Genomics era and complex disorders: Implications of GWAS with special reference to coronary artery disease, type 2 diabetes mellitus, and cancers.

The Human Genome Project (HGP) has identified millions of single nucleotide polymorphisms (SNPs) and their association with several diseases, apart from successfully characterizing the Mendelian/monogenic diseases. However, the dissection of precise etiology of complex genetic disorders still poses a challenge for human geneticists. This review outlines the landmark results of genome-wide association studies (GWAS) with respect to major complex diseases - Coronary artery disease (CAD), type 2 diabetes mellitus (T2DM), and predominant cancers. A brief account on the current Indian scenario is also given. All the relevant publications till mid-2015 were accessed through web databases such as PubMed and Google. Several databases providing genetic information related to these diseases were tabulated and in particular, the list of the most significant SNPs identified through GWAS was made, which may be useful for designing studies in functional validation. Post-GWAS implications and emerging concepts such as epigenomics and pharmacogenomics were also discussed.

Current status of understanding of the genetic etiology of coronary heart disease.

Coronary heart disease (CHD), synonymously known as coronary artery disease (CAD) is the most predominant among the cardiovascular diseases and ranked number one in prevalence among the developing countries. CHD is a multifactorial disease involving both genetic and environmental factors and is primarily caused due to a process of progressive damage of coronary arteries called atherosclerosis. We present here a comprehensive review of molecular genetic studies conducted so far on CAD. The information was gathered through the internet using appropriate search terms for CHD/CAD. We also compiled the relevant information from the following websites: http://www.bioguo.org/CADgene/and http://www.genome.gov. Besides several Mendelian forms of the CHD, ~300 more genes have been identified in different studies through candidate gene approach. Additionally 32 more loci have been identified through genome wide association studies that include 9p21.3 as the most replicated genetic locus across the globe. Nevertheless, overall, these studies have been characterized by a relative lack of consistency in the association pattern across the populations. A fair degree of ethnic variation in the nature of association of different genetic variants with the disease has also been apparent. Pleiotropic effects of genes, existence of subclinical phenotypes and genetic heterogeneity appear to have been the limiting factors for developing a genetic risk profile test for the disease. Given the high prevalence of this disease in India, the presence of environmental triggers and genetic variation, it would be prudent to conduct multi-ethnic large-scale studies in India, representing the subcontinent as a whole-there have been a very limited number of molecular genetic studies on Indian populations.

Unusual Case of Long Head of Biceps Tendon Synovial Chondromatosis.

Introduction: Synovial chondromatosis is a rare benign tumor involving the major joints. This condition results from metaplasia of synovium into chondrocytes leading to formation of multiple loose bodies. Extra articular glenohumeral joint synovial chondromatosis involving long head of biceps is very rare. Case Report: A 38-year-old male presented with history of insidious onset, dull aching pain in right shoulder for 6 months. Clinicoradiological examination revealed calcific mass around the long head of biceps tendon. The calcific mass and loose bodies were removed en bloc. Histopathological examination concurred to be synovial chondromatosis. Conclusion: We hereby report a rare case of long head biceps tendon synovial chondromatosis of shoulder which was successfully treated by combined arthroscopic and open method. The results of surgical excision are excellent.

Role of 14-bp insertion/deletion polymorphism in HLA-G among Indian women with recurrent spontaneous abortions.

Human leukocyte antigen (HLA)-G is predominantly expressed on the extravillous cytotrophoblasts at the fetal-maternal interface. The 14-bp polymorphism in exon 8 is associated with HLA-G messenger ribonucleic acid (mRNA) stability and isoform alternative splicing patterns, thereby influencing the functionality of HLA-G in pregnancy. We analysed the 14-bp indel polymorphism in 143 recurrent spontaneous abortions (RSAs) and 150 control couples. We did not find any significant difference in the 14-bp insertion/deletion allele frequencies among the RSA and control couples. Analysis for increased sharing of the polymorphism in the RSA and the control couples also did not show any significant difference. However, we found an increase in the frequency of the 14-bp deletion homozygotes in the RSA women, which could lead to extremely high levels of soluble HLA-G (sHLA-G).

HLA-G polymorphism patterns show lack of detectable association with recurrent spontaneous abortion.

