Investigating the morphology and genetics of scalp and facial hair characteristics for phenotype prediction.

Microscopic traits and ultrastructure of hair such as cross-sectional shape, pigmentation, curvature, and internal structure help determine the level of variations between and across human populations. Apart from cosmetics and anthropological applications, such as determining species, somatic origin (body area), and biogeographic ancestry, the evidential value of hair has increased with rapid progression in the area of forensic DNA phenotyping (FDP). Individuals differ in the features of their scalp hair (greying, shape, colour, balding, thickness, and density) and facial hair (eyebrow thickness, monobrow, and beard thickness) features. Scalp and facial hair characteristics are genetically controlled and lead to visible inter-individual variations within and among populations of various ethnic origins. Hence, these characteristics can be exploited and made more inclusive in FDP, thereby leading to more comprehensive, accurate, and robust prediction models for forensic purposes. The present article focuses on understanding the genetics of scalp and facial hair characteristics with the goal to develop a more inclusive approach to better understand hair biology by integrating hair microscopy with genetics for genotype-phenotype correlation research.

Differential global and MTHFR gene specific methylation patterns in preeclampsia and recurrent miscarriages: A case-control study from North India.

AIM: The purpose of the present study is to evaluate and understand the association of global and MTHFR gene specific methylation in preeclampsia and recurrent miscarriages in light of MTHFR C677T polymorphism. METHODS: The subjects comprised of recurrent miscarriage cases, their gestation matched controls, preeclampsia cases and matched controls. A set of women at full term were also recruited. Fasting blood sample (~5 ml) was drawn from all the participants followed by DNA extraction, global DNA methylation and MTHFR gene specific methylation. MTHFR C677T polymorphism was analysed by PCR followed by RFLP. RESULTS HIGHER: Global DNA methylation at maternal front (p = 0.04) and hypomethylation of MTHFR gene at fetal front (p = 0.001) might be a characteristic of preeclampsia. Recurrent miscarriage cases were having significantly (p = 0.002) hyper MTHFR gene specific methylation as compared to controls. Women carrying CT genotype were found to be having significantly (p = 0.001) higher global DNA methylation in PE cases and MTHFR gene specific methylation (p = 0.005) in RM cases. Intergenerational analysis revealed similar patterns of global DNA methylation and MTHFR gene specific methylation among both PE and RM cases at maternal and fetal fronts. CONCLUSION: The study highlights the importance of global DNA methylation in Preeclampsia and MTHFR gene specific methylation in recurrent miscarriages. MTHFR C677T gene polymorphism in association with global and gene specific methylation seem to play a pivotal role in PE and RM respectively.

Genetics of nonalcoholic fatty liver disease in Asian populations.

Nonalcoholic fatty liver disease (NAFLD) is characterized by the accumulation of fat in the liver without any history of chronic alcohol consumption. It encompasses a wide spectrum of diseases that range from simple steatosis to nonalcoholicsteatohepatitis. NAFLD is strongly associated with obesity, insulin resistance / type-2 diabetes mellitus and the metabolic syndrome. NAFLD is a complex disorder; environmental and genetic factors interact with NAFLD manifestation and determine its progression. In this review, an attempt was made to provide current information on the genetic variants of NAFLD in Asian populations. Literature search was performed by using PubMed, Medline and Google Scholar database. Candidate gene, validation and genomewide association studies (GWASs) were included in this review. A total of 41 studies fulfilled inclusion criteria of which 12 candidate gene studies exclusively focussed on the PNPLA3 gene and 17 other studies on other important candidate genes such as NCANCILP2, PPARG,AGTR1, FABP1, APOC3 etc. reported significant association with NAFLD. Eight validation studies identified associations of variants on PNPLA3, LYPLAL1, TM6SF2, ADIPOR2, STAT3, GCKR, SAMM50 etc. with NAFLD. Thus, so far, four GWASs have been conducted in Asian population that reported PNPLA3, SAMM50, PARVB and GATAD2A genes which were significantly associated with NAFLD. Findings indicate that PNPLA3, APOC3, PPARG, NCAN and GCKR genes emerge out to be the important biological markers associated with NAFLD.

Methylenetetrahydrofolate Reductase Gene-specific Methylation and Recurrent Miscarriages: A Case- Control Study from North India.

