis of variance was performed to determine the genetic structure.
Results:
Thirty-eight (38) Haplotypes were identified with GCCTG4b being the most frequent (21.2%). The most diverse polymorphism was 448G>T with a frequency of 49.9% for heterozygous. The six polymorphisms were found in genetic equilibrium and a genetic structure of populations was not evidenced (FST= 0.0038).
Conclusion:
The population studied does not present a genetic sub-structure and the polymorphisms analyzed were found in genetic equilibrium. This indicates that the population mixes randomly and there are no sub-groups capable of affecting the results of the association studies.
PMCID: PMC4001939  PMID: 24893057
Polymorphisms; blood pressure; haplotype GCCTG4b; GRK4 gene; eNOS gene
18.  Distribution of polymorphisms IL4-590 C/T and IL4 RP2 in the human populations of Madeira, Azores, Portugal, Cape Verde and Guinea-Bissau 
The IL4 gene is located on chromosome 5q23.3-31.2. Polymorphisms within this cytokine gene, like the derivative allele T of IL4-590, have been reported as being associated to elevated IgE serum levels and asthma. In the present work, the allelic and genotypic frequency of the IL4-590 and IL4 RP2 polymorphisms was carried out in 599 individuals from Madeira, Azores, Portugal mainland, Cape Verde and Guinea-Bissau and in a sample of 101 asthmatics from Madeira population. In all populations the polymorphisms were in LD and presented a significant dissimilar allelic and genotypic distribution (p<0.05) except between mainland Portugal and Madeira when compared to Azores. Significant differences regarding both loci were found between Madeira population and the group of asthmatics. Genotype 183183TT frequency is higher for African populations while 253253CC prevails in Caucasian populations. The existence of a Hardy-Weinberg Disequilibrium in Guinea-Bissau population not observed in neutral markers leads to the hypothesis of natural selection occurring in these loci probably associated to a rapid population growth an hypothesis strengthened by neutral STRs D5S818 and CSF1PO gene diversity.
PMCID: PMC3376918  PMID: 22724055
IL4-590; IL4 RP2; D5S818; CSF1PO; Asthma; Madeira; Azores; Portugal mainland; Cape Verde; Guinea-Bissau
19.  Study of interleukin-1 receptor antagonist (IL-1Ra) gene polymorphism in healthy individuals from Northern India 
Cytokines play a key role in immune responses and inflammation. IL-1Ra is a naturally occurring structural variant of IL-1 that competitively inhibits receptor binding of IL-1. We have investigated the polymorphism in intron-2 of the interleukin-1 receptor antagonist gene in North Indian population. This genetic variation has been of great interest due to its possible association with a variety of human diseases primarily of epithelial and endothelial cell origin such as urolithiasis etc. Allele frequencies of the IL-1Ra polymorphism vary among different populations but there is no data till date reported from India. The present study was carried out to determine the IL-1Ra gene Polymorphism in 165 normal unrelated individuals from North India. We obtained an allelic frequency of 63.94, 30.61, 4.55, 0.90 for A, B, C and D allele and percentage of genotypes AA, BB, CC, DD, A/B, A/C, A/D and B/C were 49.7, 18.2, 2.42, 0.60, 24.2, 3.63, 0.60, 0.60 respectively. Our results suggested that the frequency and distribution of this polymorphism in India is substantially different from other populations and ethnic groups.
doi:10.1007/BF02894269
PMCID: PMC3454213  PMID: 23105468
IL-1 Ra Polymorphism; VNTR; Single nucleotide polymorphisms (SNPs)
20.  The Impact of Artemisinin Combination Therapy and Long-Lasting Insecticidal Nets on Forest Malaria Incidence in Tribal Villages of India, 2006–2011 
PLoS ONE  2013;8(2):e56740.
Introduction
New tools for malaria control, artemisinin combination therapy (ACT) and long-lasting insecticidal nets (LLINs) were recently introduced across India. We estimated the impact of universal coverage of ACT and ACT plus LLINs in a setting of hyperendemic, forest malaria transmission.
Methods
We reviewed data collected through active and passive case detection in a vaccine trial cohort of 2,204 tribal people residing in Sundargarh district, Odisha between 2006 and 2011. We compared measures of transmission at the village and individual level in 2006–2009 versus 2010–2011 after ACT (in all villages) and LLINs (in three villages) were implemented.
Results
During 2006–2009 malaria incidence per village ranged from 156–512 per 1000 persons per year and slide prevalence ranged from 28–53%. Routine indoor residual spray did not prevent seasonal peaks of malaria. Post-intervention impact in 2010–2011 was dramatic with ranges of 14–71 per 1000 persons per year and 6–16% respectively. When adjusted for village, ACT alone decreased the incidence of malaria by 83% (IRR 0.17, 95%CI: 0.10, 0.27) and areas using ACT and LLINs decreased the incidence of malaria by 86% (IRR 0.14, 95%CI: 0.05, 0.38). After intervention, the age of malaria cases, their parasite density, and proportion with fever at the time of screening increased.
