Healthcare System Priorities for Successful Integration of Genomics: An Australian Focus

This paper examines key considerations for the successful integration of genomic technologies into healthcare systems. All healthcare systems strive to introduce new technologies that are effective and affordable, but genomics offers particular challenges, given the rapid evolution of the technology. In this context we frame internationally relevant discussion points relating to effective and sustainable implementation of genomic testing within the strategic priority areas of the recently endorsed Australian National Health Genomics Policy Framework. The priority areas are services, data, workforce, finances, and person-centred care. In addition, we outline recommendations from a government perspective through the lens of the Australian health system, and argue that resources should be allocated not to just genomic testing alone, but across the five strategic priority areas for full effectiveness

A meta-analysis of the associations between common variation in the PDE8B gene and thyroid hormone parameters, including assessment of longitudinal stability of associations over time and effect of thyroid hormone replacement

Objective Common variants in PDE8B are associated with TSH but apparently without any effect on thyroid hormone levels that is difficult to explain. Furthermore, the stability of the association has not been examined in longitudinal studies or in patients on levothyroxine (l-T4). Design Totally, four cohorts were used (n=2557): the Busselton Health Study (thyroid function measured on two occasions), DEPTH, EFSOCH (selective cohorts), and WATTS (individuals on l-T4). Methods Meta-analysis to clarify associations between the rs4704397 single nucleotide polymorphism in PDE8B on TSH, tri-iodothyronine (T3), and T4 levels. Results Meta-analysis confirmed that genetic variation in PDE8B was associated with TSH (P=1.64×10−10 0.20 s.d./allele, 95% confidence interval (CI) 0.142, 0.267) and identified a possible new association with free T4 (P=0.023, −0.07 s.d./allele, 95% CI −0.137, −0.01), no association was seen with free T3 (P=0.218). The association between PDE8B and TSH was similar in 1981 (0.14 s.d./allele, 95% CI 0.04, 0.238) and 1994 (0.20 s.d./allele, 95% CI 0.102, 0.300) and even more consistent between PDE8B and free T4 in 1981 (−0.068 s.d./allele, 95% CI −0.167, 0.031) and 1994 (−0.07 s.d./allele, 95% CI −0.170, 0.030). No associations were seen between PDE8B and thyroid hormone parameters in individuals on l-T4. Conclusion Common genetic variation in PDE8B is associated with reciprocal changes in TSH and free T4 levels that are consistent over time and lost in individuals on l-T4. These findings identify a possible genetic marker reflecting variation in thyroid hormone output that will be of value in epidemiological studies and provides additional evidence that PDE8B is involved in TSH signaling in the thyroid

Genomic Testing for Human Health and Disease Across the Life Cycle: Applications and Ethical, Legal, and Social Challenges

The expanding use of genomic technologies encompasses all phases of life, from the embryo to the elderly, and even the posthumous phase. In this paper, we present the spectrum of genomic healthcare applications, and describe their scope and challenges at different stages of the life cycle. The integration of genomic technology into healthcare presents unique ethical issues that challenge traditional aspects of healthcare delivery. These challenges include the different definitions of utility as applied to genomic information; the particular characteristics of genetic data that influence how it might be protected, used and shared; and the difficulties applying existing models of informed consent, and how new consent models might be needed

A population-based study of the clinical expression of the hemochromatosis gene

Background and Methods: Hereditary hemochromatosis is associated with homozygosity for the C282Y mutation in the hemochromatosis (HFE) gene on chromosome 6, elevated serum transferrin saturation, and excess iron deposits throughout the body. To assess the prevalence and clinical expression of the HFE gene, we conducted a population-based study in Busselton, Australia. In 1994, we obtained blood samples for the determination of serum transferrin saturation and ferritin levels and the presence or absence of the C282Y mutation and the H63D mutation (which may contribute to increased hepatic iron levels) in 3011 unrelated white adults. We evaluated all subjects who had persistently elevated transferrin-saturation values (45 percent or higher) or were homozygous for the C282Y mutation. We recommended liver biopsy for subjects with serum ferritin levels of 300 ng per milliliter or higher. The subjects were followed for up to four years. Results: Sixteen of the subjects (0.5 percent) were homozygous for the C282Y mutation, and 424 (14.1 percent) were heterozygous. The serum transferrin saturation was 45 percent or higher in 15 of the 16 who were homozygous; in 1 subject it was 43 percent. Four of the homozygous subjects had previously been given a diagnosis of hemochromatosis, and 12 had not. Seven of these 12 patients had elevated serum ferritin levels in 1994; 6 of the 7 had further increases in 1998, and 1 had a decrease, although the value remained elevated. The serum ferritin levels in the four other homozygous patients remained in the normal range. Eleven of the 16 homozygous subjects underwent liver biopsy; 3 had hepatic fibrosis, and 1, who had a history of excessive alcohol consumption, had cirrhosis and mild microvesicular steatosis. Eight of the 16 homozygous subjects had clinical findings that were consistent with the presence of hereditary hemochromatosis, such as hepatomegaly, skin pigmentation, and arthritis. Conclusions: In a population of white adults of northern European ancestry, 0.5 percent were homozygous for the C282Y mutation in the HFE gene. However, only half of those who were homozygous had clinical features of hemochromatosis, and one quarter had serum ferritin levels that remained normal over a four-year period

