Science, medicine, and the future: Postgenomic technologies: hunting the genes for common disorders

A modifiable microarray-based universal sensor: providing sample-to-results automation

A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA “universal” probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined “reporter” probes that are complementary at their 3′ termini to one or more of the universal probes and complementary to the target amplicons at their 5′ termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of Mycobacterium genitalium in a fully automated manner. Excellent correlation between traditional manual methods and the automated analysis performed by the workstation suggests that the system can provide a means to easily design and implement a variety of customized PCR-based assays. The system will be useful to researchers or clinical investigators seeking to develop their own user defined assays. As the U.S. FDA continues to pursue regulatory oversight of LDTs, the system would also allow labs to continue to develop compliant assays.

MRI of carriers of the apolipoprotein E e4 allele-evidence for structural differences in normal-appearing brain tissue in e4+ relative to e4- young adults

Apolipoprotein E is a protein involved in cholesterol and lipid transport. The gene coding for this protein has three different alleles: e2, e3 and e4. The e4 allele is recognised as a significant risk factor for the development of Alzheimer's disease in later life. Paradoxically, behavioural and functional evidence has demonstrated that the e4 allele may confer a cognitive advantage to the carrier in youth. In this article, a range of sophisticated and novel structural imaging techniques were used to identify subtle differences in the brain tissue of groups of young e4 and homozygous e3 carriers that might support this paradox. Using voxel-based morphometry of high-resolution structural MR images, we identified a higher white matter volume ratio in e4 relative to homozygous e3 carriers. Furthermore, diffusion tensor imaging and tract-based spatial statistics studies identified increases in axial diffusivity and mode of anisotropy in carriers of the e4 allele. In addition, quantitative magnetisation transfer data were analysed using tract-based spatial statistics. Evidence of a trend towards an increased transverse relaxation time of the bound proton pool was detected in e4 carriers, indicative of altered white matter composition. These changes were found to correlate with indices of cognitive performance across the two groups, supporting the notion that such subtle differences in white matter integrity may confer neural advantages that contribute to cognitive outcomes and, potentially, to performance differences, such as observed here in a test of verbal fluency and reported previously by other researchers. Copyright © 2013 John Wiley & Sons, Ltd.

The tenacity of the coronary candidate: how people with familial hypercholesterolaemia construct raised cholesterol and coronary heart disease

This article considers how people with familial hypercholesterolaemia (FH), an inherited high cholesterol condition, construct FH, high cholesterol and coronary heart disease (CHD). These data are used to explore some of the more prevalent claims about the expansion of genetic explanations for health and illness and its implications. The article draws on 31 interviews with people with FH undertaken at a large lipid clinic, a specialist outpatient clinic, in the north of England. I argue that interviewees tended to distinguish between their own `hereditary' high cholesterol and other people's `lifestyle induced' high cholesterol as a way to establish their own lack of culpability for their condition. At the same time, however, they strongly emphasized the need to take care of themselves, in particular by adhering to appropriate dietary and lifestyle regimes. Interviewees' accounts of CHD were not strongly framed in genetic terms, but tended to conform to established lay notions encapsulated by the idea of the `coronary candidate'. In sum, having FH does not seem to transform these people's understandings of the causes of high cholesterol or CHD. Their experiences were largely accommodated within existing lay frameworks. The analysis contributes to a growing reappraisal of transformative narratives about genetic knowledge.

Coexpression of gene polymorphisms involved in bilirubin production and metabolism

OBJECTIVE

The potential for genetically determined conditions to modulate the risk for developing neonatal hyperbilirubinemia is increasingly being recognized. The aims of this investigation were to (1) develop genotyping assays for an expanded panel of mutations and polymorphisms across 3 genes that are involved in bilirubin production and metabolism (glucose-6-phosphate dehydrogenase [G6PD], uridine diphosphate glucuronosyl transferase 1A1 [UGT1A1], and organic anion transporter polypeptide 1B1 [OATP1B1]) and (2) determine their allele frequencies in 450 anonymous DNA samples of US residents with ancestry from all of the major regions of the world.

