Identification of a Novel TAZ Gene Mutation in a Family With X-Linked Dilated Cardiomyopathy Barth Syndrome

Abstract Mutations in the tafazzin (TAZ) gene on chromosome Xq28 are responsible for the Barth syndrome (BTHS) phenotype resulting in a loss of function in the protein tafazzin involved in the transacylation of cardiolipin, an essential mitochondrial phospholipid. TAZ gene was investigated in the proband in our study, who died of dilated cardiomyopathy at 8 months of age, and his family by sequencing to identify the genetic cause of BTHS. Molecular analysis revealed a novel mutation in exon 5 (c.520T>G) of the TAZ gene. This novel mutation c.520T>G, pW174G, was also found in female carriers (mother and grandmother of proband) in the family. Bioinformatic analysis was carried out to examine the effect of mutation in the gene and confirmed the deleterious effect of this single mutation to the protein structure. Protein modeling and 3-dimensional structure of TAZ protein demonstrated the significantly visible changes in mutated protein leading to BTHS phenotype. Prenatal diagnosis in a subsequent pregnancy showed a carrier female, and pregnancy was continued. Child is doing well at 1 year of age.

Paleolithic spread of Y-chromosomal lineage of tribes in eastern and northeastern India.

BACKGROUND: The Indian peninsula provides a suitable region for examination of the demographic impact of migrations and invasions in historical times, because its complex recent history has involved the long-term residence of different populations with distinct geographical origins and their own particular cultural characteristics. AIM: The aim of the present study was to analyse Y chromosome haplotypes in tribes from eastern and north-eastern India, which provided the necessary phylogeographic resolution. SUBJECTS AND METHODS: A total of 32 Y-chromosome SNPs and 17 Y-STRs were genotyped in 607 males from nine populations (Munda, Birhor, Oraon, Paharia, Santhal, Ho, Lachung, Mech and Rajbanshi) residing in East and Northeastern India. RESULTS: Y-chromosomal analysis revealed high frequency of the O2a haplogroup in Austroasiatic tribes and high haplotype diversity within specific haplogroups demonstrating a lesser degree of admixture of these populations with neighbouring populations in eastern India. In addition, the presence of O3a haplogroups in Sino-Tibetan populations reflects the influx from Southeast Asia during the demographic expansion through the Northeastern corridor. CONCLUSION: The study suggested that the majority of the male gene flow of Austroasiatic tribes occurred during the late Pleistocene period. The results suggest gene flow from Southeast Asia to Northeast India, albeit more significantly among Tibeto-Burman than Austroasiatic-speaking populations.

Chemokine (CCR) and fractalkine (CX3CR) receptors and end stage renal disease.

OBJECTIVE AND DESIGN: Genetic polymorphisms of chemokines and their receptors were reported to be independent risk factors for inflammation associated disease. We explored the role of CCR5-Δ32, CCR5-G59029A, CX3CR1 V249I and T280M gene polymorphisms as susceptibility for end stage renal disease (ESRD). SUBJECTS AND METHODS: We genotyped 258 ESRD and 569 healthy controls by sequence-specific primers and RFLP and examined their association. RESULTS: There was significant difference in genotype frequencies of CCR5-G59029A (p = 0.005), and CX3CR1 V249I (p < 0.0001) between ESRD and controls. No homozygous individuals were observed for CCR5-Δ32. The haplotype analysis of all four studied genes reveled that haplotype +/A/T/I was more significant in patients and associated with higher risk (OR = 2.95) of ESRD. Further, the haplotype of CX3CR1 (T280M, V249I) gene showed 3.6-fold higher in an individual carrying T/I haplotype. No risk was seen for CCR5 haplotypes. CONCLUSIONS: These results highlight the role of CCR5 and CX3CR1 in ESRD.

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

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

Association of proinflammatory cytokines with end stage renal disease.

