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Abstract Background We report our experience of selecting tag SNPs in 35 genes involved in iron metabolism in a cohort study seeking to discover genetic modifiers of hereditary hemochromatosis. Methods We combined our own and publicly available resequencing data with HapMap to maximise our coverage to select 384 SNPs in candidate genes suitable for typing on the Illumina platform. Results Validation/design scores above 0.6 were not strongly correlated with SNP performance as estimated by Gentrain score. We contrasted results from two tag SNP selection algorithms, LDselect and Tagger. Varying r2 from 0.5 to 1.0 produced a near linear correlation with the number of tag SNPs required. We examined the pattern of linkage disequilibrium of three levels of resequencing coverage for the transferrin gene and found HapMap phase 1 tag SNPs capture 45% of the ≥ 3% MAF SNPs found in SeattleSNPs where there is nearly complete resequencing. Resequencing can reveal adjacent SNPs (within 60 bp) which may affect assay performance. We report the number of SNPs present within the region of six of our larger candidate genes, for different versions of stock genotyping assays. Conclusion A candidate gene approach should seek to maximise coverage, and this can be improved by adding to HapMap data any available sequencing data. Tag SNP software must be fast and flexible to data changes, since tag SNP selection involves iteration as investigators seek to satisfy the competing demands of coverage within and between populations, and typability on the technology platform chosen.

Background: We report our experience of selecting tag SNPs in 35 genes involved in iron metabolism in a cohort study seeking to discover genetic modifiers of hereditary hemochromatosis. Methods: We combined our own and publicly available resequencing data with HapMap to maximise our coverage to select 384 SNPs in candidate genes suitable for typing on the Illumina platform. Results: Validation/ design scores above 0.6 were not strongly correlated with SNP performance as estimated by Gentrain score. We contrasted results from two tag SNP selection algorithms, LDselect and Tagger. Varying r(2) from 0.5 to 1.0 produced a near linear correlation with the number of tag SNPs required. We examined the pattern of linkage disequilibrium of three levels of resequencing coverage for the transferrin gene and found HapMap phase 1 tag SNPs capture 45% of the >= 3% MAF SNPs found in SeattleSNPs where there is nearly complete resequencing. Resequencing can reveal adjacent SNPs ( within 60 bp) which may affect assay performance. We report the number of SNPs present within the region of six of our larger candidate genes, for different versions of stock genotyping assays. Conclusion: A candidate gene approach should seek to maximise coverage, and this can be improved by adding to HapMap data any available sequencing data. Tag SNP software must be fast and flexible to data changes, since tag SNP selection involves iteration as investigators seek to satisfy the competing demands of coverage within and between populations, and typability on the technology platform chosen.

The prevalence of iron-overload-related disease for C282Y homozygotes is examined. Findings reveal the development of iron-overload-related disease in a substantial proportion of men due to elevated levels of serum ferritin and transferrin saturation.

Hereditary haemochromatosis (HH) is an inherited disorder of iron absorption. It meets several of the key public health principles for population-based screening and is considered to be a test-case for public health genetics. However, there has been relatively little debate in the public health or wider community regarding the merits of population-based genetic screening for HH. Genetic susceptibility to HH occurs in about 1:200 people and although mortality is low (age-standardised rate 2.75/million), there are potentially serious clinical manifestations of iron overload. Regular venesection is a simple and effective treatment for early stage iron overload. DNA-based testing is available and iron overload may be identified using serum transferrin saturation and ferritin tests. However, there are important gaps in knowledge relevant to screening for HH. The limited data on penetrance of HFE genotypes, and thus the uncertain probability that genetically susceptible individuals will develop clinically significant disease, is a major impediment to population-based genetic screening. Clinical evidence supports treating early-stage disease but no randomised controlled trials of the effectiveness of screening in reducing the burden of disease have been conducted. In addition, the natural history of early stages of HH and factors that may modify progression are unclear. Two international consensus panels on HH concluded that there is insufficient evidence for population-based screening at present. We present recommendations to advance the debate on screening for HH in Australia.

Objectives. The purpose of this study was to describe the establishment of a national surveillance system for newly acquired human immunodeficiency virus (HIV) infection and present the first 3 years' results. Methods. All new cases of diagnosed HIV infection were reported to the national HIV surveillance center through state and territory health authorities. Information sought on each case included evidence of whether the infection had been newly acquired, defined by the diagnosis of HIV seroconversion illness or by the report of a negative or indeterminate HIV antibody test result occurring within the 12 months prior to diagnosis of infection. Results. Of 3602 reported cases of HIV infection in adults and adolescents newly diagnosed in Australia between 1991 and 1993,11.4% were identified as newly acquired. The majority (85%) of cases of newly diagnosed HIV infection occurred among men who reported homosexual contact, and 15% of these cases were identified as newly acquired. Average age at diagnosis was 31 years for cases of newly acquired infection and 34 years for other cases. Conclusions. Surveillance for newly acquired HIV infection has been established at a national level in Australia and provides valuable information for planning primary HIV prevention programs. (Am J Public Health. 1994;84:1923-1928), National surveillance data on newly acquired HIV infections in Australia appear to indicate a significant increase in the number of cases contracted between 1991 and 1993. Each health authority in Australia is required to report cases of HIV infection to the national HIV surveillance center. Data suggest there were 410 (11.4%) newly acquired HIV cases among a total of 3602 new infections reported between 1991 and 1993. Most of the cases involved men who were an average of 31 years of age and had homosexual contacts. The marked increase in new infections, from 131 in 1991 to 327 in 1993, may be due to higher reporting accuracy or reflect actual prevalence changes. The relatively low incidence of HIV infection linked to heterosexual activity and intravenous drug use is consistent with previous prevalence data in Australia.