AIM: This study aimed to understand the association of gene-specific methylation of the promoter region of methylenetetrahydrofolate reductase (MTHFR) in the causation of recurrent miscarriages (RMs) both independently and also in light of MTHFR C677T polymorphism, hyperhomocysteinemia, folate, and Vitamin B12 deficiency. SETTINGS AND DESIGN: This was a hospital-based, case-control, observational study. METHODS: The proposed study included a total of 85 RM cases and 121 nonpregnant controls. Biochemical (homocysteine, folate, and Vitamin B12) investigations, MTHFR polymorphism (C677T), and MTHFR allele-specific methylation were done on all the samples. RESULTS: Methylation-specific polymerase chain reaction of MTHFR gene revealed that methylated allele (single dose) was found to pose a significant 3.6-fold increased risk for RM. The degree of risk of methylated allele for RM was found to be aggravated from the normal genotype CC (2.8 folds) to CT (7.5 folds) individuals. Vitamin B12 deficiency and folate repletion were found to be posing an increased risk in association with methylated allele for recurrent miscarriages as compared to the respective controls. CONCLUSION: Recurrent miscarriage cases were found to be hypermethylated with respect to MTHFR gene-specific methylation as compared to the controls. High prevalence of folate repletion causing imbalance between folate and Vitamin 12 levels may lead to hypermethylation among recurrent miscarriage cases. The present study highlights the significance of the epigenetic mechanisms in the causation of the recurrent miscarriages.

Role of ACE and IL-1ß Gene Polymorphisms in Erythropoeitin Hyporesponsive Patients with Chronic Kidney Disease with Anemia.

BACKGROUND: Hyporesponse to erythropoietin is a common problem seen in around 5-10% of patients. Recently the focus from these remediable factors has been shifted to the non-modifiable innate factors i.e polymorphism of ACE and IL-1B gene and studies have shown that DD genotype and IL-1B CC genotype have lower erythropoietin requirement. The aim of our study was to evaluate the role of ACE and IL-1B gene polymorphisms in erythropoietin hyporesponse in CKD patients with anemia. METHODS: A total of 50 patients were selected. After taking pre-informed written consent, they were segregated into two groups, group A and B with 25 patients in each group. Group A included CKD stage III-IV patients and Group B included CKD stage V patients who were on regular maintenance. All patients were given erythroepoietin and response was monitored using erythropoietin resistance index (ERI). Genotyping of ACE and IL-1B genes were done and serum levels of ACE and IL-1B were measured. Mean values of ERI were compared between different genotype subgroups and analysed using binary regression analysis. RESULTS: The study group included 6 patients with diabetic nephropathy and out of these 4(66.6%) had DD genotype. On comparing the effect of ACE polymorphism on ERI levels it was seen that the mean ERI values in DD subgroup were significantly lower (16.97±5.35, 21.88±6.25, 22.69±8.35 at 1,3 and 5th month) as compared to ID (18.16±3.39, 24.17±3.66, 32.74±9.95 and II (20.73±5.17, 27.74±7.30, 41.08±13.83 U/Kg/g/dL). In the case of IL-1B the mean ERI values were lowest in the TT subgroup (16.46±4.45, 21.96±5.77,23.98±8.48) as compared to CC (19.49 ±5.62,25.46±7.07, 33.59±12.61) and CT (18.12±4.27,24.14±5.70, 31.89±13.83 U/Kg/g/dL). The mean serum values of ACE were in a decreasing trend i.e DD> ID> II (238.05 ± 52.46, 194.73±50.28 and 162.99±39.71 ng/ml, (p < 0.05). The mean serum values of IL1B in CC, CT and TT were 23.24±28.77, 18.32±16.25, 23.34±13.83 pg/ml (p>0.05). CONCLUSIONS: D allele positively affected the serum ACE level but there was no association between IL-1B genotype and its levels. ACE gene polymorphism has an important role in determining the response to EPO and progression of CKD. Pre-treatment screening for genotype may help in predicting the patients at risk and poor responders.

'Mendelian randomization': an approach for exploring causal relations in epidemiology.

OBJECTIVES: To assess the current status of Mendelian randomization (MR) approach in effectively influencing the observational epidemiology for examining causal relationships. METHODS: Narrative review on studies related to principle, strengths, limitations, and achievements of MR approach. RESULTS: Observational epidemiological studies have repeatedly produced several beneficiary associations which were discarded when tested by standard randomized controlled trials (RCTs). The technique which is more feasible, highly similar to RCTs, and has the potential to establish a causal relationship between modifiable exposures and disease outcomes is known as MR. The technique uses genetic variants related to modifiable traits/exposures as instruments for detecting causal and directional associations with outcomes. CONCLUSIONS: In the last decade, the approach of MR has methodologically developed and progressed to a stage of high acceptance among the epidemiologists and is gradually expanding the landscape of causal relationships in non-communicable chronic diseases.

An assessment study of CVD related risk factors in a tribal population of India.