METHODS

Genotyping assays were developed on the basis of allele-specific hybridization and melting peak analysis of the probe set and the match or mismatch template. Allele frequencies and the complexity of coinheritance of multiple genetic variants across G6PD, UGT1A1, and OATP1B1 genes in DNA samples from the DNA Polymorphism Discovery Resource of the National Human Genome Research Institute were determined by using this expanded panel.

RESULTS

Genetic polymorphisms of the UGT1A1 promoter, specifically the T-3279G phenobarbital responsive enhancer module and the (thymidine-adenine)(7) dinucleotide repeat TATAA box variants, were common. Similarly, OATP1B1 coding sequence gene variants were frequently observed. Moreover, in more than three quarters of the samples, >or=2 variants were detected, reflecting a high degree of polymorphism coexpression across these genes, including those who carried the African A(-) G6PD mutation.

CONCLUSIONS

We conclude that this expanded panel of mutations and polymorphisms can serve as an effective instrument to study the genetic architecture of hyperbilirubinemia and speculate an important role for genetic polymorphism coinheritance in determining hyperbilirubinemia risk in newborns.

A genetic future for coronary heart disease?

This paper is concerned with changing conceptions of genetic disease. It is based on an analysis of biomedical literature and focuses on the treatment of coronary heart disease (CHD) in four published commentary papers. The aim of this analysis is to explore the ways in which CHD is constructed as genetic and the place of genetic discourses in the wider set of ideas that circulate about the disease. This analysis is then used to consider some of the claims of the geneticisation thesis (Lippman 1991, 1992). The analysis suggests that a genetic vision for understanding and managing CHD has emerged, which has many of the hallmarks of the geneticisation imagined by Lippman. However, a number of alternative and competing models of CHD are also supported within the biomedical discourse. These are related to the different disciplines with a stake in the field of CHD, and their struggles for authority. In conclusion, it is suggested that the geneticisation thesis, as a universal claim, is at odds with the diffuse and distributed nature of biomedical knowledge and practice. Rather than analysing geneticisation in a literal way, it may be more fruitful to see the thesis, itself, as a form of boundary work (Gieryn 1983).

Pharmacogenomics and nutrigenomics: synergies and differences

The success of the Human Genome Project and the spectacular development of broad genomics tools have catalyzed a new era in both medicine and nutrition. The terms pharmacogenomics and nutrigenomics are relatively new. Both have grown out of their genetic forbears as large-scale genomics technologies have been developed in the last decade. The aim of both disciplines is to individualize or personalize medicine and food and nutrition, and ultimately health, by tailoring the drug or the food to the individual genotype. This review article provides an overview of synergies and differences between these two potentially powerful science areas. Individual genetic variation is the common factor on which both pharmacogenomics and nutrigenomics are based. Each human is genetically (including epigenetics) unique and phenotypically distinct. One of the expectations of both technologies is that a wide range of gene variants and related single-nucleotide polymorphism will be identified as to their importance in health status, validated and incorporated into genotype based strategies for the optimization of health and the prevention of disease. Pharmacogenomics requires rigorous genomic testing that will be regulated and analyzed by professionals and acted on by medical practitioners. As further information is obtained on the importance of the interaction of food and the human genotype in disease prevention and health, pharmacogenomics can provide an opportunity driver for nutrigenomics. As we move from disease treatment to disease prevention, the two disciplines will become more closely aligned.

