Genetic affinities of the central Indian tribal populations

Background

The central Indian state Madhya Pradesh is often called as ‘heart of India’ and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers.

Methodology/Principal Findings

Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results.

Conclusions/Significance

Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn''t unequivocally follow the genetic footprints.     

Analysis of methionine synthase reductase polymorphism (A66G) in Indian Muslim population

BACKGROUND AND OBJECTIVES:

Methionine synthase reductase (MTRR) is a vital enzyme of homocysteine/methionine metabolic pathway and is required for the conversion of inactive form of methionine synthase (MTR) to its active form. A clinically important allelic variant of MTRR A66G, with less enzymatic activity is reported with worldwide prevalence rate of ~ 30%. The present study was designed to determine the frequency of MTRR A66G polymorphism in rural Sunni Muslim population of Eastern Uttar Pradesh.

MATERIALS AND METHODS:

Total 56 subjects were analyzed for MTRR A66G polymorphism. A66G mutation analysis was carried out according to the polymerase chain reaction-restriction fragment length polymorphism method of Wilson et al. [1] amplification with MTRR specific primers followed by amplicon digestion with NdeI enzyme was used for the identification of different MTRR genotypes in subjects.

RESULTS AND DISCUSSION:

The AA genotype was found in 5 subjects, AG in 23 subjects, and GG genotype in 28 subjects. Genotype frequencies of AA, AG, and GG were 0.089, 0.41, and 0.5 respectively. The allele frequency of A allele was found to be 0.298 and G allele was 0.705.

CONCLUSION:

It is evident from the present study that the percentage of homozygous genotype GG and frequency of G allele is high in the target Muslim population.     

Prevalence of methylenetetrahydrofolate reductase C677T polymorphism in eastern Uttar Pradesh

AIM:

This study was aimed to evaluate the 5, 10-methylenetetrahydrofolate reductase (MTHFR) C677T mutation in eastern Uttar Pradesh population.

MATERIALS AND METHODS:

Polymerase chain reaction (PCR) using specific primers followed by amplicon digestion by Hinf I restriction enzyme was used for MTHFR C677T polymorphism analysis. Total 250 subjects were analyzed.

RESULTS:

The CC genotype was found in 192 subjects, followed by CT in 56 subjects and TT in 2 subject. Genotype frequencies of CC, CT and TT were 0.768, 0.224 and 0.008, respectively. The frequency of C allele was found to be 0.88 and that of T allele was 0.12.

CONCLUSION:

It is evident from the results of the present study that the percentage of homozygous genotype (CC) is highest in the target population.     

Measuring opportunity for natural selection: Adaptation among two linguistically cognate tribes inhabiting two eco-situations of North-East India

BACKGROUND:

Numerous literature on the migration of Mishings point out to the fact that the Mishing and the Minyong are two culturally and linguistically cognate tribes that co-existed in the same ecology in the hills of Arunachal Pradesh. The Mishing tribe after migration, now inhabits flood-prone areas of Brahmaputra valley of Assam.

AIM:

The study aims to measure the adaptation process of these two cognate tribes inhabiting two different ecologies at present: Hills and plains by calculating the index of selection intensity by Crow’s and Johnston and Kensinger’s formulae.

MATERIALS AND METHODS:

The reproductive histories of 77 Mishing mothers of completed fertility inhabiting a flood affected village of Assam and 74 Minyong mothers inhabiting a hilly village of Arunachal Pradesh are selected.

RESULTS AND DISCUSSION:

The Minyongs show higher average fertility than the Mishings. The proportion of embryonic death is higher, and child death is lower among the Mishings (0.1661; 0.1623) than the Minyongs (0.1319; 0.2238). The index of selection due to mortality component is contributing more toward the total index of selection in both the tribes.

CONCLUSION:

The contribution of mortality component is sizeable to the total selection like many other tribes of North-East India. Higher proportion of embryonic deaths among the Mishings infers that the causes are mostly biological whereas, the higher proportion of child deaths among the Minyongs infers that the causes are mostly socio-cultural.     

Recombination in human leukocyte antigen region in two Asian Indian families

BACKGROUND:

Recombination (crossing over) may generate novel haplotypes that can be beneficial to a population against recently introduced pathogens. It may lead to the generation of new alleles.

SETTINGS AND DESIGN:

A prospective study at a tertiary care centre.

