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Archive for category: E-News

E-News

Researchers link Kawasaki Disease in childhood with increased risk of adult heart disease

, 26 August 2020/in E-News /by 3wmedia

Cedars-Sinai researchers have linked Kawasaki Disease, a serious childhood illness that causes inflammation of blood vessels throughout the body, with early-onset and accelerated atherosclerosis, a leading cause of heart disease in adults.
In a study, an American Heart Association peer-reviewed medical journal, a team of researchers showed how Kawasaki Disease in young mice predisposed them to develop accelerated atherosclerosis, often called hardening of the arteries, in young adulthood. The study also suggests that aggressive early treatment of the blood vessel inflammation caused by Kawasaki Disease may reduce the future risk of developing accelerated atherosclerosis. Up to 25 percent of children with Kawasaki Disease will develop inflammation of the coronary arteries, making it the leading cause of acquired heart disease among children in developed countries.
‘Heart disease is the leading cause of death in this country and this study suggests that adult cardiovascular diseases likely start during childhood and that Kawasaki Disease may play a role in the childhood origin of adult heart disease,’ said Moshe Arditi, MD, executive vice chair of research in Cedars-Sinai’s Department of Pediatrics in the Maxine Dunitz Children’s Health Center and director of the Division of Pediatric Infectious Diseases and Immunology. ‘By recognising the connection between this vascular inflammatory disease and hardening of the arteries in young adults, physicians will be better prepared to provide preventive care to these vulnerable patients.’
Arditi said the study’s findings also may have implications for children with Kawasaki Disease in that they may need to be closely monitored for future development of early-onset atherosclerosis. Also, doctors treating children who have had Kawasaki Disease should closely monitor other known cardiovascular disease risk factors such as obesity, high blood pressure, high cholesterol and smoking, Arditi said.
Kawasaki Disease is diagnosed in approximately 5,000 U.S. children every year, predominantly affecting children younger than five. Boys are more likely than girls to acquire Kawasaki Disease, which starts with a sudden, persistent fever and causes swollen hands and feet, red eyes and body rash. Scientists suspect Kawasaki Disease is the body’s immune reaction to a virus that has yet to be identified.
Atherosclerosis occurs when fat, cholesterol, and other substances build up in the walls of arteries and form hard structures called plaques. Over the course of years, plaque buildup makes it harder for blood to flow because the plaque narrows arteries and makes them stiffer. When pieces of plaque break off and move to smaller vessels, they can cause stroke, heart attack or pulmonary embolism.
In the study, which was funded with a grant from the National Institute of Allergy and Infectious Diseases, mice with Kawasaki Disease were fed a high-fat diet and then compared to mice that did not have Kawasaki Disease but did eat the same high-fat diet. The Kawasaki mice developed significantly more atherosclerotic plaque at a younger age.
‘This study suggests that timely diagnosis and aggressive initial treatment of the vascular inflammation may be important in preventing this potentially serious future complication,’ said co-author Prediman K. Shah, MD, director of cardiology, director of the and the Shapell and Webb Family Chair in Clinical Cardiology at the Cedars-Sinai Heart Institute. EurekAlert

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New TB test promises to be cheap and fast