Association of hypertension with single nucleotide polymorphisms in the quantitative trait locus for abdominal obesity-metabolic syndrome on chromosome 17

Genome scan in Chinese revealed an association of blood pressure with the microsatellite marker D17S1303, which lies in a quantitative trait locus for the abdominal obesity-metabolic syndrome (AOMS2) at 17p12 on chromosome 17. We previously reported that D17S1303 was associated with hypertension and obesity. Therefore, we studied 10 single nucleotide polymorphisms (SNP) within 3 kb of D17S1303. One hundred and eighty hypertensive subjects (91 men, 89 women, age 53+/-12 years) and 180 normotensive matched controls (91 men, 89 women, age 52+/-11) were genotyped using the Sequenom genotyping platform. Allelic frequencies in these Chinese subjects differed from those reported for Caucasians. Three SNPs (rs11656507, rs1357926, rs852319) were homozygous in our subjects. The genotype frequencies of rs852320, rs852321 and rs852322 did not differ between hypertensive and normotensive subjects. However, there were significant differences for rs1525402 (P=0.048), rs2692343 (P=0.022), rs2692344 (P=0.017) and rs2321313 (P=0.028). A four-locus haplotype comprising G at rs1525402, C at rs2692343, C at rs2692344 and G at rs2321313 was associated with lower systolic blood pressure (P=0.023) and normotension (P=0.048). Our results provide further evidence that there is a gene, as yet unidentified, influencing blood pressure in the vicinity of D17S1303 in a quantitative trait locus for abdominal obesity-metabolic syndrome at 17p12.

Vitamin D receptor gene polymorphisms in patients with urolithiasis

Urolithiasis is a multifactorial disease, the onset and severity of which is influenced by both genetic and environmental factors. This study represents an investigation of the role of vitamin D receptor (VDR) gene polymorphisms (ApaI, BsmI, and TaqI) and combined genotypes in urolithiasis in a Turkish population. We studied 110 patients with urinary stones and 150 control subjects. The polymorphic regions were amplified using polymerase chain reaction, followed by digestion with restriction enzymes BsmI, ApaI, and TaqI, and analyzed electrophoretically. Genotype and allele frequencies were calculated, and the association with urolithiasis, family history, and recurrence of stone was investigated. Our data provide no evidence for an association between urolithiasis and VDR ApaI, BsmI, and TaqI genotypes. We also analyzed the effects of VDR ApaI, BsmI, and TaqI genotypes in combination; the "GTT" VDR haplotype, constructed from three adjacent restriction fragment length polymorphisms was overrepresented among the urolithiasis patients. However, no significant differences between heterozygous carriers (OR 1.302; 95% CI 0.527-3.215) and homozygous carriers (OR 3.39; 95% CI 0.719-15.985) were observed in our study population. A significant association was found only between the ApaI polymorphism and family history (P=0.017; chi (2)=5.657). Our data indicate that the VDR ApaI, BsmI, and TaqI polymorphisms do not confer a significant risk for urolithiasis.

Risk factors of atherosclerosis: A review of genetic epidemiology data from a Serbian population

Determining common risk factors for the onset and progression of atherosclerosis and cardiovascular diseases, which are known to be multi-factorial and polygenic diseases, represents a challenge for medicine in the future. In recent years, there have been breakthroughs in the determination of pathogenesis, risk estimating methodologies, modifications of genetic risk in prophylaxis and in establishing new therapeutic targets in pharmacology. The role of genetic epidemiology is to provide necessary data about genetic characteristics of different populations, as well as gene-gene and gene-environment interactions, that lead to the development of diseases. The aim is to define high-risk haplotypes and primary targets for a new generation of pharmaceutical products and tools designed for the diagnosis and therapy of these disorders. The present review provides examples from the authors' genetic epidemiology studies regarding the association of candidate genes with risk factors of atherosclerosis, such as dyslipidemias, hypertension and diabetes mellitus, in a Serbian population, along with basic assumptions that come with this type of research. The main results of these studies are discussed, as well as problems that should be taken into consideration in future evaluations of disease risk in a population.

