EYE on bioinformatics: dissecting complex disease traits in silico

Bioinformatics has provided an unprecedented power and resource for us to decipher the enigma of complex diseases. It can reveal otherwise promiscuous information from the tremendous amount of data generated by the new, powerful and high-throughput technologies of genomics and proteomics. In this paper, we review the cutting edge developments in complex disease trait mapping, databases, computational gene recognition, gene function prediction, pathway reconstruction and disease classification by expression profiling, and computational modelling of living systems. Integration of all this knowledge and the different technologies, alongside cooperation between experts from different fields, will enhance our understanding of the molecular and mechanistic abnormalities in disease state, and greatly assist the rational development of effective therapies.     

Coeliac disease in primary care: case finding study

ObjectivesTo provide evidence of underdiagnosis of coeliac disease and to describe the main presenting symptoms of coeliac disease in primary care.DesignCase finding in a primary care setting by testing for coeliac disease by using the endomysial antibody test.SettingNine surgeries in and around a market town in central England, serving a population of 70 000.ParticipantsFirst 1000 patients screened from October 1996 to October 1997.ResultsThe 30 patients (out of 1000 samples) with positive results on the endomysial antibody test all had histological confirmation on small intestine biopsy. The commonest mode of presentation (15/30) was anaemia of varying severity. Most patients (25/30) presented with non-gastrointestinal symptoms. Specificity of the endomysial antibody test was 30/30.ConclusionsUnderdiagnosis and misdiagnosis of coeliac disease are common in general practice and often result in protracted and unnecessary morbidity. Serological screening in primary care will uncover a large proportion of patients with this condition and should be made widely available and publicised. Coeliac disease should be considered in patients who have anaemia or are tired all the time, especially when there is a family history of the disease.

Key messages

• General practitioners currently see many people with undiagnosed coeliac disease
• The most likely presentation is a combination of microcytic anaemia, past or present, a family history of the disease, and feeling tired all the time
• Estimations of endomysial antibody and IgA are reliable diagnostic tools
• The prevalence of coeliac disease in Britain is higher than the accepted figure of 1:1000 population
• Increased awareness of the extra intestinal manifestations of coeliac disease, coupled with a low threshold for serological testing, will uncover a large portion of undiagnosed coeliac disease

     

Coeliac disease and immunological disorders.

Out of 314 patients with coeliac disease, 63 had associated disorders of known or suspected immunological cause (excluding aphthous stomatitis and dermatitis herpetiformis). Autoimmune diseases appeared to occur more often in patients with coeliac disease than in the normal population, 52 such diseases being found in 45 patients. Of individual disorders, diabetes mellitus, thyroid diseases, and ulcerative colitis seemed to be more common than expected. Atopy (asthma and eczema) occurred in 7% of the patients. Most of these immunological disorders developed when the patients were on normal diet. A gluten-free diet and virtually normal jejunum did not prevent their development, and the diet had little ameliorating effect on their course apart from an occasional dramatic improvement in atopic patients.     

Coeliac disease with farmers' lung.

Two patients with allergic alveolitis due to mouldy hay antigens (farmer''s lung) were shown to have malabsorption due to coeliac disease. As similar associations have been found with other alveolar diseases, this association is probably not fortuitous and further population screening should be done.     

Vitiligo as an inflammatory skin disorder: a therapeutic perspective

From a therapeutic standpoint, vitiligo is still regarded by many physicians as a simple problem of regenerative medicine, with the main aim to repopulate the depigmented skin with functional melanocytes from the margins of the lesions or from intact progenitors in hair follicles. However, recent research in vitiligo suggests that various local triggers alert the skin immune innate system and may precede adaptive immune responses targeting melanocytes. This scenario is close to that of other common skin inflammatory disorders like psoriasis and atopic, and suggests to target as a priority this clinically silent inflammatory component of he disease. This perspective highlights possible targets for intervention.     

Coronary heart disease: a disorder of growth

A new 'developmental' model for the origins of coronary heart disease and the related disorders of type 2 diabetes, hypertension and stroke is emerging. The finding that people who develop these disorders have altered growth in utero, during infancy and childhood provides a new starting point for research. The immediate prospect for prevention is through protecting infant growth and preventing accelerated weight gain in children made vulnerable to later disease by small size at birth and during infancy. Ultimately we need to optimize maternal diet and composition before and during pregnancy. Despite current levels of nutrition in Western countries the nutrition of many fetuses and infants remains suboptimal because the nutrients available are unbalanced or because their delivery is constrained by the long and vulnerable fetal supply line.     

Tourette's disorder and associated complex behaviors: a case report

A case of a man with Tourette's disorder associated with obsessive-compulsive disorder, multiple sexual paraphilias, and aggressive behavior is described. Treatment with haloperidol led to improvement in the characteristic tics of Tourette's disorder as well as to improvement in these three complex-associated behaviors. After haloperidol was discontinued, an exacerbation of tics and the associated behaviors occurred.     