AIM:

To report two rare cases of crossing over in HLA region.

MATERIALS AND METHODS:

Tissue-typing was done by sequence specific primers (SSP) for DR locus and by both SSP and serology for Class I which was reconfirmed on fresh samples.

RESULTS:

In one patient crossing over had taken place in the region of A locus resulting in inheritance of A*01 instead of expected A*11. In second family crossing over had taken place in region of DRB1 locus and the sibling inherited DRB1*08 instead of DRB1*10.

CONCLUSIONS:

Possibility of recombination must be considered when interpreting implausible tissue-typing results of families worked up for BMT.     

Distribution of CC-chemokine receptor-5-?32 allele among the tribal and caste population of Vidarbha region of Maharashtra state

BACKGROUND:

Genetic relationships among the ethnic groups are not uniform across the geographical region. Considering this assumption, we analyzed the frequency of the CC-chemokine receptor-5 (CCR5)-∆32 allele of the CCR5 chemokine receptor, which is considered a Caucasian marker, in Bhil tribal and Brahmin caste sample sets from the population.

MATERIALS AND METHODS:

108 blood samples were collected from 6 tribe''s populations and a caste population from the district of Vidarbha region.

RESULTS AND DISCUSSION:

The presence of low frequencies of CCR5-Δ32 in an individual of Bhil tribe (0.034, χ² value 0.017) in the present study implies that these communities may have a better resistance toward human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) than the other studied tribe sample, as non-show such mutation.

CONCLUSION:

The marginal presence of the allele seen in the studied tribal population could be due to gene flow from the people of European descent. However, lack of the homozygous CCR5-Δ32 mutation and the low prevalence of heterozygous CCR5-Δ32 mutations suggest that the Indians are highly susceptible to HIV/AIDS, and this correlates with the highest number of HIV/AIDS infected individuals in India.     

Genetic markers for idiopathic scoliosis on chromosome 19p 13.3 among Saudi Arabian girls: A pilot study

BACKGROUND AND OBJECTIVE:

Genetic locus linked to chromosome 19p for Adolescent idiopathic scoliosis (AIS) has been described. This study was carried out with the aim to find any significant linkage or association between three microsatellite markers (D19S216, D19S894, and DS1034) of chromosome 19p13.3 in Saudi Arabian girls with AIS.

MATERIALS AND METHODS:

In eleven unrelated Saudi Arabian girls who were treated for AIS with Cobb angle of ≥30 degrees and in 10 unrelated healthy individuals, linkage analysis was performed using parametric and nonparametric methods by use of GENEHUNTER version 2.1. Multipoint linkage analysis was used in specifying an autosomal dominant trait with a gene frequency of 0.01 and an estimated penetrance of 80% at the genotype and the allele level. Fisher''s exact test was used in the analysis of contingency tables for the D19S216, D19S894, and DS1034 markers.

RESULTS:

The analysis between the patient group and healthy girls showed that at genotypic level there was no significant association of the markers and scoliosis D19S216 (P = 0.21), D19S894 (P = 0.37), and DS1034 (P = 0.25). Whereas, at the allele level, there was statistically significant association between the marker DS1034 (P = 0.008) and no significant association with the other two markers D19S216 (P = 0.25) and D19S894 (P = 0.17).

CONCLUSIONS:

Our study shows that at genotypic level none of the markers reported earlier were associated with scoliosis but at allele level, marker DS1034 was significantly associated with patients with AIS. This allele marker on chromosome 19p appears important in the etiology of AIS.     

Identification of a rare blood group, "Bombay (Oh) phenotype," in Bhuyan tribe of Northwestern Orissa, India

BACKGROUND:

Blood group serology plays a vital role in transfusion medicine. The Bombay (Oh) phenotype is characterized by the absence of A, B, and H antigens on red cells and occurs rarely, especially in tribal populations of India.

AIMS AND OBJECTIVES:

This is a field-based random population study in the Bhuyan tribal community. The study reports three cases of the rare Bombay (Oh) phenotype for the first time in the Bhuyan tribe of Sundargarh district in North-Western Orissa.