BACKGROUND: Non communicable diseases (NCDs) have become a major concern for global health. Cardiovascular diseases (CVDs) contribute 48 % towards the deaths due to NCDs in India. Though studies have been conducted in urban and rural areas, data related to tribal communities is limited. The present study aims to examine various CVD related risk factors including hypertension, elevated fasting blood glucose, obesity and metabolic syndrome among a tribal population. METHODS: The present study was an observational, cross- sectional study conducted on Rang Bhotias, a tribal population of India. The participants were adults of age between 20 and 60 years. Prior to blood sample collection, interview schedule was administered which included relevant information like age, lifestyle, socio-economic status, education and occupation In addition to this, various anthropometric and physiological measurements were taken. Logistic regression was used to examine the association of the various health disorders related to CVDs with age, gender and behavioural factors (smoking, alcohol consumption and physical activity). RESULTS: A total of 288 participants were surveyed for the study including 104 males and 184 females. High BMI (56.6 %), hypertension (43.4 %), metabolic syndrome (39.2 %) and abdominal obesity (33.7 %) were the most prevalent CVD risk factors observed in the population. The multivariate logistic regression analysis, conducted to examine the contribution of risk factors including behavioural risk factors on the studied abnormalities, revealed age to be a significant risk factor for all the abnormalities except elevated fasting blood glucose. Gender and physical inactivity contributed significantly towards development of hypertension. Physical inactivity was also found to be associated with high BMI levels. CONCLUSION: In the present study, hypertension, high BMI levels, MS and abdominal obesity have been found to be high among the studied population. The status of the population with respect to these abnormalities implicates susceptibility of the community towards various common disorders. The prevention and treatment intervention programs should be implemented taking into consideration age and gender.

Opportunity for natural selection among five population groups of Manipur, North East India.

Opportunity for natural selection among five population groups of Manipur in comparison with other North East Indian population has been studied. Crow's index as well as Johnston and Kensinger's index for natural selection were calculated based on differential fertility and mortality. The mortality component was found to be lower compared to fertility component in all the populations which may attribute to comparatively improved and easily accessible health care facilities. However, different selection pressures, artificial and natural, seem to be influencing the selection intensity through induced abortion and spontaneous abortion among the two non-tribal migrant groups: Bamon and Muslims, respectively. This study highlights the probable interaction of artificial and natural selection in determining the evolutionary fate of any population group.

APOE, MTHFR, LDLR and ACE polymorphisms among Angami and Lotha Naga populations of Nagaland, India.

Several common polymorphisms in the ApoE, ACE, MTHFR and LDLR genes have been implicated in the pathogenesis of common complex diseases across world populations. This study investigates the prevalence of five known and clinically important common polymorphisms in Angami and Lotha Naga populations. A total of 112 unrelated healthy volunteers (52 Lotha Nagas and 60 Angami Nagas) participated in the study. All the five genes were found to be polymorphic in the studied populations. The Lotha Nagas displayed higher mutant allele frequencies than the Angami Nagas except for the T allele frequency of the AvaII polymorphism of the LDLR gene, though chi square did not reveal any significant population differences by genotypes. In view of the relatively high mutant allele frequencies in both the populations, they are likely to be at a high risk of developing various complex diseases as they shift from an active and rigorous lifestyle to a more sedentary one.

A validation study of type 2 diabetes-related variants of the TCF7L2, HHEX, KCNJ11, and ADIPOQ genes in one endogamous ethnic group of north India.

The aim of this study was to validate the single nucleotide polymorphisms (SNPs) of four candidate genes (TCF7L2, HHEX, KCNJ11, and ADIPOQ) related to type 2 diabetes (T2D) in an endogamous population of north India; the Aggarwal population, having 18-clans. This endogamous population model was heavily supported by recent land mark work and we also verified the homogeneity of this population by clan-based stratification analysis. Two SNPs (rs4506565; rs7903146) in TCF7L2 were found to be significant (p-value = 0.00191; p-value = 0.00179, respectively), and odds ratios of 2.1 (dominant-model) and 2.0 (recessive-model) respectively, were obtained for this population. The TTT haplotype in the TCF7L2 gene was significantly associated with T2D. Waist-Hip ratio (WHR), systolic blood pressure (SBP), and age were significant covariates for increasing risk of T2D. Single-SNP, combined-SNPs and haplotype analysis provides clear evidence that the causal mutation is near to or within the significant haplotype (TTT) of the TCF7L2 gene. In spite of a culturally-learned sedentary lifestyle and fat-enriched dietary habits, WHR rather than body-mass-index emerged as a robust predictor of risk for T2D in this population.

A genomic insight into diversity among tribal and nontribal population groups of Manipur, India.

Twenty autosomal markers, including linked markers at two gene markers, are used to understand the genomic similarity and diversity among three tribal (Paite, Thadou, and Kom) and one nontribal communities of Manipur (Northeast India). Two of the markers (CD4 and HB9) are monomorphic in Paite and one (the CD4 marker) in Kom. Data suggest the Meitei (nontribal groups) stand apart from the three tribal groups with respect to higher heterozygosity (0.366) and presence of the highest ancestor haplotypes of DRD2 markers (0.228); this is also supported by principal co-ordinate analysis. These populations are found to be genomically closer to the Chinese population than to other Indian populations.