Coeliac disease in endocrine diseases of autoimmune origin

Abstract Coeliac disease (CD, sometimes called gluten-sensitive enteropathy or nontropical sprue) is an inflammatory disorder of the small intestine of autoimmune origin. It occurs in genetically predisposed people and is induced by a gluten protein, which is a component of wheat. The prevalence of histologically confirmed CD is estimated in screening studies of adults in the United States and Europe to be between 0.2% and 1.0%. The results of previous studies have indicated that the prevalence of CD is increased in patients with other autoimmune disorders such as: autoimmune thyroid diseases, type 1 diabetes mellitus, and Addison's disease. A coincidence of the above diseases constitutes autoimmune polyglandular syndrome (APS). The high prevalence of CD in APS is probably due to the common genetic predisposition to the coexistent autoimmune diseases. The majority of adult patients have the atypical or silent type of the disease. This is the main reason why CD so often goes undiagnosed or the diagnosis is delayed. CD, if undiagnosed and untreated, is associated with many medical disorders including haematological (anaemia), metabolical (osteopenia/osteoporosis), obstetric-gynaecological (infertility, spontaneous abortions, late puberty, early menopause), neurological (migraine, ataxia, epilepsy) as well as with an increased risk of malignancy, especially: enteropathy-associated T-cell lymphoma, small intestine adenocarcinoma, and oesophageal and oropharyngeal carcinomas. Early introduction of a gluten-free diet and lifelong adherence to this treatment decreases the risk of these complications.     

Hypersensitivity pneumonitis: a complex lung disease

Hypersensitivity pneumonitis (HP), also called extrinsic allergic alveolitis, is a respiratory syndrome involving the lung parenchyma and specifically the alveoli, terminal bronchioli, and alveolar interstitium, due to a delayed allergic reaction. Such reaction is secondary to a repeated and prolonged inhalation of different types of organic dusts or other substances to which the patient is sensitized and hyper responsive, primarily consisting of organic dusts of animal or vegetable origin, more rarely from chemicals. The prevalence of HP is difficult to evaluate because of uncertainties in detection and misdiagnosis and lacking of widely accepted diagnostic criteria, and varies considerably depending on disease definition, diagnostic methods, exposure modalities, geographical conditions, agricultural and industrial practices, and host risk factors. HP can be caused by multiple agents that are present in work places and in the home, such as microbes, animal and plant proteins, organic and inorganic chemicals. The number of environment, settings and causative agents is increasing over time. From the clinical point of view HP can be divided in acute/subacute and chronic, depending on the intensity and frequency of exposure to causative antigens. The mainstay in managing HP is the avoidance of the causative antigen, though the complete removal is not always possible due to the difficulties to identify the agent or because its avoidance may lead to major changes in life style or occupational settings. HP is a complex syndrome that needs urgently for more stringent and selective diagnostic criteria and validation, including wider panels of IgG, and a closer collaboration with occupational physicians, as part of a multidisciplinary expertise.     

A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits

Background

Genotyping-by-sequencing (GBS) is a high-throughput genotyping approach that is starting to be used in several crop species, including bread wheat. Anchoring GBS tags on chromosomes is an important step towards utilizing them for wheat genetic improvement. Here we use genetic linkage mapping to construct a consensus map containing 28644 GBS markers.

Results

Three RIL populations, PBW343 × Kingbird, PBW343 × Kenya Swara and PBW343 × Muu, which share a common parent, were used to minimize the impact of potential structural genomic variation on consensus-map quality. The consensus map comprised 3757 unique positions, and the average marker distance was 0.88 cM, obtained by calculating the average distance between two adjacent unique positions. Significant variation of segregation distortion was observed across the three populations. The consensus map was validated by comparing positions of known rust resistance genes, and comparing them to wheat reference genome sequences recently published by the International Wheat Genome Sequencing Consortium, Rye and Ae. tauschii genomes. Three well-characterized rust resistance genes (Sr58/Lr46/Yr29, Sr2/Yr30/Lr27, and Sr57/Lr34/Yr18) and 15 published QTLs for wheat rusts were validated with high resolution. Fifty-two per cent of GBS tags on the consensus map were successfully aligned through BLAST to the right chromosomes on the wheat reference genome sequence.

Conclusion

The consensus map should provide a useful basis for analyzing genome-wide variation of complex traits. The identified genes can then be explored as genetic markers to be used in genomic applications in wheat breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1424-5) contains supplementary material, which is available to authorized users.     

Chimaeras and mosaics for dissecting complex mutant phenotypes.

Back at the first half of the 1980s, there was no mammalian experimental embryology in Hungary. One of us, AN, took up the challenge of establishing a small group in the field. In the absence of local information, AN and his former colleague, Andras Paldi (AP), used their tourist passport to visit several laboratories in Western Europe and collect information and advice. This is how AN and AP ended up one day sitting in Anne McLaren's office in the MRC Mammalian Development Unit at University College, London. They never forgot her endless enthusiasm and the way she clearly explained the important points of preimplantation embryo manipulation, chimaera making and embryo transfer. As well as the extremely useful suggestions, which were crucial to starting the lab in Hungary, they also took back her deep love for embryo development. They remember her telling them, 'never waste an embryo--there is always another unanswered question it can solve'. Many who have been lucky and experienced Anne's spirit and advice later realized how useful it was to generate 'new' ideas by following the 'not wasting' principle. Our views on chimaeras presented below definitely contain elements which grew out from this principle.