, 26 August 2020/in E-News /by 3wmedia

Biomedical engineers at UC Davis have developed a microfluidic chip to test for latent tuberculosis. They hope the test will be cheaper, faster and more reliable than current testing for the disease.
‘Our assay is cheaper, reusable, and gives results in real time,’ said Ying Liu, a research specialist working with Professor Alexander Revzin in the UC Davis Department of Biomedical Engineering.
The team has already conducted testing of blood samples from patients in China and the United States.
About one-third of the world’s population is infected with the bacteria that cause tuberculosis, a disease that kills an estimated 1.5 million people worldwide every year, according to the U.S. Centers for Disease Control and Prevention.
Most infected people have latent TB, in which the bacteria are kept in check by the immune system. Patients become sick only when the immune system is compromised, enabling the bacteria to become active. People with HIV are at especially high risk.
Current tests for latent TB are based on detecting interferon-gamma, a disease-fighting chemical made by cells of the immune system. Commercially available tests require sending samples to a lab, and can be used just once.
Liu and Revzin used a novel approach: They coated a gold wafer with short pieces of a single-stranded DNA segment known to stick specifically to interferon-gamma. They then mounted the wafer in a chip that has tiny channels for blood samples. If interferon-gamma is present in a blood sample, it sticks to the DNA, triggering an electrical signal that can be read by a clinician.
‘If you see that the interferon-gamma level is high, you can diagnose latent TB,’ Liu said.
The researchers plan to refine the system so that the microfluidic sensor and electronic readout are integrated on a single chip. UC Davis

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Researchers studying chromosomal abnormalities uncover new genes contributing to autism and related neurodevelopmental disorders

, 26 August 2020/in E-News /by 3wmedia

When chromosomes replicate, sometimes there is an exchange of genetic material within a chromosome or between two or more chromosomes without a significant loss of genetic material. This exchange, known as a balanced chromosomal abnormality (BCA), can cause rearrangements in the genetic code.
Researchers from 15 institutions in three countries including Brigham and Women’s Hospital (BWH), Massachusetts General Hospital, Harvard Medical School, and the Broad Institute found that due to these rearrangements, BCAs harbour a reservoir of disruptions in the code that could lead to autism and other neurodevelopmental disorders. The researchers also uncovered 22 new genes that may contribute to or increase the risk of autism or abnormal neurodevelopment.
The researchers used a strategy that involved directly sequencing BCAs to reveal genes at the breakpoints and show that these genes are related to autism and other neurodevelopmental disorders.
This study is part of a larger, ongoing collaborative endeavour, the Developmental Genome Anatomy Project (DGAP), to identify genes critical in human development.
The researchers discovered that the genetic code can be disrupted at various distinct sites and still result in autism. The disruptions occur in several different groups of genes, including those already individually suspected to be associated with abnormal neurodevelopment; those which illuminate a single gene as important in large regions previously defined as genomic disorders; as well as those associated with psychiatric disorders that can have much later onset than neurodevelopmental disorders.
‘BCAs provide a unique opportunity to pinpoint a gene and validate it in a disorder,’ said Cynthia Morton, PhD, BWH director of cytogenetics, and principal investigator of DGAP. ‘These discoveries can illuminate biological pathways that may be a window to a new therapy. We are all grateful to the individuals and their families who make these fundamental findings possible through their participation as subjects in these studies.’ Brigham and Women’s Hospital

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Genome-wide analysis shows previously undetected abnormalities in parents of affected children