Deficiency of knowledge of genetics and genetic tests among general practitioners, gynecologists, and pediatricians: A global problem

PURPOSE

The objective of this study was to assess knowledge of genetics and awareness of genetic tests among Dutch general practitioners (GPs), gynecologists (GYNs), and pediatricians (PEDs), as well as factors influencing their knowledge and awareness.

METHODS

An anonymous questionnaire inquiry was used, validated with a sample of 52 clinical geneticists (CGs). The study was carried out in primary care (general practice) and secondary care (general and university hospitals) in The Netherlands. A random sample of 200 GPs, 300 GYNs, and 265 PEDs received a questionnaire. In addition, all registered CGs (58) received a questionnaire for validation. In total, 122 GPs, 187 GYNs, 164 PEDs, and 52 CGs returned a completed questionnaire. The main outcome measures were differences in knowledge scores between physicians working in different disciplines and factors influencing these scores.

RESULTS

Knowledge scores of GPs (mean 64% correct answers, 61%-66% [95% confidence interval]), GYNs (mean 75% correct answers, 73%-76% [95% confidence interval]), and PEDs (mean 81% correct answers, 79%-82% [95% confidence interval]) were lower than those in the CG validation group (mean 95% correct answers, 94%-96% [95% confidence interval]). The 5th percentile of GPs, GYNs, and PEDs was at approximately 40%, 52% and 62% correct answers, respectively. There was a specific lack of knowledge about DNA testing. In addition to specialty, important factors positively associated with the knowledge scores of nongeneticists are more recent graduation, having taken an elective course in genetics, and providing genetic counseling in their own practice.

CONCLUSION

The overall knowledge levels of genetics in many nongeneticist health care providers show clear deficiencies. This is in line with reports from other countries, showing that these deficiencies are a global problem.

Family, kinship, memory and temporality in the age of the new genetics

The new genetics has now become an integral part of contemporary biomedicine, promising great advances in alleviating disease. Like any scientific endeavor, beliefs in the new genetics tend to give new meanings to people's lives and therefore have significant implications for people's lived experience. Drawing on fieldwork in the USA and research in various literatures, the aim of this article is to explore the role the new genetics plays in mainstream American society as revealed in people's narratives of their families' medical histories. An anthropological analysis of these narratives illuminates multilayered cultural meanings of genetic inheritance and the role biomedical conceptualizations play not only in explaining disease etiologies and treatment, but also in addressing concerns that bear on the postmodern experience of family, kinship, choice, memory, time-space, relatedness, sociality and immortality.

Association of essential hypertension with a microsatellite marker on chromosome 17

Hypertension is related to sodium intake, and many patients with essential hypertension are overweight and have the metabolic syndrome. We therefore studied microsatellite markers close to the thiazide-sensitive Na-Cl cotransporter on chromosome 16 and a quantitative trait locus for abdominal obesity-metabolic syndrome (AOMS2) on chromosome 17, which have been found to be linked to hypertension in a previous genome scan in Chinese. There were 84 hypertensive subjects (44 men, 40 women, age 53+/-13 years) and 88 normotensive controls (40 men, 48 women, age 54+/-13 years) recruited. Specific oligonucleotide primers were used to amplify genomic DNA spanning the microsatellite markers D16S3396 and D17S1303 that consist of ATA and GATA repeats, respectively. We did not find any association between D16S3396 and blood pressure. In contrast, the distribution of D17S1303 genotypes differed between hypertensive subjects and normal controls (P = 0.014). The number of GATA repeats correlated inversely with diastolic blood pressure (r = -0.18, P = 0.02) and body mass index (r = -0.12, P = 0.01). Nine GATA repeats in D17S1303 were associated with hypertension (OR 2.19, 95% CI 1.08-4.44, P = 0.027), while 14 GATA repeats were associated with normotension (OR 0.26, 95% CI 0.10-0.66, P = 0.002). The diastolic blood pressure in those with or without the (GATA)9 allele was 85.9+/-13.6 and 79.2+/-13.6 mmHg respectively (P = 0.01), and in those with or without the (GATA)14 allele it was 73.8+/-11.0 and 81.8+/-14.0 mmHg respectively (P = 0.003). Our results provide further evidence that a gene predisposing to hypertension in Chinese is in the vicinity of the microsatellite D17S1303.