MATERIALS AND METHODS:

Taking informed consent, red blood cells of 836 Bhuyan subjects were tested with three antisera, i.e., anti-A, anti-B, and anti-H (lectin) for forward reaction. Agglutinations of plasma with A, B, and O (H) red cells (reverse reaction) were also tested for the presence or absence of antibodies in the serum. Specialized tests like absorption-elution, titration of naturally occurring antibodies at different temperatures, inhibition of anti-H by O saliva secretor, and determination of secretor status were performed.

RESULTS:

Three cases of a rare blood group, Bombay (Oh) phenotype, (2 out of 244 Khandayat Bhuyan and 1 out of 379 Paudi Bhuyan from Hemgiri and Lahunipara blocks, respectively) in the Bhuyan tribe of Sundargarh district in North-Western Orissa were detected, giving an incidence of 1 in 122 in Khandayat Bhuyan and 1 in 379 in Paudi Bhuyan, with an average of 1 in 278 among the Bhuyan tribal population. This incidence is high in comparison to earlier studies reported from India.

CONCLUSIONS:

The practice of tribal and territorial endogamy in a smaller effective populations (for example, there are only 3,521 individuals in Paudi Bhuyan) results in smaller marital distance and inbreeding, leading to increased homozygous expression of rare recessive genetic characters like the Bombay (Oh) phenotype. This study further testifies that the incidence is higher in those states of India where the consanguinity is a common practice.     

Genetic diversity of 15 autosomal short tandem repeats loci using the AmpFLSTR? Identifiler? kit in a Bhil Tribe Population from Gujarat state,India

MATERIALS AND METHODS:

The genetic diversity and forensic parameters based on 15 autosomal short tandem repeats (STR) loci; D8S1179,D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317,D16S539, D2S1338, D19S433, vWA, TPOX, D18S51,D5S818, and FGA in AmpFLSTR® Identifiler™ kit from Applied Biosystems, Foster City, CA, USA were evaluated in saliva samples of 297 unrelated individuals from the Bhil Tribe population of Gujarat state, India to study genetic diversities and relatedness of this population with other national and international populations.

RESULTS:

Statistical analysis of the data revealed all loci were within Hardy-Weinberg Equilibrium expectations with the exception of the locus vWA (0.019) and locus D18S51 (0.016). The neighbour joining phylogeny tree and Principal Co-ordinate Analysis plot constructed based on Fst distances from autosomal STRs allele frequencies of the present study and other national as well as international populations show clustering of all the South Asian populations in one branch of the tree, while Middle Eastern and African populations cluster in a separate branch.

CONCLUSION:

Our findings reveal strong genetic affinities seen between the Indo-European (IE) speaking Bhil Tribe of Gujarat and Dravidian groups of South India.     

Inter and intra ethnic variation of vitamin K epoxide reductase complex and cytochrome P450 4F2 genetic polymorphisms and their prevalence in South Indian population

BACKGROUND:

Genetic variation in the vitamin K epoxide reductase complex (VKORC1) and cytochrome P450 4F2 (CYP4F2) genes were found to be strongly associated with the oral anticoagulant (OA) dose requirement. The distribution of genetic variation in these two genes was found to show large inter- and intra-ethnic difference.

MATERIALS AND METHODS:

A total of 470 unrelated, healthy volunteers of South Indians of either sex (age: 18-60 years) were enrolled for the study. A 5 ml of venous blood was collected and the genomic deoxyribonucleic acid (DNA) was extracted by using phenol-chloroform extraction method. Real-time quantitative polymerase chain reaction (RT-PCR) method was used for genotyping.

RESULTS:

The variant allele frequencies of VKORC1 rs2359612 (T), rs8050894 (C), rs9934438 (T) and rs9923231 (A) were found to be 11.0%, 11.8%, 11.7% and 12.0%, respectively. The variant allele VKORC1 rs7294 was (80.1%) more frequent and the variant allele CYP4F2 * 3 was found to be 41.8% in South Indians. The allele, genotype and haplotype frequencies of VKORC1 and CYP4F2 gene were distinct from other compared HapMap populations (P < 0.0001).

CONCLUSION:

The findings of our study provide the basic genetic information for further pharmacogenetic based investigation of OA therapy in the population.     

Haptoglobin polymorphism among the tribal groups of southern Gujarat

BACKGROUND:

Gujarat is located at the western most point of the Indian subcontinent. Valsad and Surat districts are part of the ‘tribal belt’of Gujarat and constitute 29.1% of total tribal population of Gujarat. These tribal populations are a rich source of gaining insights in the patterns of genetic diversity and genetico-environmental disorders against the back drop of their ecological, historical and ethnographic aspects.

