Genetics, statistics and human disease: analytical retooling for complexity

Molecular biologists and geneticists alike now acknowledge that most common human diseases with a genetic component are likely to have complex etiologies. Yet despite this belief, many statistical geneticists continue applying, in slightly new and different ways, methodologies that were developed to dissect much simpler etiologies. In this article, we characterize, with examples, the various factors that can complicate genetic analysis and demonstrate their shared features and how they affect genetic analysis. We describe a variety of approaches that are currently available, revealing methodological gaps and suggesting new directions for method development. Finally, we propose a comprehensive two-step approach to analysis that systemically addresses the different genetic factors that are likely to underlie complex diseases.     

综述:基于人多潜能干细胞的人类疾病研究与治疗

人多潜能干细胞(hPSC)包括人胚胎干细胞(hESC)和诱导性多潜能干细胞(hiPSC),理论上具有分化成为人类所有细胞类型的能力.基于hPSC的基因打靶技术,不但可以纠正人基因组中的遗传突变用于细胞治疗,还可以通过反向遗传学的方式向hPSC引入疾病特异的突变.将携带人类疾病遗传基因的hPSC分化为特定的细胞类型,在理论上可以在体外模拟人类疾病的发生,研究人类疾病发生的机理,并建立体外筛选平台寻找治疗性药物.基因编辑和干细胞技术的结合将为人类疾病的机制研究和再生医学治疗带来革命性的突破.     

Linkage disequilibrium--understanding the evolutionary past and mapping the medical future

Linkage disequilibrium--the nonrandom association of alleles at different loci--is a sensitive indicator of the population genetic forces that structure a genome. Because of the explosive growth of methods for assessing genetic variation at a fine scale, evolutionary biologists and human geneticists are increasingly exploiting linkage disequilibrium in order to understand past evolutionary and demographic events, to map genes that are associated with quantitative characters and inherited diseases, and to understand the joint evolution of linked sets of genes. This article introduces linkage disequilibrium, reviews the population genetic processes that affect it and describes some of its uses. At present, linkage disequilibrium is used much more extensively in the study of humans than in non-humans, but that is changing as technological advances make extensive genomic studies feasible in other species.     

Evolution and medicine in undergraduate education: a prescription for all biology students

The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine.     

Problems and possibilities in the differential diagnosis of Syndrome Spinocerebellar Ataxia

Differential diagnosis in neurologic patients with spinocerebellar syndrome is complex as a result of the great degree of variability in phenotypic and genetic aspects of more than 200 nosological entities. In the past decade, genetic etiology has been discovered in part of the diseases and the term 'spinocerebellar ataxia' has become, from a neurologic point of view, a loose definition applied to a group of autosomal dominant diseases. Topical extensive literature about differential diagnoses of ataxias usually refers to genetics classification or is produced by a group of radiologists, elektrophysiologists and biologists as well as others in the field. A further problem is that the majority of studies do not take into account other acquired illnesses and diseases which may fundamentally alter the symptomology and course of a primary disease, not to mention the possibility of concomitancy in hereditary diseases. The following article was prompted by daily contact with ataxic patients and related issues raised by colleagues; its goal is to clarify problems faced by child neurologists and neurologists in clinical practice.     

Enteric nervous system development and Hirschsprung's disease: advances in genetic and stem cell studies

The enteric nervous system (ENS) has been explored by developmental neurobiologists and medical researchers for decades. Whereas developmental biologists have been unravelling the molecular mechanisms underlying the migration, proliferation and differentiation of the neural crest derivatives that give rise to the ENS, human geneticists have been uncovering the genetic basis for diseases of the ENS, notably Hirschsprung's disease. Here we discuss the exciting recent advances, including novel transgenic and genetic tools, a broadening range of model organisms, and the pursuit of ENS stem cells as a therapeutic tool, that are bringing these fields closer together.     

Network-Based Study Reveals Potential Infection Pathways of Hepatitis-C Leading to Various Diseases

Protein-protein interaction network-based study of viral pathogenesis has been gaining popularity among computational biologists in recent days. In the present study we attempt to investigate the possible pathways of hepatitis-C virus (HCV) infection by integrating the HCV-human interaction network, human protein interactome and human genetic disease association network. We have proposed quasi-biclique and quasi-clique mining algorithms to integrate these three networks to identify infection gateway host proteins and possible pathways of HCV pathogenesis leading to various diseases. Integrated study of three networks, namely HCV-human interaction network, human protein interaction network, and human proteins-disease association network reveals potential pathways of infection by the HCV that lead to various diseases including cancers. The gateway proteins have been found to be biologically coherent and have high degrees in human interactome compared to the other virus-targeted proteins. The analyses done in this study provide possible targets for more effective anti-hepatitis-C therapeutic involvement.     