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry

The cost-effectiveness of point of care testing in a general practice setting: results from a randomised controlled trial

Extent: 11p.Background: While point of care testing (PoCT) for general practitioners is becoming increasingly popular, few studies have investigated whether it represents value for money. This study aims to assess the relative cost-effectiveness of PoCT in general practice (GP) compared to usual testing practice through a pathology laboratory. Methods: A cost-effectiveness analysis based on a randomized controlled trial with 4,968 patients followed up for 18 months and fifty-three general practices in urban, rural and remote locations across three states in Australia. The incremental costs and health outcomes associated with a clinical strategy of PoCT for INR, HbA1c, lipids, and ACR were compared to those from pathology laboratory testing. Costs were expressed in year 2006 Australian dollars. Nonparametric bootstrapping was used to generate 95% confidence intervals. Results: The point estimate of the total direct costs per patient to the health care sector for PoCT was less for ACR than for pathology laboratory testing, but greater for INR, HbA1c and Lipids, although none of these differences was statistically significant. PoCT led to significant cost savings to patients and their families. When uncertainty around the point estimates was taken into account, the incremental cost-effectiveness ratio (ICER) for PoCT was found to be unfavourable for INR, but somewhat favourable for ACR, while substantial uncertainty still surrounds PoCT for HbA1c and Lipids. Conclusions: The decision whether to fund PoCT will depend on the price society is willing to pay for achievement of the non-standard intermediate outcome indicator. Trial registration: Australian New Zealand Clinical Trial Registry ACTRN12605000272695Caroline O Laurence, John R Moss, Nancy E Briggs, Justin J Beilby for PoCT Trial Management Grou

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Relationship between wearer prickle response with fibre and garment properties and Wool ComfortMeter assessment

The prickle evoked by 48 knitted fabrics was assessed by wearers under a defined evaluation protocol. The relationship between the average wearer prickle score and known properties of constituent fibre, yarns and fabrics and fabric evaluation using the Wool ComfortMeter (WCM) was determined using linear modelling. After log transformation, the best model accounted for 87.7% of the variance. The major share of variation could be attributed to differences between mean fibre diameter (MFD) and WCM values. Low prickle scores were linearly associated with lower MFD, lower WCM and lower yarn linear density. There was an indication that yarn twist affected prickle scores and that fabrics composed of cotton evoked less prickle. Measures of fibre diameter distribution or coarse fibre incidence and other fabric properties were not significant. The analysis indicates that wool garments can be constructed to keep wearer assessed prickle to barely detectable levels and textile designers can manipulate a range of parameters to achieve similar wearer comfort responses

APOE ε2 resilience for Alzheimer’s disease is mediated by plasma lipid species: Analysis of three independent cohort studies

Introduction The apolipoprotein E (APOE) genotype is the strongest genetic risk factor for late-onset Alzheimer\u27s disease. However, its effect on lipid metabolic pathways, and their mediating effect on disease risk, is poorly understood. Methods We performed lipidomic analysis on three independent cohorts (the Australian Imaging, Biomarkers and Lifestyle [AIBL] flagship study, n = 1087; the Alzheimer\u27s Disease Neuroimaging Initiative [ADNI] 1 study, n = 819; and the Busselton Health Study [BHS], n = 4384), and we defined associations between APOE ε2 and ε4 and 569 plasma/serum lipid species. Mediation analysis defined the proportion of the treatment effect of the APOE genotype mediated by plasma/serum lipid species. Results A total of 237 and 104 lipid species were associated with APOE ε2 and ε4, respectively. Of these 68 (ε2) and 24 (ε4) were associated with prevalent Alzheimer\u27s disease. Individual lipid species or lipidomic models of APOE genotypes mediated up to 30% and 10% of APOE ε2 and ε4 treatment effect, respectively. Discussion Plasma lipid species mediate the treatment effect of APOE genotypes on Alzheimer\u27s disease and as such represent a potential therapeutic target