AIM:

The objectives were to find out a) the genetic diversity among the tribes of Gujarat with reference to haptoglobin (Hp) locus b) the relationship between Hp polymorphism and sickle cell anemia/trait.

MATERIALS AND METHODS:

431 individuals belonging to eight tribal groups were studied for Hp polymorphism using polyacrylamide disc gel electrophoresis (PAGE). Hb*S was screened by dithionate tube turbididy (DTT) test and confirmed using cellulose acetate membrane electrophoresis (CAME).

STATISTICAL ANALYSIS:

Allele frequency was calculated by direct gene counting method. Average heterozygosity and gene diversity were computed using software DISPAN. Analysis of molecular variance (AMOVA) was estimated using software ARLEQUIN version 3.1.

RESULTS AND CONCLUSIONS:

Pattern of allele frequency distribution showed preponderance of Hp² allele in all the eight tribal groups, which is in accordance with its frequency in different populations of Indian subcontinent. Total average heterozygosity (H_T) was found to be low (0.160) but the level of genetic differentiation (G_ST) was found to be moderately high (5.6%). AMOVA analysis indicated least among group variance between west and south Indian populations (-0.04%) indicating the affinities of the tribes of Gujarat with that of Dravidian speaking groups. Analysis of Hp phenotypes among sickle cell anemia/ trait individuals revealed a high frequency of Hp 0-0 phenotype (92.7%) among SS individuals as opposed to only 9.7% among AS individuals, reaffirming the selective advantage of HbAS state in relation to hemolytic disorders.     

Identification of FVIII gene mutations in patients with hemophilia A using new combinatorial sequencing by hybridization

BACKGROUND:

Standard methods of mutation detection are time consuming in Hemophilia A (HA) rendering their application unavailable in some analysis such as prenatal diagnosis.

OBJECTIVES:

To evaluate the feasibility of combinatorial sequencing-by-hybridization (cSBH) as an alternative and reliable tool for mutation detection in FVIII gene.

PATIENTS/METHODS:

We have applied a new method of cSBH that uses two different colors for detection of multiple point mutations in the FVIII gene. The 26 exons encompassing the HA gene were analyzed in 7 newly diagnosed Italian patients and in 19 previously characterized individuals with FVIII deficiency.

RESULTS:

Data show that, when solution-phase TAMRA and QUASAR labeled 5-mer oligonucleotide sets mixed with unlabeled target PCR templates are co-hybridized in the presence of DNA ligase to universal 6-mer oligonucleotide probe-based arrays, a number of mutations can be successfully detected. The technique was reliable also in identifying a mutant FVIII allele in an obligate heterozygote. A novel missense mutation (Leu1843Thr) in exon 16 and three novel neutral polymorphisms are presented with an updated protocol for 2-color cSBH.

CONCLUSIONS:

cSBH is a reliable tool for mutation detection in FVIII gene and may represent a complementary method for the genetic screening of HA patients.     

Coryphoid Palm Leaf Fossils from the Maastrichtian–Danian of Central India with Remarks on Phytogeography of the Coryphoideae (Arecaceae)

Premise of research

A large number of fossil coryphoid palm wood and fruits have been reported from the Deccan Intertrappean beds of India. We document the oldest well-preserved and very rare costapalmate palm leaves and inflorescence like structures from the same horizon.

Methodology

A number of specimens were collected from Maastrichtian–Danian sediments of the Deccan Intertrappean beds, Ghughua, near Umaria, Dindori District, Madhya Pradesh, India. The specimens are compared with modern and fossil taxa of the family Arecaceae.

Pivotal results

Sabalites dindoriensis sp. nov. is described based on fossil leaf specimens including basal to apical parts. These are the oldest coryphoid fossil palm leaves from India as well as, at the time of deposition, from the Gondwana- derived continents.

Conclusions

The fossil record of coryphoid palm leaves presented here and reported from the Eurasian localities suggests that this is the oldest record of coryphoid palm leaves from India and also from the Gondwana- derived continents suggesting that the coryphoid palms were well established and wide spread on both northern and southern hemispheres by the Maastrichtian–Danian. The coryphoid palms probably dispersed into India from Europe via Africa during the latest Cretaceous long before the Indian Plate collided with the Eurasian Plate.     