Measuring the reinforcing strength of abused drugs

Animal models for human diseases are highly valued for their utility in developing new therapies. Animals have long provided suitable platforms for the development of innovative surgical procedures and for the study of disease states that are relatively easy to produce in otherwise healthy animals, such as diabetes or hypertension. Increasingly, new strains of animals susceptible to common human illnesses are being introduced into medical research, promising new inroads into the treatment of a variety of organic disorders. Despite these advances in model development, psychiatric disorders, by and large, remain among the hardest to induce experimentally, and the search for reasonable animal procedures to study diseases of the mind is an ongoing challenge for experimental biologists. An exception to this limitation, however, comes in the study of drug abuse. Major developments in this area of research over the last several decades have steadily advanced our ability to identify pharmacological, genetic, and environmental determinants that contribute to the development of drug dependence and addictive behavior.     

综述: 人类早衰症的发病机制及干预方法

衰老是一种在细胞和组织水平逐渐发生功能衰退的过程.早衰症是一类罕见的人类遗传性疾病,以加速衰老为特征.对早衰症的研究有助于理解人类衰老的生理过程,对衰老相关疾病的防治具有借鉴意义.成人早衰症和儿童早衰症是两种著名的人类早衰症,本文将综述这两种早衰症的发病机制及干预方法.     

DR-GAS: A database of functional genetic variants and their phosphorylation states in human DNA repair systems

We present DR-GAS¹, a unique, consolidated and comprehensive DNA repair genetic association studies database of human DNA repair system. It presents information on repair genes, assorted mechanisms of DNA repair, linkage disequilibrium, haplotype blocks, nsSNPs, phosphorylation sites, associated diseases, and pathways involved in repair systems. DNA repair is an intricate process which plays an essential role in maintaining the integrity of the genome by eradicating the damaging effect of internal and external changes in the genome. Hence, it is crucial to extensively understand the intact process of DNA repair, genes involved, non-synonymous SNPs which perhaps affect the function, phosphorylated residues and other related genetic parameters. All the corresponding entries for DNA repair genes, such as proteins, OMIM IDs, literature references and pathways are cross-referenced to their respective primary databases. DNA repair genes and their associated parameters are either represented in tabular or in graphical form through images elucidated by computational and statistical analyses. It is believed that the database will assist molecular biologists, biotechnologists, therapeutic developers and other scientific community to encounter biologically meaningful information, and meticulous contribution of genetic level information towards treacherous diseases in human DNA repair systems. DR-GAS is freely available for academic and research purposes at: http://www.bioinfoindia.org/drgas.     

Elevation of urinary hyaluronic acid in Werner's syndrome and progeria

Werner's syndrome and Hutchinson-Gilford progeria syndrome (progeria) are human genetic diseases which may serve as models for the study of premature aging. The basic defects underlying these diseases are unknown. An abnormally high level of urinary hyaluronic acid (HA) excretion has been previously reported in several Werner's and one progeria subject, all from Japan. To determine if a high HA level is a reliable marker for these diseases, we quantitated the urinary excretion of HA in three progeria subjects, one subject with an atypical progeroid syndrome, and a Werner's syndrome subject. Compared to controls, the total urinary HA was found to be markedly increased in the three progeria samples and in the Werner's syndrome sample. These findings support the previous observations indicating elevated HA may be a specific marker for these diseases.     

Detecting short tandem repeats from genome data: opening the software black box

Short tandem repeats, specifically microsatellites, are widely used genetic markers, associated with human genetic diseases, and play an important role in various regulatory mechanisms and evolution. Despite their importance, much is yet unknown about their mutational dynamics. The increasing availability of genome data has led to several in silico studies of microsatellite evolution which have produced a vast range of algorithms and software for tandem repeat detection. Documentation of these tools is often sparse, or provided in a format that is impenetrable to most biologists without informatics background. This article introduces the major concepts behind repeat detecting software essential for informed tool selection. We reflect on issues such as parameter settings and program bias, as well as redundancy filtering and efficiency using examples from the currently available range of programs, to provide an integrated comparison and practical guide to microsatellite detecting programs.     