, 26 August 2020/in E-News /by 3wmedia

The use of genome-wide array analysis in parents whose children are suspected of having a genetic disease shows that the parents frequently also have previously undetected genetic abnormalities, a researcher from The Netherlands told the annual conference of the European Society of Human Genetics. Being aware of this is important to parents because it means that their risk of having another affected child is significantly increased.
Dr. Nicole de Leeuw, a clinical laboratory geneticist in the Department of Human Genetics of the Radboud University Nijmegen Medical Centre in Nijmegen, and colleagues performed genome-wide SNP array analysis in 6,500 patients and 1,874 parents. The patients had intellectual disability and/or congenital abnormalities, and the parents of those in whom an aberration was detected were tested in a similar way to determine whether they had the same aberration as their child. Mosaic aberrations, where both genetically normal and abnormal cells are present in an individual, were not only found in one in every 300 patients, but in one in every 270 parents as well. ‘These abnormalities occurred more frequently than we had expected’, said Dr. de Leeuw. ‘Armed with this knowledge, we can try to understand not only why, but also how genetic disease arises in individuals, and this can help us to provide better genetic counselling.’
Analysis of patients’ genomes showed 6.5% de novo (spontaneously arising) genomic imbalances, 9.1% of rare, inherited imbalances, and 0.8% of X-linked abnormalities. Moreover, with the additional data from their SNP array test results, the researchers were able to subsequently find pathogenic mutations in recessive disease genes, uniparental disomies (where a single chromosome is doubled leading to two genetically identical ones), and mosaic aneuploidies (an extra or missing chromosome in some of the cells of the body) in about 30 patients.
‘In at least seven families, these findings meant that what we had thought of as a spontaneously arising, non-inherited genetic abnormality in a child was in fact already present in some form in the parent’, said Dr. de Leeuw. ‘Furthermore, when we tested in different cell lines – for example, DNA from blood and that from a mouth swab – we often found that results varied. This is because mosaic aberrations can occur in cells in some organs and not in others, and underlines the importance of not just relying on one type of cell line for this kind of genetic diagnosis.’
In two cases these tissue-dependent differences changed over time, and the researchers believe that this was due to an attempt by the body to correct and rescue the situation. ‘Such rescue attempts are best known in cases of trisomy, where there are three chromosomes instead of two in a cell, or monosomy, where there is only one. In both these cases, the body may try to correct the situation by respectively deleting or adding (doubling) a chromosome. Such rescue mechanisms may be more common than we expected, and by using genome-wide SNP array analysis it will help us to reveal them. For some patients, it would be particularly interesting if we could test multiple samples of these patients over time’, said Dr. de Leeuw. EurekAlert

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Lack of basic evidence hampering prevention of sudden heart attacks in sport

, 26 August 2020/in E-News /by 3wmedia

Big gaps in basic knowledge about the numbers and causes of apparently inexplicable heart attacks among young sportsmen and women are seriously hampering our ability to prevent them, says a sport and exercise medicine specialist in the British Journal of Sports Medicine.
At the very least, we need to start building reliable databases of all such events across sport, in a bid to start plugging these knowledge gaps, say Dr Richard Weiler and colleagues.
His comments come in the wake of the recent high profile case of premier league footballer, Fabrice Muamba, who collapsed on pitch, in front of a stadium packed with spectators, after sustaining a sudden heart attack.
Fortunately, Mr Muamba recovered, but cases like these, although rare, are still likely to occur despite screening programmes, and they are poorly understood, emphasises Dr Weiler.
These cases have prompted improvements in pitch-side and acute sports medicine, including emergency life support, defibrillation and the development of practical education courses and emergency care guidelines, says Dr Weiler.
None the less, he says: ‘We still lack many answers to basic questions about these afflictions. We do not know the exact numbers and trends in prevalence or incidence, and do not understand the [multiple causes] that trigger sudden cardiac death in previously healthy athletes.’
Issues that still need further investigation are the roles of gender and ethnicity, geography and genes, he says.
For example, Sub-Saharan Africa may be a ‘cardiac hotspot,’ with recent research linking sudden heart attacks to sickle cell trait.
Other research suggests that African Americans are three times more prone to sudden cardiac death/arrest than white athletes, although the rates vary considerably depending on the type of sport played.
And another study found that heart (ECG) tracing patterns differ between white and black athletes, although whether this is normal or indicates a higher risk for sudden cardiac death is not known, says Dr Weiler.
Screening programmes throw up a considerable number of false positive results, and it is still far from clear whether screening actually cuts the number of deaths, whether it is cost effective, and how to manage any abnormal findings, he says.
‘It is vital that we start to answer these questions based on reliable science and evidence,’ he insists. ‘To achieve this, we propose the collection and recording of reliable data across sport of every sudden cardiac death/arrest,’ he writes.
But for this to happen, co-operation and collaboration will be needed among sporting organisations, federations, and clubs, in addition to the establishment of sport specific and national registries for these incidents, he suggests.
Dr Weiler cites a FIFA (International Football Federation) initiative. This requires a medical assessment before a match for all FIFA competitions, and includes a recently established database for all its 208 member associations in a bid to build up an evidence base and better understand the condition.
‘This is one of many efforts needed to fill knowledge gaps and enable us to mitigate the risks of sudden cardiac arrest/death,’ concludes Dr Weiler, adding that minimum standards of pitch-side medical care across all sports are essential. EurekAlert