CD14 C-159T polymorphism and its association with chronic lung diseases: A pilot study on isocyanate exposed population of Central India

CONTEXT:

CD14 functions as a multifunctional receptor for bacterial cell wall components including endotoxin and lipopolysaccharide and is likely to influence the cytokine profile and subsequent immunoglobulin E production in response to antigen/allergen contact in allergic phenotypes.

AIMS:

The present study was to investigate genetic polymorphism in CD14 gene - 159C/T, which may be one of the risk factor for increased prevalence of Chronic Lung Diseases in the Central India.

SETTINGS AND DESIGN:

Survivors of Methyl isocyanates toxicity in Bhopal still suffering from various respiratory ailments were examined.

MATERIALS AND METHODS:

Polymerase chain reaction-restriction fragment length polymorphism was performed to determine the polymorphism of C-159T.

RESULTS:

The genotype and allelic frequencies were in Hardy-Weinberg’s equilibrium. Prevalence of CC, CT, and TT were 5.5%, 22.2% and 9.25% respectively in asthmatics; 16.6%, 20.3% and 5.5% respectively in chronic obstructive pulmonary disease (COPD) patients and 5.5%, 14.8% and 1.85 respectively among interstitial lung disorder (ILD) patients; whereas the control cohort with no methyl isocyanate exposure displayed (CC, CT, and TT) cytosine, thymine as 2%, 1.6% and 2% respectively. Increased risk of Asthma among those carrying TT genotype and T allele (odds ratio [OR] =2.61 and 2.02 respectively).

CONCLUSION:

COPD risk significantly found among those with CC genotype and C allele (OR = 2.81 and 1.50 respectively), whereas ILD risk found significantly among CT genotype and C allele (OR = 1.75 and 1.40 respectively). Therefore, single nucleotide polymorphism (SNP) C-159T polymorphism in CD14 gene might be a risk factor for development of CLD in this population.     

Methylenetetrahydrofolate reductase polymorphism is not risk factor for Down syndrome in North India

BACKGROUND:

Down syndrome (DS) is the most common cause of mental retardation of genetic etiology with the prevalence rate of 1/700 to 1/1000 live births worldwide. Several polymorphisms in folate/homocysteine metabolism pathways genes have been reported as a risk factor in women for bearing DS child, but very few studies investigated these polymorphisms in DS cases whether there are a risk factor for being DS or not.

OBJECTIVE:

We have investigated the association of methylenetetrahydrofolate reductase (MTHFR) with the occurrence of DS in Indian population. MTHFR is one of the key regulatory enzymes involved in the metabolic pathway of homocysteine responsible for the reduction of methyltetrahydrofolate. A total of 32 DS cases and 64 age, sex matched controls were genotyped for MTHFR C677T polymorphism by polymerase chain reaction-restriction fragment length polymorphism.

RESULTS:

The observed genotype frequencies were CC = 0.81; CT = 0.17 and TT = 0.02 in controls and CC = 0.81 and CT = 0.19 in DS cases. Frequency of T allele in DS and controls were 0.09 and 0.1, respectively. Significant difference in the distribution of mutant 677T allele was not observed between DS cases and controls (odds ratio = 0.915; 95% confidence intervals: 0.331-2.53; P = 0.864).

CONCLUSION:

Results of this study indicate that MTHFR C677T polymorphism is not risk factor for DS.     

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe,Asia and Africa

Background

Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × -48×).

Results

We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency.

Conclusion

This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-963) contains supplementary material, which is available to authorized users.     

Analysis of association of TaqI VDR gene polymorphism with the chronic periodontitis in Dravidian ethnicity

AIM:

The aim of this study is to analyze the association of TaqI vitamin D receptor (VDR) gene polymorphism with the chronic periodontitis (CP) in Dravidian ethnicity.

MATERIALS AND METHODS:

A total of 120 subjects were recruited for this study, which included 60 CP and 60 healthy controls. TaqI VDR gene polymorphism was analyzed using specific primers and amplified by polymerase chain reaction (PCR) and visualized under 2% agarose gel.

RESULTS:

Our study results showed that Tt and tt genotype had a higher frequency of occurrence in CP compared with controls. Similarly, t allele was found to be associated with CP.