Newborn screening: new developments, new dilemmas

Scientific and technological advances are lending pressure to expand the scope of newborn screening. Whereas this has great potential for improving child health, it also challenges our current perception of such programmes. Standard newborn screening programmes are clearly justified by the fact that early detection and treatment of affected individuals avoids significant morbidity and mortality. However, proposals to expand the scope and complexity of such testing are not all supported by a similar level of evidence for unequivocal benefit. We argue that screening for genetic susceptibility to complex disorders is inherently different from standard screening and, while of potential value, must be considered separately from conventional testing.

Genetics and public health--evolution, or revolution?

During the 19th and early 20th century, public health and genetics shared common ground through similar approaches to health promotion in the population. By the mid-20th century there was a division between public health and genetics, with eugenicists estranged and clinical genetics focused on single gene disorders, usually only relevant to small numbers of people. Now through a common interest in the aetiology of complex diseases such as heart disease and cancer, there is a need for people working in public health and genetics to collaborate. This is not a comfortable convergence for many, particularly those in public health. Nine main concerns are reviewed: fear of eugenics; genetic reductionism; predictive power of genes; non-modifiable risk factors; rights of individuals compared with populations; resource allocation; commercial imperative; discrimination; and understanding and education. This paper aims to contribute to the thinking and discussion about an evolutionary, multidisciplinary approach to understanding, preventing, and treating complex diseases.

The changing legal and conceptual shape of health care privacy

The contributions of Professor Bernard Dickens to health law and bioethics span the era in which these fields have emerged as distinct domains of teaching, scholarship and professional and public conversation. Neither field exists in a vacuum. The concerns of bioethics, like the content of health law, are a product of social forces. The bureaucratization of medical care, the possibilities and uncertainties created by developments in medical technology, not to mention glaring health inequalities, have been destabilizing forces in medicine. Writing in 1974, American sociologist Renée Fox noted that medicine had reached “a stage of development characterized by diffuse ethical and existential self-consciousness.” This new medical introspection was evidenced by intense engagement with issues of biomedical regulation, and with the growth of professional codes and processes for resolving value-laden issues within clinical settings.

While sometimes described as a process or site for discussion and “engagement,” bioethics evolved rapidly into a domain of governance, with direct implications for clinical practice.

Association of TAP2 gene polymorphisms in Chinese patients with rheumatoid arthritis

The aim of this study was to investigate the association between the polymorphism of transporters associated with antigen processing ( TAP1/TAP2) genes and rheumatoid arthritis in Chinese patients. A total of 100 RA patients and 99 healthy control subjects were enrolled. Analyses with polymerase chain reaction (PCR) based restrictions were used to identify the polymorphisms of the TAP1 and TAP2 genes, which were mapped on chromosome 6. There was a significant difference in the distribution of the TAP2 gene codon 565 polymorphism frequency between the RA patients and healthy control subjects ( p<0.001). The odds ratio for the risk of the 'A' allele in RA patients was 1.60 (95% CI: 0.82-2.92). No statistical associations in the distribution of the TAP1 gene polymorphism frequency were found between RA patients and controls. There were some physical links found between TAP1/TAP2 gene polymorphism loci. However, there was no linkage observed from TAP1/TAP2 gene polymorphisms and HLA-DRB1*04 between RA patients and healthy controls. We concluded that the TAP2 gene codon 565 'A' allele was associated with RA in Chinese patients in Taiwan. Individuals possessing the 'A' allele had a higher incidence of RA. A lack of association of TAP1 gene polymorphisms between RA patients and healthy individuals was noted. The results of this study provide genetic evidence that TAP2 gene codon 565 polymorphism may play a role in RA.