Human leukocyte antigen-G (HLA-G) is a class I non-classical molecule that is predominantly expressed on the extravillous cytotrophoblasts at foetal-maternal interface during pregnancy. We recruited 143 recurrent spontaneous abortion (RSA) and 150 control couples for the study. DNA-based typing of the HLA-G was carried out to explore if we can validate the patterns of association reported elsewhere or find association of novel HLA-G alleles with RSA in the Indian population. We also evaluated the role of allele sharing in couples with RSA. We did not find association of any of the HLA-G alleles with RSA in our study. There is a general trend of increase in sharing among the RSA couples, but the increase is not significant. The results suggest that the HLA-G alleles or the allele sharing by couples may not play a significant role in the manifestation of RSA in the Indian context albeit more studies are required before making any definitive statement.

Microsatellite diversity among the primitive tribes of India.

The present study was undertaken to determine the extent of diversity at 12 microsatellite short tandem repeat (STR) loci in seven primitive tribal populations of India with diverse linguistic and geographic backgrounds. DNA samples of 160 unrelated individuals were analyzed for 12 STR loci by multiplex polymerase chain reaction (PCR). Gene diversity analysis suggested that the average heterozygosity was uniformly high ( >0.7) in these groups and varied from 0.705 to 0.794. The Hardy-Weinberg equilibrium analysis revealed that these populations were in genetic equilibrium at almost all the loci. The overall G(ST) value was high (G(ST) = 0.051; range between 0.026 and 0.098 among the loci), reflecting the degree of differentiation/heterogeneity of seven populations studied for these loci. The cluster analysis and multidimensional scaling of genetic distances reveal two broad clusters of populations, besides Moolu Kurumba maintaining their distinct genetic identity vis-à-vis other populations. The genetic affinity for the three tribes of the Indo-European family could be explained based on geography and Language but not for the four Dravidian tribes as reflected by the NJT and MDS plots. For the overall data, the insignificant MANTEL correlations between genetic, linguistic and geographic distances suggest that the genetic variation among these tribes is not patterned along geographic and/or linguistic lines.

Mitochondrial DNA variation and substructure among the tribal populations of Andhra Pradesh, India.

We analyzed mtDNA HVR-I variation among six tribal populations-Andh, Pardan, Gond, Naikpod, Kolam and Chenchu--from Andhra Pradesh. These tribes belong to the Dravidian and Indo-European linguistic group. Except for Chenchu, the rest of the tribal samples were collected from two or more than two locations. The analysis of molecular variance (AMOVA) of the sequences yields a significant F(ST) value (0.045), suggesting a fair degree of genetic differentiation among these tribes. When the tribal samples collected from different locations were considered as subpopulations in AMOVA, it is found that the variation among the subunits within the tribal groups is smaller than among the tribes. However, when Chenchu is removed from the analysis, the magnitude of within and between groups diversity becomes similar. In the multidimensional scaling plot based on F(ST) distances the Chenchu is found to be the extreme outlier. Exclusion of Chenchu from AMOVA analysis and multidimensional scaling plot does not result in any specific pattern of population clustering. Mismatch distribution suggest that Chenchu might have undergone a bottleneck effect and does not show evidence of past demographic expansion as shown by the other five tribal groups. A comparison of AP tribes with some other caste and tribal populations of India suggests common maternal genetic heritage.

STR data for the Amp FlSTR Profiler Plus loci among 27 populations of different social hierarchy from southern part of Andhra Pradesh, India.

Allele frequency for the 9 STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) were estimated from a total of 1096 individuals belonging to 27 endogamous populations from the state of Andhra Pradesh, India, covering the entire gamut of socio-economic variation of the linguistic region. These loci are found to be highly polymorphic within the populations with high levels of average heterozygosity (>0.80). However, the allele frequency distributions are fairly uniform across the populations in case of these loci suggesting relatively greater homogeneity among the populations. Regrouping populations into five broad socio-economic categories further reiterated the homogenous pattern of genetic diversity.

Antigenic determinants of human serum retinol binding protein as probed with monoclonal antibodies.

Monoclonal antibodies raised against human serum retinol-binding protein (hRBP) were used as probes for the study of the antigenic determinants of hRBP and those shared with the same protein from other species. The antibodies could be classified into four distinct groups and react with the homologous proteins from the rat as well as the rabbit sera. Three of these antibodies recognize sequential or continuous epitopes while the remaining antibody is directed against a discontinuous or conformational epitope. By chemical cleavage with cyanogen bromide, the domains recognized by the monoclonal antibodies could be delineated. By solid-phase synthetic approach, the core sequences recognized by two of these monoclonal antibodies were identified to amino acid sequences 45-51 and 128-131 of the primary amino acid sequence of hRBP.