CONCLUSION:

Our study concludes that TaqI VDR gene polymorphism is associated with CP in Dravidian ethnicity.     

THE +1245G/T POLYMORPHISMS IN THE COLLAGEN TYPE I ALPHA 1 (COL1A1) GENE IN POLISH SKIERS WITH ANTERIOR CRUCIATE LIGAMENT INJURY

Objectives

The aim of this study was to examine the association of +1245G/T polymorphisms in the COL1A1 gene with ACL ruptures in Polish male recreational skiers in a case-control study.

Methods

A total of 138 male recreational skiers with surgically diagnosed primary ACL ruptures, all of whom qualified for ligament reconstruction, were recruited for this study. The control group comprised 183 apparently healthy male skiers with a comparable level of exposure to ACL injury, none of whom had any self-reported history of ligament or tendon injury. DNA samples extracted from the oral epithelial cells were genotyped for the +1245G/T polymorphisms using real-time PCR method.

Results

Genotype distributions among cases and controls conformed to Hardy-Weinberg equilibrium (p = 0.2469 and p = 0.33, respectively). There was a significant difference in the genotype distribution between skiers and controls (p = 0.045, Fisher''s exact test). There was no statistical difference in allele distribution: OR 1.43 (0.91-2.25), p = 0.101 (two-sided Fisher''s exact test).

Conclusions

The risk of ACL ruptures was around 1.43 times lower in carriers of a minor allele G as compared to carriers of the allele T.     

Insertion-deletions burden in copy number polymorphisms of the Tibetan population

BACKGROUND:

Many studies have been conducted to identify either insertions-deletions (inDels) or copy number variations (CNVs) in humans, but few studies have been conducted to identify both of these forms coexisting in the same region.

AIMS AND OBJECTIVES:

To map the functionally significant sites within human genes that are likely to influence human traits and diseases.

MATERIALS AND METHODS:

In this report, we describe an inDel map in the 1051 Tibetan CNV regions obtained through CNV genotyping using Affymetrix Genome-wide single nucleotide polymorphism 6.0 chip. InDel polymorphisms in these copy number polymorphism regions were identified with a computational approach using the 2500 deoxyribonucleic acid sequences obtained from the 1000 Genome Project.

RESULTS:

The study identified a total of 95935 inDels that range from 1 bp to several bps in length which were found scattered across regulatory regions, exons and in introns of genes underlying the CNVs. A study on the distribution of inDels revealed that the majority of inDels were found in coding regions of the genome than the noncoding, while within the genes, inDels in intron regions were more followed by exonic regions and finally the regulatory regions.

CONCLUSION:

Study of inDels in CNV regions contribute to the enhanced understanding of the role played by the two variations and their collective influence on the genome. Further, a collection of these inDel genetic markers will aid in genetic mapping, further understanding of the phenotypic variability, identification of disease genes and in detecting novel CNVs.     

Risk conferred by FokI polymorphism of vitamin D receptor (VDR) gene for essential hypertension

BACKGROUND:

The vitamin D receptor (VDR) gene serves as a good candidate gene for susceptibility to several diseases. The gene has a critical role in regulating the renin-angiotensin system (RAS) influencing the regulation of blood pressure. Hence determining the association of VDR polymorphisms with essential hypertension is expected to help in the evaluation of risk for the condition.

AIM:

The aim of this study was to evaluate association between VDRFok I polymorphism and genetic susceptibility to essential hypertension.

MATERIALS AND METHODS:

Two hundred and eighty clinically diagnosed hypertensive patients and 200 normotensive healthy controls were analyzed for Fok I (T/C) [rs2228570] polymorphism by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis. Genotype distribution and allele frequencies in patients and controls, and odds ratios (ORs) were calculated to predict the risk for developing hypertension by the individuals of different genotypes.

RESULTS:

The genotype distribution and allele frequencies of Fok I (T/C) [rs2228570] VDR polymorphism differed significantly between patients and controls (χ² of 18.0; 2 degrees of freedom; P = 0.000). FF genotype and allele F were at significantly greater risk for developing hypertension and the risk was elevated for both the sexes, cases with positive family history and habit of smoking.

CONCLUSIONS:

Our data suggest that VDR gene Fok I polymorphism is associated with the risk of developing essential hypertension