Houseofficers' reactions to media coverage about the sequencing of the human genome

After the announcement that sequencing of the human genome was nearly complete, media coverage was extensive. In light of ample evidence that the media are a primary source of health and science information, even for health professionals, media portrayals are often inaccurate or misleading, and discoveries that emanate from sequencing the human genome are likely to influence future health care, it is important to assess physicians' interpretations of media coverage about the human genome announcement. This paper describes the reactions of a sample of new physicians in the United States to this announcement, as well as the content of the stories they read or heard. Semi-structured surveys were distributed to all incoming houseofficers during Orientation at one major academic medical center. Eighty-one percent of 190 houseofficers returned a survey; 123 completed surveys were analyzed. Fifty-four percent of respondents thought the media message was only positive and 21% thought it was negative or mixed. Participants who reported radio as their media source were less likely to recall positive messages (p<0.05). Sixty-five percent and 76%, respectively, had positive perceptions of the impact of the accomplishment on people and on the medical profession. Overall, 48% were enthusiastic and 52% were guarded about the accomplishment. Enthusiasm was related to being an adult primary care houseofficer (p=0.07) or to having heard about it on television or in the newspaper (p<0.05). Of the 36 stories analyzed, newspaper and television reports focused more on medical implications and radio reports focused more on ethical issues. The degree of enthusiasm about the accomplishment reflects the content of the media coverage, and, at least for adult primary care houseofficers, probably reflects the increasing relevance of genetic discoveries to medical practice. Since physicians obtain much of their health and science information from the media, they can play an instrumental role in helping their patients interpret media coverage of advances in genetics and their impact on health care. However, this will require that physicians develop an appreciation of the newsmaking process, and how subtle interactions between politics, the media and science influence the "framing" of media coverage.

Genetics education for primary-care providers

In an era of growing knowledge about genetics and health, primary-care physicians will have increasing responsibility for evaluating genetic risk and using genetic tests. Although most have little knowledge of genetics, their expertise in the prudent use of technology is relevant to the task. Successful educational programmes will need to forge partnerships between primary care and genetics.

Typing of multiple single nucleotide polymorphisms in cytokine and receptor genes using SNaPshot

Associations have been described between polymorphisms in cytokine genes and severity of autoimmune diseases, outcome of infectious disease, and outcome following transplantation. Many methods now exist for typing single nucleotide polymorphisms (SNPs) and these can be applied to typing cytokine gene and cytokine receptor gene variation. A system for typing multiple cytokine and receptor gene polymorphisms using a primer extension method, SNaPshot (Applied Biosystems, Foster City, CA, USA), has been assessed. The development of this methodology may enable other laboratories to type for cytokine SNPs in different populations and facilitate research into the effect of genetic polymorphism in the cytokine network in transplantation and disease.

Urokinase gene 3'-UTR T/C polymorphism is associated with urolithiasis

OBJECTIVES

To study single nucleotide polymorphisms to investigate the possibility that urokinase is involved in the formation of urolithiasis, which, although lacking in genetic evidence, has been previously proposed.

METHODS

A total of 153 patients with recurrent calcium stones and 105 controls were studied. Polymerase chain reaction-based restriction analysis was used to identify the C/T polymorphism of the urokinase gene, which is mapped on the 3'-untranslated region (3'-UTR) on chromosome 10.

RESULTS

A significant difference was found in the distribution of the urokinase gene 3'-UTR C/T polymorphism frequency between patients with stones and normal controls (P <0.05). The odds ratio for the risk of the "T" allele in patients with stones was 3.088 (95% confidence interval 1.06 to 8.99).

CONCLUSIONS

The results of our study demonstrate that the urokinase gene 3'-UTR "T" allele is associated with calcium stone disease. Individuals possessing the "T" allele have a higher incidence of calcium oxalate stone disease. The results of this study provide genetic evidence that the urokinase gene may play a role in stone formation.