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Detecting breast cancer’s fingerprint in a droplet of blood

, 26 August 2020/in E-News /by 3wmedia

One in eight women will be diagnosed with breast cancer during her lifetime. The earlier cancer is detected, the better the chance of successful treatment and long-term survival. However, early cancer diagnosis is still challenging as testing by mammography remains cumbersome, costly, and in many cases, cancer can only be detected at an advanced stage. A team based in the Dept. of Biomedical Engineering at McGill University’s Faculty of Medicine has developed a new microfluidics-based microarray that could one day radically change how and when cancer is diagnosed.
For years, scientists have worked to develop blood tests for cancer based on the presence of the Carcinoembryonic Antigen (CEA), a protein biomarker for cancer identified over 40 years ago by McGill’s Dr. Phil Gold. This biomarker, however, is also found in healthy people and its concentration varies from person to person depending on genetic background and lifestyle. As such, it has not been possible to establish a precise cut-off between healthy individuals and those with cancer.
‘Attempts have been made to overcome this problem of person-to-person variability by seeking to establish a molecular ‘portrait’ of a person by measuring both the concentration of multiple proteins in the blood and identifying the signature molecules that, taken together, constitute a characteristic ‘fingerprint’ of cancer,’ explains Dr. David Juncker, the team’s principal investigator. ‘However, no reliable set of biomarkers has been found, and no such test is available today. Our goal is to find a way around this.’
Dr. Mateu Pla-Roca, the study’s first author, along with members of Juncker’s team, began by analysing the most commonly used existing technologies that measure multiple proteins in the blood and developing a model describing their vulnerabilities and limitations. Specifically, they discovered why the number of protein targets that can be measured simultaneously has been limited and why the accuracy and reproducibility of these tests have been so challenging to improve. Armed with a better understanding of these limitations, the team then developed a novel microfluidics-based microarray technology that circumvents these restrictions. Using this new approach, it then became possible to measure as many protein biomarkers as desired while minimising the possibility of obtaining false results.
Juncker’s biomedical engineering group, together with oncology and bioinformatics teams from McGill’s Goodman Cancer Research Centre, then measured the profile of 32 proteins in the blood of 11 healthy controls and 17 individuals who had a particular subtype of breast cancer (oestrogen receptor-positive). The researchers found that a subset of six of these 32 proteins could be used to establish a fingerprint for this cancer and classify each of the patients and healthy controls as having or not having breast cancer.
‘While this study needs to be repeated with additional markers and a greater diversity of patients and cancer subsets before such a test can be applied to clinical diagnosis, these results nonetheless underscore the exciting potential of this new technology,’ said Juncker.
Looking ahead, Juncker and his collaborators have set as their goal the development of a simple test that can be carried out in a physician’s office using a droplet of blood, thereby reducing dependence on mammography and minimizing attendant exposure to X-rays, discomfort and cost. His lab is currently developing a hand-held version of the test and is working on improving its sensitivity so as to be able to accurately detect breast cancer and ultimately, many other diseases, at the earliest possible stage. McGill University

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Quick, simple test developed to identify patients who will not respond to the painkiller tramadol