A common epitope of beta-lactoglobulin and serum retinol-binding proteins: elucidation of its core sequence using synthetic peptides.

One of the monoclonal antibodies raised against bovine beta-lactoglobulin reacted with human serum retinol binding protein. The finding that this monoclonal antibody also reacted with the serum retinol binding proteins isolated from other animals, suggested that this epitopic conformation is conserved among these proteins. Using ELISA and various synthetic peptides of defined sequence, we show in this paper that the epitope defined by this monoclonal antibody comprises of the highly conserved core sequence of DTDY present in beta-lactoglobulin and retinol binding proteins.

Genetic variation among the Golla pastoral caste subdivisions of Andhra Pradesh, India, according to the HLA system.

The HLA allele frequency distributions have been characterized for the HLA class I and class II loci of the Golla pastoral caste, from Southeast India, subdivided into the subcastes (Puja, Punugu, Kurava, Pokanati, Karnam, and Doddi). Genetic distances, neighbor-joining, correspondence, and haplotype analyses all indicate that the subcastes exhibit a high haplotype variability and that their genetic substratum may be the result of European-Middle East/Asian admixture with the autochthonous populations. The Karnam subcaste seems to be the one that has undergone a higher degree of admixture, when compared with the other subcastes. The Golla speak an old Indian Dravidian language and should theoretically represent the basic Indian substratum that existed before the postulated "Aryan" invasion.

Anacardoside from the seeds of Semecarpus anacardium.

From the seeds of Semecarpus anacardium, a new phenolic glucoside, anacardoside, was isolated, and its structure and configuration were elucidated by a combination of NMR techniques as 1-O-beta-D-glucopyranosyl-(1-->6)-beta-D-glucopyranosyloxy-3-hydro xy-5-methylbenzene.

Acylated C-21 steroidal bisdesmosidic glycosides from Caraluma umbellata.

From the whole plant of Caraluma umbellata, three new C-21 steroidal glycosides, named as carumbellosides III-V, were isolated and their structures elucidated by extensive spectroscopic experiments, devoid of any derivatisation, as caralumagenin 3-O-beta-D-glucopyranosyl(1-->4)-beta-D-digitalopyranoside-20-O-be ta- D-glucopyranoside, caralumagenin 3-O-beta-D-glucopyranosy(1-->4)- beta-D-digitalopyranoside-20-O-(2-O- benzoyl)-beta-D-glucopyranoside and caralumagenin 3-O-[6-O-benzoyl-beta-D-glucopyranosyl(1-->4)]-beta-D- digitalopyranoside-20-O-(2-O-benzoyl)-beta-D-glucopyranoside. The determination of the absolute configuration of the aglycone as (20 R), the conformations of the sugars and the unambiguous assignments of their NMR spectroscopic signals were achieved by a combination of 2D-NMR techniques. The isolates were devoid of significant cytotoxity in the UIC human cancer cell panel.

Antinociceptive and anti-inflammatory activity of Sida rhomboidea leaves.

Various organic extracts of Sida rhomboidea leaves were studied for antinociceptive and anti-inflammatory activity at a dose of 200 mg/kg. Ethyl acetate extract has shown significant (P < 0.01) antinociceptive activity. Percentage inhibition of edema by butanolic extract (33.05, P < 0.001) is comparable to that of phenylbutazone, 100 mg/kg inhibition (38.83%). Phytochemical screening of the extracts indicated the presence of alkaloids, steroids and/or triterpenoids and their glycosides, tannins, flavonoids and their glycosides, carbohydrates and absence of cardiac glycosides.

Antinociceptive and anti-inflammatory activity of a flavonoid isolated from Caralluma attenuata.

Luteolin-4'-O-neohesperidoside, i.e. luteolin-4'-O-[alpha-(L-rhamnopyranosyl-(1-->2)-beta-D-glucopyranoside)] has significant anti-inflammatory action. It is more potent than ibuprofen. Its antinociceptive activity is less pronounced when compared with its anti-inflammatory activity.

Antinociceptive and anti-inflammatory activity of carumbelloside-I isolated from Caralluma umbellata.

