DNA sequence variation and haplotype structure of the ICAM1 and TNF genes in 12 ethnic groups of India reveal patterns of importance in designing association studies.

We have examined the patterns of DNA sequence variation in and around the genes coding for ICAM1 and TNF, which play functional and correlated roles in inflammatory processes and immune cell responses, in 12 diverse ethnic groups of India. We aimed to (a) quantify the nature and extent of the variation, and (b) analyse the observed patterns of variation in relation to population history and ethnic background. At the ICAM1 and TNF loci, respectively, the total numbers of SNPs that were detected were 28 and 12. Many of these SNPs are not shared across ethnic groups and are unreported in the dbSNP or TSC databases, including two fairly common non-synonymous SNPs at positions 13487 and 13542 in the ICAM1 gene. Conversely, the TNF-376A SNP that is reported to be associated with susceptibility to malaria was not found in our study populations, even though some of the populations inhabit malaria endemic areas. Wide between-population variation in the frequencies of shared SNPs and coefficients of linkage disequilibrium have been observed. These findings have profound implications in case-control association studies.

Prenatal diagnosis of beta-thalassaemia and other haemoglobinopathies in India.

This paper reports prenatal diagnosis of 787 fetuses of beta-thalassaemia and other haemoglobinopathies in Indian high-risk communities. DNA based diagnosis was offered in the first, as well as the second trimester, in 489 pregnancies (with five twins) on fetal tissues such as chorionic villus (CV) and amniocytes using the amplification refractory mutation system (ARMS) and restriction fragment length polymorphism (RFLP) techniques. Two hundred and ninety-two women (with one twin), who either presented late in the second trimester or whose DNA diagnosis was not informative, were offered prenatal diagnosis using globin chain synthesis (GCS) on fetal blood cells. Maternal contamination of fetal DNA was ruled out by variable number tandem repeat (VNTR) analysis using sites in four different genes (Apo-B, D1S-80, Ig-JH and Ha-ras), while contamination of fetal blood was checked by a particle size distribution channelyzer. Using both techniques we were able to offer complete diagnosis in 99.8% cases. Out of 494 fetuses tested by DNA analysis, 135 were found to be normal, 201 were carriers, whereas 146 were affected. Out of 293 fetuses analysed by GCS, 215 were unaffected and 71 were affected. In this study, both fetuses were tested in twin pregnancies, of which three required selective termination of one fetus. Because of social, religious taboos and family influences, genetic counselling was found to be an important guideline for couples selecting options for prenatal diagnosis. Our experience suggests that because of late presentation by many couples to the diagnostic centres, in developing countries like India, both the techniques of DNA analysis and GCS should be made available at major referral centres for maximum benefit to couples.

The molecular basis of beta thalassaemia in Punjabi and Maharashtran Indians includes a multilocus aetiology involving triplicated alpha-globin loci.

We have analysed 201 beta-thalassaemia (beta-thal) genes from natives of the Punjab (156) and Maharashtra states of India and found the causative mutation in 200 of them. The most common beta-globin gene mutations differed significantly between these two groups and between these groups and Indian immigrants in the U.S.A. and the U.K. In the Punjabi Indians the IVS-1, nt 1 (G-T) mutation accounted for nearly one-quarter of beta-thal genes, whereas it was 5% or less in the other groups. Likewise, the cap + 1 mutation was much more prevalent in the Punjabis, whereas the nonsense codon 15 allele had a higher frequency in the Maharashtrans of the Bombay region. The common IVS-1, nt5 allele had a frequency of 60% of beta-thal genes in the Maharastrans, 35% in North American immigrants, and only 23% in the Punjabis. Two-thirds of all beta-thal genes in Punjab were found in the merchant caste (Khatri-Arora), whereas the menial caste (Shudra) was highly represented among those with beta-thal genes in Maharashtra. Two novel beta-globin alleles were each found once; a frameshift codon 55 (+A) in Maharashtrans and a frameshift codons 47-48 (+ATCT) in Punjabis. Of three Punjabi patients with beta-thal intermedia in whom only a single severe beta-globin gene mutation was found, two had six alpha-globin genes (homozygosity for a triplicated alpha-globin locus) instead of the normal alpha-globin gene number of four. Thus, these two individuals had a multilocus aetiology of beta-thal and their parents have the unusual recurrence risk of 1 in 8 for conceiving a third with beta-thal intermedia. Since 15% of 126 alpha-globin clusters studies in Punjabis contained either single (10%) or triplicated (5%) alpha-globin genes, the alpha-globin gene number is a frequent modifier of the phenotype of beta-thal in this ethnic group.

Thalassemia in Bombay: the role of medical genetics in developing countries.

This study of 200 families with thalassaemic children in Bombay showed that these children's treatment and needs place a significant, unavoidable and increasing demand on the public health services. At the same time, owing to the potentially large number of patients and the difficulties of long-term management, the situation is characterized by evasion of the problem, failure of planning, no provisions for prevention, and inadequate treatment leading to premature death among the affected children. The burden on such families is greater in developing than in developed countries because, besides caring for the chronically sick child, their lives are dominated by the high costs of treatment, often amounting to 20-30% of the income for many families. Seven mothers with no healthy children and 27 with only one healthy child had been sterilized; 90% of reproductive-age couples felt that prenatal diagnosis was a necessity. Also, ignorance and prejudice in the community led to social isolation for forty families. The experience in Europe shows that improved treatment is the key step in controlling thalassaemia. A well-organized day-transfusion service is cost-effective, soon restoring the children to health and leading to increased optimism. The formation of associations by parents could mobilize community support for improved treatment and prevention, and increase public awareness of the problem. Thus cost-effective management and prevention through screening, genetic counselling, and prenatal diagnosis are at least as important in the developing as in developed countries.

Thalassaemia in Bombay: The role of medical genetics in developing countries

This study of 200 families with thalassaemic children in Bombay showed that these children's treatment and needs place a significant, unavoidable and increasing demand on the public health services. At the same time, owing to the potentially large number of patients and the difficulties of long-term management, the situation is characterized by evasion of the problem, failure of planing, no provisions for prevention, and inadequate treatment leading to premature death among the affected children. The burden on such families is greater in developing than in developed countries because, besides caring for the chronically sick child, their lives are dominated by the high cost of treatment, often amounting to 20-30 per cent of the income for many families. Seven mothers with no healthy children and 27 with only one healthy child had been sterilized; 90 per cent of reproductive-age couples felt that prenatal diagnosis was a necessity. Also, ignorance and prejudice in the community led to social isolation for the forty families

The experience in Europe shows that improved treatment is the key step in controlling thalassaemia. A well-organized day-transfusion service is cost-effective, soon restoring the children to health and leading to increased optimism. The formulation of associations by parents could mobilize ...(AU)