, 26 August 2020/in E-News /by 3wmedia

French researchers have found a way to identify quickly the 5-10% of patients in whom the commonly used painkiller, tramadol, does not work effectively. A simple blood test can produce a result within a few hours, enabling doctors to switch a non-responding patient on to another painkiller, such as morphine, which will be able to work in these patients.
Dr Laurent Varin, an anaesthesiologist at the Caen Teaching Hospital (Caen, France), presented the findings.
Tramadol is a synthetic opioid that is metabolised in the liver via an enzyme called cytochrome P450 2D6 (CYP2D6) to produce a small molecule (or ‘metabolite’) called O-demethyltramadol (ODT). ODT is between two and four times better at inducing analgesia than tramadol that is not metabolised successfully. This is because ODT has a 200-fold higher affinity to the opioid receptors in humans than un-metabolised tramadol, meaning that it binds to the receptors more successfully, blocking out the signals for pain.
Dr Varin said: ‘In our hospital we frequently use tramadol after surgery – about 50-60% of patients are treated with it, while the rest are treated with nefopam, which is a non-opioid painkiller. However, in about 5-10% of Caucasian patients the CYP2D6 enzyme is inefficient and does not produce enough ODT to bind effectively to the opioid receptors; these patients are known as ‘poor metabolisers’ and will have poorly controlled pain unless the problem is identified quickly and they are switched to morphine or nefopam.’
In order to identify the ‘poor metabolisers’, Dr Varin and his colleagues decided to investigate the ratio between tramadol and ODT in patients’ blood to see if this would give an indication of how efficiently CYP2D6 was working. They recruited 294 Caucasian patients who were receiving tramadol after surgery for a number of digestive conditions such as stomach, bowel and liver cancer, or for surgery on the spleen, gall bladder or pancreas. They collected blood samples after 24 and 48 hours post-surgery, and tested them for concentrations of tramadol and ODT using ‘high performance liquid chromatography tandem mass spectrometry’, which separates out the different components in the blood.
The researchers also used genotyping to analyse and identify the DNA make-up of the patients to discover which of them had inefficient CYP2D6. This revealed that eight per cent (23) of the patients were ‘poor metabolisers’. Then the researchers assessed the ratio of tramadol to ODT in the blood samples of the ‘poor metabolisers’ and the other patients.
‘We found that, after 24 hours, an ODT/tramadol ratio of less than 0.1 indicated a deficient CYP2D6 activity with an accuracy of 87% sensitivity – the test’s ability to correctly identify positive results – and 85% specificity – the test’s ability to correctly identify negative results,’ said Dr Varin. ‘This means that this ratio is highly accurate at detecting ‘poor metabolisers’ who need to be switched to another painkiller.’
Dr Varin and his colleagues believe that the ODT/tramadol ratio gives doctors a new tool to identify ‘poor metabolisers’ in the clinic. ‘This test is simple and cheap, costing only about 30 Euros. It can be performed quickly in just a few hours, instead of many days when the genotyping method is used, and will enable clinicians to make the best treatment choices for their patients. If a patient is suffering unrelieved postoperative pain and the blood test reveals an ODT/tramadol ratio of less than 0.1, then the clinicians can switch quickly to morphine, rather than trying to increase the dose of tramadol and risk adverse drug effects by overdosing. EurekAlert

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Towards TB elimination: ECDC and ERS introduce new guidelines on tuberculosis care in Europe

, 26 August 2020/in E-News /by 3wmedia

The European Respiratory Society (ERS) and the European Centre for Disease Prevention and Control (ECDC) have published their jointly developed European Union Standards for Tuberculosis Care (ESTC). The 21 patient-centred standards aim to guide healthcare workers to ensure optimal diagnosis, treatment and prevention of TB in Europe – with nearly 74,000 reported TB cases in the EU/EEA in 2010 clearly showing that TB remains a public health challenge across the region. The new EU-specific guidelines were developed by a panel of 30 experts and aim to bridge current gaps in the case management of TB that were identified in a recent survey. In the process, the ERS has taken the lead in developing the clinically related standards and ECDC has developed the public health related standards. The ESTC are based on the same recommendations as the International Standards for TB Care (ISTC), but feature additional supplements and replacement information relevant for healthcare providers in the EU. The new guidelines include the following: All people showing signs, symptoms, history or risk factors linked with TB should be examined for TB. All people diagnosed with TB should undergo drug susceptibility testing in a laboratory setting, to rule out drug-resistance and help combat the growing number of multidrug-resistant cases of TB (MDR-TB). Patients with, or highly likely to have, TB caused by drug-resistant organisms (especially MDR-TB) should be treated for at least 20 months, with the recommended intensive phase of treatment being 8 months. It should be ensured that all newly admitted patients who are suspected of having infectious TB are subject to respiratory isolation until their diagnosis is confirmed or excluded following an appropriate infection control plan. The guidelines also include an additional section on how policymakers and healthcare professionals can adopt and introduce the recommendations to a healthcare setting.