The phytochemical study using Caralluma umbellata (Asclepiadaceae) whole plant allowed the isolation of a novel pregnane glycoside named carumbelloside-I (3-O-beta-D-glucopyranosyl-(1-->6)-beta-D-glucopyranosyl-3beta,14beta -dihydroxypregn-5-en-20-one). Carumbelloside-I was evaluated for both antinociceptive activity and anti-inflammatory activity. The antinociceptive activity was evaluated in mice using the writhing test method, while the anti-inflammatory activity was evaluated in rats using the paw edema test with carrageenin. Carumbelloside-I has significant antinociceptive action. It has no anti-inflammatory activity.

Patterns of variation in a caste-cluster of Dhangars of Maharashtra, India.

We study patterns of variation among the 20 endogamous groups of Dhangars, a caste-cluster from Maharashtra State of India, who are semi-nomadic shepherds and cattle herders. To understand patterns of variation, we subjected the data on fourteen anthropometric measurements of about 2,500 adult males and data on 6 genetic markers, published among 13 of the 20 Dhangar castes, to R-matrix analysis, Harpending and Ward model of regression of heterozygosity on the distance from centroid of the populations, spatial autocorrelation analysis and Mantel statistics of matrix correspondence of the distances--geographic, anthropometric and genetic. Results of multiple regression analysis suggest a high degree of association between allele frequencies and the geographic longitude and latitude; R2 value suggests that about 70% of the variance in RH7 and ACP can be assigned to geographic distribution of groups. In case of anthropometry, this association with body size is found to be even stronger. Results of spatial autocorrelation analysis, as suggested by Moran's (I), are somewhat complementary to those based on multiple regression analysis. Mantel test indicates significant association between anthropometric distances and the geographic distances, not between geographic and genetic distances. The extent of differentiation of Dhangar sub-castes is much higher in anthropometric traits (F(ST) = 0.068) when compared to the genetic markers (F(ST) = 0.023). Yet, the F(ST) value obtained forgenetic markers is larger than the average for the Indian populations, based on similar class of markers. The positioning of the groups in the multivariate space reflects primarily geographic proximity of the groups with reference to anthropometric dimensions while no tangible pattern is evident forgenetic markers. The plot of average heterozygosity of the groups versus their distance from the gene frequency centroid seems to reflect population size variation, rather than group variation in external gene flow.

A case of primary ovarian lymphoma with autoimmune hemolytic anemia achieving complete response with Rituximab-based combination chemotherapy.

Ovarian involvement as primary or secondary lymphomatous process is extremely uncommon. In most cases, the diagnosis is usually not suspected initially and is confirmed only after detailed histopathological evaluation. We report a patient with primary ovarian diffuse large B-cell lymphoma (DLBCL) and associated auto-immune hemolytic anemia (AIHA) who achieved complete remission after treatment with Rituximab-cyclophosphamide-doxorubicin-vincristine and prednisolone (R-CHOP) chemotherapy. This patient was a 50 year old female, who presented with fever, abdominal pain, vomiting, weight loss and anemia. Computed tomography scan of the abdomen and pelvis revealed a large left ovarian mass with bilateral hydronephrosis. We performed exploratory laparotomy and partial resection of the mass was done due to the adhesions. Histopathology confirmed the diagnosis of DLBCL. After six R-CHOP chemotherapy cycles, patient achieved complete response with correction of anemia. To our knowledge, this may be the first case report till date of primary ovarian DLBCL with AIHA treated with R-CHOP chemotherapy who achieved complete remission in terms of primary disease as well as hemolytic anemia.

Present status of understanding on the G6PD deficiency and natural selection.

G6PD deficiency is a common hemolytic genetic disorder, particularly in the areas endemic to malaria. Individuals are generally asymptomatic and hemolytic anemia occurs when some anti-malarial drugs or other oxidizing chemicals are administered. It has been proposed that G6PD deficiency provides protection against malaria. Maintaining of G6PD deficient alleles at polymorphic proportions is complicated because of the X-linked nature of G6PD deficiency. A comprehensive review of the literature on the hypothesis of malarial protection and the nature of the selection is being presented. Most of the epidemiological, in vitro and in vivo studies report selection for G6PD deficiency. Analysis of the G6PD gene also reveals that G6PD-deficient alleles show some signatures of selection. However, the question of how this polymorphism is being maintained remains unresolved because the selection/fitness coefficients for the different genotypes in the two sexes have not been established. Prevalence of G6PD deficiency in Indian caste and tribal populations and the different variants reported has also been reviewed.