Broadening the application of evolutionarily based genetic pest management

Insect- and tick-vectored diseases such as malaria, dengue fever, and Lyme disease cause human suffering, and current approaches for prevention are not adequate. Invasive plants and animals such as Scotch broom, zebra mussels, and gypsy moths continue to cause environmental damage and economic losses in agriculture and forestry. Rodents transmit diseases and cause major pre- and postharvest losses, especially in less affluent countries. Each of these problems might benefit from the developing field of Genetic Pest Management that is conceptually based on principles of evolutionary biology. This article briefly describes the history of this field, new molecular tools in this field, and potential applications of those tools. There will be a need for evolutionary biologists to interact with researchers and practitioners in a variety of other fields to determine the most appropriate targets for genetic pest management, the most appropriate methods for specific targets, and the potential of natural selection to diminish the effectiveness of genetic pest management. In addition to producing environmentally sustainable pest management solutions, research efforts in this area could lead to new insights about the evolution of selfish genetic elements in natural systems and will provide students with the opportunity to develop a more sophisticated understanding of the role of evolutionary biology in solving societal problems.     

Genetics in hereditary spastic paraplegias: Essential but not enough

Hereditary spastic paraplegias consist of a group of rare neurodegenerative diseases characterized by lower limb spasticity. These inherited Mendelian disorders show high genetic variability associated with wide clinical diversity. Pathophysiological investigations have suggested that mutations in genes affecting the same cellular pathway generally lead to similar clinical symptoms, highlighting the importance of genetic mutation in these diseases. However, phenotype-genotype correlations have failed to explain the observed large inter-individual variability linked to mutations in a single gene, suggesting that genetics alone is not sufficient to explain symptom diversity. The identification of biomarkers, such as neurofilament light chain, could fill the gap and predict disease evolution.     

Getting under the skin of epidermal morphogenesis

At the surface of the skin, the epidermis serves as the armour for the body. Scientists are now closer than ever to understanding how the epidermis accomplishes this extraordinary feat, and is able to survive and replenish itself under the harshest conditions that face any tissue. By combining genetic engineering with cell-biological studies and with human genome data analyses, skin biologists are discovering the mechanisms that underlie the development and differentiation of the epidermis and hair follicles of the skin. This explosion of knowledge paves the way for new discoveries into the genetic bases of human skin disorders and for developing new therapeutics.     

Meckel-Gruber syndrome and the role of primary cilia in kidney,skeleton, and central nervous system development

The ciliopathies are a group of related inherited diseases characterized by malformations in organ development. The diseases affect multiple organ systems, with kidney, skeleton, and brain malformations frequently observed. Research over the last decade has revealed that these diseases are due to defects in primary cilia, essential sensory organelles found on most cells in the human body. Here we discuss the genetic and cell biological basis of one of the most severe ciliopathies, Meckel-Gruber syndrome, and explain how primary cilia contribute to the development of the affected organ systems.     

Meckel-Gruber syndrome and the role of primary cilia in kidney,skeleton, and central nervous system development

The ciliopathies are a group of related inherited diseases characterized by malformations in organ development. The diseases affect multiple organ systems, with kidney, skeleton, and brain malformations frequently observed. Research over the last decade has revealed that these diseases are due to defects in primary cilia, essential sensory organelles found on most cells in the human body. Here we discuss the genetic and cell biological basis of one of the most severe ciliopathies, Meckel-Gruber syndrome, and explain how primary cilia contribute to the development of the affected organ systems.     

Storage diseases: new insights into sphingolipid functions

Studying human diseases can help us to uncover important processes in normal cells. Cell biologists have recently focused on inherited sphingolipid-storage diseases. Eukaryotic life is characterized by internal membranes of various compositions, and sphingolipids are a small but important part of these membranes. Compositional differences between cellular membranes are maintained by sorting and sphingolipids are thought to organize this process by forming ordered domains of increased thickness in the bilayer. Here, we describe the impact of sphingolipid accumulation on the sorting of endocytic membranes and discuss the proposed basis for the pathology of these diseases at the cellular level.     

Evolution, revolution and heresy in the genetics of infectious disease susceptibility

Infectious pathogens have long been recognized as potentially powerful agents impacting on the evolution of human genetic diversity. Analysis of large-scale case-control studies provides one of the most direct means of identifying human genetic variants that currently impact on susceptibility to particular infectious diseases. For over 50 years candidate gene studies have been used to identify loci for many major causes of human infectious mortality, including malaria, tuberculosis, human immunodeficiency virus/acquired immunodeficiency syndrome, bacterial pneumonia and hepatitis. But with the advent of genome-wide approaches, many new loci have been identified in diverse populations. Genome-wide linkage studies identified a few loci, but genome-wide association studies are proving more successful, and both exome and whole-genome sequencing now offer a revolutionary increase in power. Opinions differ on the extent to which the genetic component to common disease susceptibility is encoded by multiple high frequency or rare variants, and the heretical view that most infectious diseases might even be monogenic has been advocated recently. Review of findings to date suggests that the genetic architecture of infectious disease susceptibility may be importantly different from that of non-infectious diseases, and it is suggested that natural selection may be the driving force underlying this difference.