http://tinyurl.com/d88ylrc
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Exposure to antibiotics linked to severity of allergic asthma

, 26 August 2020/in E-News /by 3wmedia

Widely used antibiotics may increase incidence and severity of allergic asthma in early life, according to a University of British Columbia study.
The study shows that certain antibiotics that affect intestinal bacteria also had a profound impact on allergic asthma.
‘It has long been suspected that kids exposed to more antibiotics – like those in developed countries – are more prone to allergic asthma,’ says the study’s author, UBC microbiologist Brett Finlay. ‘Our study is the first experimental proof that shows how.’
Finlay’s team at UBC’s Dept. of Microbiology and Immunology and Michael Smith Laboratories examined how two widely used antibiotics – streptomycin and vancomycin – affected the bacterial ‘ecosystem’ in the gut. They found that vancomycin profoundly alters the bacterial communities in the intestine and increases severity of asthma in mouse models.
The same antibiotics do not impact adult mice’s susceptibility to asthma, indicating that early life is a critical period of establishing a healthy immune system.
Allergic asthma affects more than 100 million people worldwide and its prevalence is increasing on average by 50 per cent every decade, particularly among children in industrialized countries. According to the Asthma Society of Canada, asthma affects at least 12 per cent of Canadian children.
The human gut is colonised by approximately 100 trillion bacteria, and contains upwards of 1,000 bacterial species. While not fully understood, these micro-organisms, known as ‘gut flora,’ perform a host of useful functions, says Finlay.
‘Modern societal practices, such as improved sanitation methods and widespread antibiotic use, are causing the disappearance of ancestral species of bacteria in our gut that may be critical to a healthy immune system,’ says Finlay.
‘Our study shows this is the case with certain antibiotics and allergic asthma, and the gut-lung connection is also consistent with observations that incidence of asthma has not increased significantly in developing countries where antibiotic use is less prevalent – and in turn, the gut flora is permitted to fully develop.’ University of British Columbia

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Evolutionary information improves discovery of mutations associated with diseases