Conclusions
ACT, and LLINs along with ACT, effectively reduced malaria incidence in a closely monitored population living in a forest ecotype. It is unclear whether LLINs were impactful when prompt and quality antimalarial treatment was available. In spite of universal coverage, substantial malaria burden remained.
doi:10.1371/journal.pone.0056740
PMCID: PMC3577711  PMID: 23437229
21.  Interactions of miR-34b/c and TP53 Polymorphisms on the Risk of Intracranial Aneurysm 
Several lines of evidence indicate that inflammatory processes play a key role in the happening and development of intracranial aneurysm (IA). Recently, polymorphisms in the TP53 gene were shown to be associated with inflammation and inflammatory disease. The aim of this study was to investigate the interactions of miR-34b/c and TP53 Arg72-Pro polymorphisms on the risk of IA in a Chinese population. A total of 590 individuals (including 164 patients with IA and 426 controls) were involved in this study. The polymorphisms (i.e., miR-34b/c rs4938723 and TP53 Arg72-Pro) were genotyped by polymerase chain reaction-restriction fragment length polymorphism assay and DNA sequencing. We found that the CC genotype of miR-34b/c rs4938723 was significantly associated with a decreased risk of IA compared with the TT genotype. Moreover, a significant gene interaction of the carriers with the combined genotypes of miR-34b/c rs4938723CC and TP53 Arg72Pro CG/CC/GG had a decreased risk of IA, compared with those carrying miR-34b/c rs4938723CT/TT+TP53 Arg72Pro GG/CG/CC combined genotypes. These findings suggest that the miR-34b/c rs4938723CC and TP53 Arg72-Pro polymorphisms may be involved in the susceptibility to IA.
doi:10.1155/2012/567586
PMCID: PMC3403301  PMID: 22844323
22.  Repeat variation in the human PER2 gene as a new genetic marker associated with cocaine addiction and brain dopamine D2 receptor availability 
Translational Psychiatry  2012;2(3):e86-.
Low dopamine D2 receptor (D2R) levels in the striatum are consistently reported in cocaine abusers; inter-individual variations in the degree of the decrease suggest a modulating effect of genetic makeup on vulnerability to addiction. The PER2 (Period 2) gene belongs to the clock genes family of circadian regulators; circadian oscillations of PER2 expression in the striatum was modulated by dopamine through D2Rs. Aberrant periodicity of PER2 contributes to the incidence and severity of various brain disorders, including drug addiction. Here we report a newly identified variable number tandem repeat (VNTR) polymorphism in the human PER2 gene (VNTR in the third intron). We found significant differences in the VNTR alleles prevalence across ethnic groups so that the major allele (4 repeats (4R)) is over-represented in non-African population (4R homozygosity is 88%), but not in African Americans (homozygosity 51%). We also detected a biased PER2 genotype distribution among healthy controls and cocaine-addicted individuals. In African Americans, the proportion of 4R/three repeat (3R) carriers in healthy controls is much lower than that in cocaine abusers (23% vs 39%, P=0.004), whereas among non-Africans most 3R/4R heterozygotes are healthy controls (10.5% vs 2.5%, P=0.04). Analysis of striatal D2R availability measured with positron emission tomography and [11C]raclopride revealed higher levels of D2R in carriers of 4R/4R genotype (P<0.01). Taken together, these results provide preliminary evidence for the role of the PER2 gene in regulating striatal D2R availability in the human brain and in vulnerability for cocaine addiction.
doi:10.1038/tp.2012.11
PMCID: PMC3309530  PMID: 22832851
cocaine addiction; dopaminergic signaling; human brain; human brain imaging; Period 2 gene
23.  Association of ABO blood group with severe falciparum malaria in adults: case control study and meta-analysis 
Malaria Journal  2011;10:309.
Background
Erythrocyte-associated antigenic polymorphisms or their absence have perhaps evolved in the human population to protect against malarial infection. Studies in various populations consistently demonstrate that blood group 'O' confers resistance against severe falciparum infection. In India, Odisha state has one of the highest incidences of Plasmodium falciparum infection and contributes to the highest number of deaths by falciparum malaria. This study aims to evaluate the relationship between ABO blood group and severe malaria in an adult population at the tertiary care centre in Odisha.
Methods
A total of 353 P. falciparum infected subjects and 174 healthy controls were screened for ABO blood group. Falciparum-infected individuals were categorized as severe malaria and uncomplicated malaria. Severe malaria was further clinically phenotyped into cerebral malaria, non-cerebral severe malaria and multi-organ dysfunction. A meta-analysis was performed to assess the role of ABO blood group in severe malaria.