MTHFR C677T polymorphisms among the Ahirs and Jats of Haryana (India).

Methylenetetrahydrofolate reductase (MTHFR) is a vital enzyme catalyzing the nicotinamide adenine dinucleotide phosphate (NADPH) linked reduction of 5,10-methylenetetrahydrofolate to 5-methylenetetrahydrofolate, which serves as cofactor in methylation of homocysteine to methionine. Three clinically important mutations of the MTHFR gene namely C677T, A1298C, and T1317C are reported to be associated with various pathological conditions. The present study deals with the screening of C677T mutation among two endogamous groups viz. Ahirs and Jats of Haryana (India). The mutation is reported to be significantly associated with thrombosis, hypertension, stroke and myocardial infraction, neural tube defects (NTDs), and recurrent pregnancy loss. The T allele among Jats is found to be more frequent (0.06) than Ahirs (0.03). Moreover, the Jats population shows a significant deviation from Hardy-Weinberg equilibrium with respect to C677T mutation. This could probably be due to some selection pressure operating in the population.

Genetic variation of 13 STR loci in the four endogamous tribal populations of Eastern India.

We have analysed 13 autosomal STR loci in four endogamous tribal populations from two eastern states (Orissa and Nagaland) of India. The Gadaba, Kuvi Khond and Lotha Naga populations have not been analysed for microsatellite genetic variation previously. The allele frequencies for all loci are within the range observed in the geographical region and racial background, though some alleles showed greater variation. Departures from the Hardy-Weinberg equilibrium were tested by three methods and two loci (THO1 and TPOX) showed significant departures for all measures in Gadaba and Lotha Naga populations. The exclusion probability and discrimination probability were high for all analysed loci in all populations. There is no evidence for association of alleles among the STR loci studied. This allele frequency information will be useful for forensic, paternity and population genetic studies.

Evidence of a common founder for SCA12 in the Indian population.

Spinocerebellar ataxia type 12 (SCA12) is an autosomal dominant cerebellar ataxia associated with the expansion of an unstable CAG repeat in the 5' region of the PPP2R2B gene on chromosome 5q31-5q32. We found that it accounts for approximately 16% (20/124) of all the autosomal dominant ataxia cases diagnosed in AIIMS, a major tertiary referral centre in North India. The length of the expanded allele in this population ranges from 51-69 CAG triplets. Interestingly, all the affected families belong to an endogamous population, which originated in the state of Haryana, India. We identified four novel SNPs and a dinucleotide marker spanning approximately 137 kb downstream of CAG repeat in the PPP2R2B gene. Analysis of 20 Indian SCA12 families and ethnically matched normal unrelated individuals revealed one haplotype to be significantly associated with the affected alleles (P= 0.000), clearly indicating the presence of a common founder for SCA12 in the Indian population. This haplotype was not shared by the American pedigree with SCA12. Therefore, the SCA12 expansion appears to have originated at least twice.

Genetic variation at three VNTR loci (D1S80, APOB, and D17S5) in two tribal populations of Andhra Pradesh, India.

This study reports the genetic variation at three variable number of tandem repeat (VNTR) loci (APOB, D17S5 and D1S80) in two tribes (Thoti and Kolam) of Andhra Pradesh, India. Kolams constitute 1% of the total scheduled tribal population of Andhra Pradesh, while Thoti is a numerically small tribe. All three genetic loci were genotyped using the polymerase chain reaction (PCR) technique and were polymorphic in both populations. At the D1S80 locus, both populations showed higher frequencies of allele *31 (9-14%) than other Indian populations. In the APOB system, Thoti showed a very high frequency of allele *37 (54%) and for D17S5 system allele *4 was the most common in Thoti (32%) and allele *2 in Kolam (28%). Both tribes differed statistically significantly from other tribal populations of the region. The level of gene differentiation was low (GST = 0.038) for Indian tribal populations. The allele frequency distribution, heterozygosity and genetic diversity analysis shows that the observed genetic variation is socially and geographically structured.

6-phosphogluconate dehydrogenase typing from dried bloodstains--under Indian conditions.

As yet, there is no report available on the stability studies of 6-phosphogluconate dehydrogenase enzyme in India. 469 bloodstains prepared in the laboratory using a variety of substrates commonly encountered in case examination have been analysed by starch gel electrophoresis. The utility of this parameter under various climatic conditions prevalent in India has also been evaluated. Except in the cases of relatively fresh samples of blood, the PGD isoenzyme system seems not to be very suitable in Indian conditions.