CONTEXT: Cytokines play an important role in the pathogenesis of kidney disease and its progression to ESRD. Macrophage migration inhibitory factor (MIF) is a proinflammatory cytokine that is released by macrophages and lymphocytes and interferon-gamma (IFN-gamma) plays an important pathogenetic role in several inflammatory diseases. OBJECTIVES: We have explored the role of MIF -173 G/C, INF-gamma +874 A/T and INF-gamma CA repeat microsatellite gene polymorphisms as a susceptibility for ESRD. PARTICIPANTS AND METHODS: We genotyped MIF and IFN-gamma gene polymorphisms in 258 patients with ESRD and 569 healthy controls free of any renal disease using PCR-RFLP, gene sequencing and gene scanning methods. RESULTS: The frequency of high producer MIF -173 CC genotype was higher (10.1%) in ESRD than in controls (1.2%) (p=0.0001, OR=8.9; 95%CI=3.8-21.0). It was observed that there was significant differences in the genotype frequencies of the IFN-gamma +874 A/T at genotypic as well as at allelic level (p=0.0023 and p=0.001) among patients and controls. A significant difference was found in the frequency distribution between the two groups at IFN-gamma CA microsatellite polymorphism (p=0.0001) (CA(17))/(CA(17)). Combined analysis revealed a higher risk ( approximately 9-fold) in ESRD patients with high MIF -173 G/C and high INF-gamma +874 A/T protein producing phenotypes. CONCLUSIONS: These results highlight the role of MIF and IFN-gamma in ESRD disease.

Use of Multiplex Ligation-Dependent Probe Amplification (MLPA) in screening of subtelomeric regions in children with idiopathic mental retardation.

OBJECTIVE: To detect subtelomeric copy number variations (deletions and duplications) using Multiplex Ligation-Dependent Probe Amplification (MLPA) technique in children with idiopathic mental retardation. METHODS: All children presenting to the genetics out-patient department for evaluation of mental retardation or developmental delay over a period of two years, for whom no identifiable cause could be found by clinical evaluation, karyotyping, neuroimaging and other relevant investigations. RESULTS: In the present study, two cases deletions and one case of duplication were detected amongst 65 cases with idiopathic mental retardation/ global developmental delay. The overall detection rate is 4.6%. The detection rate is higher (13%) in children with facial dysmorphism. CONCLUSION: MLPA for subtelomeric regions is recommended for evaluation of children with idiopathic mental retardation/ global developmental delay were included in the study.

Presence of three different paternal lineages among North Indians: a study of 560 Y chromosomes.

BACKGROUND: The genetic structure, affinities, and diversity of the 1 billion Indians hold important keys to numerous unanswered questions regarding the evolution of human populations and the forces shaping contemporary patterns of genetic variation. Although there have been several recent studies of South Indian caste groups, North Indian caste groups, and South Indian Muslims using Y-chromosomal markers, overall, the Indian population has still not been well studied compared to other geographical populations. In particular, no genetic study has been conducted on Shias and Sunnis from North India. AIM: This study aims to investigate genetic variation and the gene pool in North Indians. SUBJECTS AND METHODS: A total of 32 Y-chromosomal markers in 560 North Indian males collected from three higher caste groups (Brahmins, Chaturvedis and Bhargavas) and two Muslims groups (Shia and Sunni) were genotyped. RESULTS: Three distinct lineages were revealed based upon 13 haplogroups. The first was a Central Asian lineage harbouring haplogroups R1 and R2. The second lineage was of Middle-Eastern origin represented by haplogroups J2*, Shia-specific E1b1b1, and to some extent G* and L*. The third was the indigenous Indian Y-lineage represented by haplogroups H1*, F*, C* and O*. Haplogroup E1b1b1 was observed in Shias only. CONCLUSION: The results revealed that a substantial part of today's North Indian paternal gene pool was contributed by Central Asian lineages who are Indo-European speakers, suggesting that extant Indian caste groups are primarily the descendants of Indo-European migrants. The presence of haplogroup E in Shias, first reported in this study, suggests a genetic distinction between the two Indo Muslim sects. The findings of the present study provide insights into prehistoric and early historic patterns of migration into India and the evolution of Indian populations in recent history.

Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh.

BACKGROUND: India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000-85,000 years before present (ybp). It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians) from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. RESULTS: We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst) were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119) as compared to the Asians (DA 0.1694 and Fst - 0.0718). The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20 geo-ethnic populations. The three phylogenetic assessments revealed that north Indians are clustering with Caucasians. CONCLUSION: The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and both upper caste and Muslim populations are genetically closer to the Caucasians.