Results
Frequency of blood group 'B' was significantly higher in patients with severe malaria compared to the uncomplicated cases (P < 0.0001; OR = 4.09) and healthy controls (P < 0.0001; OR = 2.79). Irrespective of the level of clinical severity, blood group 'B' was significantly associated with cerebral malaria (P < 0.0001; OR = 5.95), multi-organ dysfunction (P < 0.0001; OR = 4.81) and non-cerebral severe malaria patients (P = 0.001; OR = 3.02) compared to the uncomplicated category. Prevalence of 'O' group in uncomplicated malaria (P < 0.0001; OR = 2.81) and healthy controls (P = 0.0003; OR = 2.16) was significantly high compared to severe malaria. Meta-analysis of previous studies, including the current one, highlighted the protective nature of blood group 'O' to severe malaria (P = 0.01). On the other hand, carriers of blood group 'A' (P = 0.04) and 'AB' (P = 0.04) were susceptible to malaria severity.
Conclusions
Results of the current study indicate that blood group 'O' is associated with reduced and 'B' blood group with increased risk of development of severe malaria in Odisha, India. Meta-analysis also supports the protective nature of blood group 'O' from severe falciparum infection.
doi:10.1186/1475-2875-10-309
PMCID: PMC3215225  PMID: 22011404
ABO blood group; severe malaria; cerebral malaria; multi-organ dysfunction; non-cerebral severe malaria; uncomplicated malaria; meta-analysis
24.  Community Based Assessment of Biochemical Risk Factors for Cardiovascular Diseases in Rural and Tribal Area of Himalayan Region, India 
Context. Evident change in nutrition and lifestyle among individuals of urban and rural areas raises suspicion for similar change in tribal area population of India. Aim. To study the biochemical risk factor for CVDs in rural and tribal population of Sub-Himalayan state of India. Settings and Design. Cross-sectional study in rural (low altitude) and tribal (high altitude) area of Himachal Pradesh, India. Methodology. Blood lipid profile using standard laboratory methods. Statistical Analysis. Chi-square test and multiple linear regression analysis. Results. Total of 900 individuals were studied in both areas. As per Asian criteria, obesity (BMI 27.5–30.0 kg/m2) was observed to be significantly high (P = 0.00) as 13.7% in tribal area as compared to 5.5% in rural area. Normal level of TC (<200 mg/dL) and LDL (<130 mg/dL) was observed in the majority of the population of both areas, whereas, at risk level of HDL (<40 mg/dL) was present in half of the population of both rural and tribal areas. The prevalence of borderline to high level of TGs was observed to be 60.2% and 55.2% in rural and tribal (P = 0.10) area, respectively. Conclusion. Prevalent abnormal lipid profile in tribal area demands establishment of an effective surveillance system for development of chronic diseases.
doi:10.1155/2013/696845
PMCID: PMC3881340  PMID: 24455263
25.  Associations of IL-4, IL-4R, and IL-13 Gene Polymorphisms in Coal Workers' Pneumoconiosis in China: A Case-Control Study 
PLoS ONE  2011;6(8):e22624.
Background
The IL-4, IL-4 receptor (IL4R), and IL-13 genes are crucial immune factors and may influence the course of various diseases. In the present study, we investigated the association between the potential functional polymorphisms in IL-4, IL-4R, and IL-13 and coal workers' pneumoconiosis (CWP) risk in a Chinese population.
Methods
Six polymorphisms (C-590T in IL-4, Ile50Val, Ser478Pro, and Gln551Arg in IL-4R, C-1055T and Arg130Gln in IL-13) were genotyped and analyzed in a case-control study of 556 CWP and 541 control subjects.
Results
Our results revealed that the IL-4 CT/CC genotypes were associated with a significantly decreased risk of CWP (odds ratio (OR) = 0.74, 95% confidence interval (CI) = 0.58–0.95), compared with the TT genotype, particularly among subgroups of age <65 years (OR = 0.68, 95%CI = 0.46–0.99) and dust exposure years ≥26 years (OR = 0.69, 95%CI = 0.50–0.94). Moreover, the polymorphism was significantly associated with risk of CWP patients with stage I. In addition, a combined effect was observed in a dose-dependent manner with increasing numbers of risk variant alleles (Ptrend = 0.023), and individuals with 11–12 risk alleles had a 47% higher risk of CWP than those with 0–8 risk alleles (OR = 1.47, 95% CI = 1.05–2.05).
Conclusions
Our results suggest that the IL-4 C-590T polymorphism is involved in the etiology of CWP and susceptibility to this disease. Larger studies are warranted to validate our findings.
doi:10.1371/journal.pone.0022624
PMCID: PMC3150141  PMID: 21857939

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