, 26 August 2020/in E-News /by 3wmedia

A book containing misprints may cause annoyance for the reader, but typos in an individual’s genetic blueprint (DNA) can mean serious disease or even death. The search for genetic correlates for the wide range of diseases plaguing humankind has inspired a wealth of research falling under the heading of genome-wide association studies (GWAS).
According to Sudhir Kumar, director of the Center for Evolutionary Medicine and Informatics at Arizona State University’s Biodesign Institute, however, results from many such studies become less useful when gene variants or alleles implicated in disease in a given population fail to be discovered in subsequent independent studies. ‘Often, we do not discover the same set of mutations for the same disease in different populations,’ he says. ‘This is a huge problem in genomic medicine.’
Kumar and colleagues Joel T. Dudley, Rong Chen, Maxwell Sanderford, and Atul J. Butte, have developed a statistical method to remedy this problem by using evolutionary information. It is capable of significantly enhancing the likelihood of identifying disease-associated alleles that show better consistency across populations, improving the reliability of GWAS studies. The method makes use of phylogenetics – the comparative study of species genomes through long-term evolutionary history.
The new method is now available to use via the web, so that researchers worldwide can apply it as an aid to discovering disease-associated mutations that are more consistently reproducible and therefore useable as diagnostic markers. Kumar refers to this new approach, combining standard comparative genomic studies with phylogenetic data as phylomedicine, a rapidly developing field that promises to streamline genomic information and improve its diagnostic power.
‘We can take this method and apply it to all the data that has been published,’ Kumar says. ‘It will lead to new discoveries that were sitting right there, but nobody knew about.’
The new method boosts the discovery of reproducible mutations by integrating evolutionary history of humans with contemporary genomic information. Applying the new rankings to a large GWAS study improved the discovery of reliable mutation correlates of complex diseases, which will advance personalised medicine based on each patient’s genomic code.
The basic idea behind GWAS is simple: compare the genomes of two populations of subjects, one with disease trait and a control group without the disease. Next, identify the disparities at each position of the genome in the two populations. Find the alleles occurring in the diseased population that are less frequent in the healthy population and you have just pinpointed the gene mutations associated with disease.
Or have you?
As Kumar explains, matters are not so simple. The mutations studied in such studies are known as SNPs (for single-nucleotide polymorphisms). This simply means that for a given gene sequence, one of the four nucleotides (A,T,C and G) found commonly in the population is replaced by something else. For example, the majority of healthy subjects may carry the ‘A’ at a particular position in the genome, but disease individuals may be more likely to carry a ‘C’ at the same position. If the difference between the groups is striking, the SNP may be associated with the disease trait.
Human genomes are vast structures – consisting of some 3 billion base pairs of nucleotides. Most are littered with SNPs and teasing out which ones sit there without apparent effect and which may translate to disease is often a vexing affair. For some diseases, a one-to-one correspondence between gene mutation and disease exists. Generally, these afflictions, known as monogenic diseases, have particular characteristics. They result from a mutation in just a single gene, rather than multiple genes. They are early-onset diseases, taking their toll when the patient is still young.
Monogenic diseases, which include cystic fibrosis, Tay sachs disease, sickle cell anemia and Huntington’s disease are usually not the targets for genome-wide association studies, because the relationship between gene mutation and occurrence of the disease is straightforward and reliable.
By contrast, so-called complex diseases tend to occur later in life, are triggered by mutations occurring at multiple sites along the genome and often have a significant environmental– that is, non-genetic – component. Finding the alleles responsible for such diseases, which include hypertension, rheumatoid arthritis, Alzheimer’s disease, type II diabetes and countless others through GWAS studies has often been a bewildering endeavor, as alleles identified in one study population frequently fail to turn up in different studies with different populations.
GWAS studies compute the odds of an allele along the genome being disease-related and translate this into a statistic known as the P value. Alleles with the lowest P value are least likely to have occurred by random chance. In the current research, a meta-analysis is conducted using results from thousands of previous GWAS studies and phylogenetics are applied to unearth evolutionary trends in the data.
‘Every position in the human genome among the billions of base pairs has evolved over time,’ Kumar says. ‘As the genome evolves, some positions permit change frequently while others do not.’ The positions least likely to change with time and across mammalian species are known as evolutionarily conserved positions. The group conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. ‘Even if a GWAS variant does not have a functional role in a disease, evolutionary information is still very relevant, because every position in the human genome has an evolutionary signature that gives us prior information on how alleles at that position are likely to vary in modern human populations,’ says Dudley, the study’s lead author.
An analysis of existing data found that most of the presumptively disease-related alleles uncovered in the GWAS studies occurred at relatively slow-evolving, highly conserved sites. According to Kumar, this fact accounts for the poor reproducibility of many putative disease alleles across different populations, as alleles occurring at conserved sites tend to be rare. As Kumar explains ‘You can keep finding rare alleles like this all day, but they would have limited clinical utility in a broader population.’
The new ranking system, known as E-ranking, incorporates phylogenetic information from multi-species studies of mammals, and applies it to human GWAS data. The effect is to remove the inherent sampling bias for rare alleles, allowing the more common alleles occurring at fast-evolving sites in the genome to be more readily discovered. ‘Our method removes this bias, which gives a boost to high-frequency common variants that are more likely to reproduce across populations due to the evolutionary history of the genomic position where they are found,’ says Dudley. Arizona State University

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