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News Article | October 26, 2016
Site: www.eurekalert.org

MONTREAL, Oct. 20, 2016 - A Canada-US study led by Luis Barreiro, a professor at the University of Montreal's Department of Pediatrics and researcher at the Sainte-Justine University Hospital Center, has demonstrated that Americans of African descent have a stronger immune response to infection compared to Americans of European descent. The study establishes for the first time this difference in immune responses and shows that it is mostly genetic -- inherited from our ancestors and influenced by a relatively recent natural selection. The study is published today in the scientific journal Cell. The study was conducted among 175 Americans, half of which were of African descent, the other half being of European descent, in collaboration with the University of California, Wayne State University, Cornell University, the University of Minnesota, and Duke University. While the immune system of African Americans responds more strongly, Professor Barreiro is careful to qualify it as better: "The immune system of African Americans responds differently, but we cannot conclude that it is better, since a stronger immune response also has negative effects, including greater susceptibility to autoimmune inflammatory diseases such as Crohn's disease. Too much inflammation can damage organs and leave sequelae. In short, a strong immune response can be beneficial in some areas but a disadvantage in others. The immune system reacts to infection by causing inflammation (redness, heat, swelling, etc.) to neutralize and eliminate the infection. It was already known to scientists that African Americans are more susceptible to autoimmune inflammatory diseases and thus more likely to suffer from tuberculosis or scleroderma, for example. The 175 participants in Professor Barreiro's study provided blood samples, from which were extracted macrophages ¬-- cells of the immune system whose role is to kill pathogens responsible for infection. The research team then infected the macrophages with two kinds of bacteria (Listeria and Salmonella) to observe various immune responses: after 24 hours of infection, the macrophages from African Americans killed the bacteria three times faster. The research team also uncovered the molecular mechanisms acting on the genes responsible for these differences in immune responses. "This is one of the firsts of our study," said Barreiro. People of African and European descent have intermingled over the past centuries, and we are even able to determine which part of an individual's immune system is associated with African ancestry and which part with European ancestry." "Although we found these differences in immune responses between African and European Americans, we are still unable to demonstrate what evolutionary pressures led to the observed differences. One of our hypotheses is that in the prehistoric period, after human populations had migrated out of Africa, they were exposed to fewer pathogens (bacteria, viruses, parasites), which reduced the immune response and thus tissue inflammation. This reduction in the immune response (and inflammation) was most likely an advantage because of the adverse consequences of acute or chronic inflammation, which are major contributors to the development of autoimmune inflammatory diseases." Another hypothesis is that the weaker immune response detected in Europeans is the result of a less vigorous natural selection in an environment in which there were fewer, or at least different, pathogens compared to Africa. Neanderthals also played a role in the immune response to infection. Neanderthals, before disappearing, colonized Europe, but not Africa. In the process, they mixed their genes with African Cro-Magnons, who were spread throughout Europe. The analysis of Barreiro's team shows that about 3% of the genes involved in the differences in immune responses between African and European Americans come from Neanderthals! "There is still much to do. For example, we have not yet studied the immune response to viruses and parasites. In addition, genetics explains only about 30% of the observed differences in immune responses. Our future studies should focus on other factors, emphasizing the influence of the environment and our behaviour. The idea is to find immune mechanisms to help understand why some individuals react differently from others in the presence of certain viruses and bacteria," said Barreiro. Luis Barreiro specializes in the evolution of immune responses and was named one of the "40 under 40" (most promising researchers) published in 2014 by the prestigious journal Cell. The first time he set foot in a laboratory after completing his graduate studies in biotechnology at the University of Lisbon in his native Portugal, he found his vocation. After graduating, he obtained a six-month internship in mycobacterial genetics at the Pasteur Institute in Paris. Within five years he had completed a doctorate in human population genetics. After receiving his Ph.D., Barreiro moved to the United States, where he did a postdoctoral fellowship in functional genomics at the University of Chicago's Department of Human Genetics. Today, the same theme runs through Luis Barreiro's work at the University of Montreal and the Sainte-Justine University Hospital Research Center, which he joined in 2011. He is the holder of the Canadian Research Chair in Functional and Evolutionary Genomics of the Immune System. The main project of his laboratory is to discover and define the genetic bases of the variations underlying the differences in immune responses between individuals and human populations. While Barreiro's team is among the two or three groups in the world interested in immune responses and their genetic basis, it is the only one to explore this issue among different species of primates. http://www. Y. Nedelec, J. Sanz, G. Baharian, Z. A. Szpiech, A. Pacis, A. Dumaine, J.-C. Grenier, A. Freiman, A. J. Sams, S. Hebert, A. Pagé Sabourin, F. Luca, R. Blekhman, R. D. Hernandez, R. Pique-Regi, J. Tung, V. Yotova et L. B. Barreiro published the article "Genetic ancestry and natural selection drive population differences in immune responses to pathogens in human" in the journal Cell on October 2016. This study was funded by the Canadian Institutes of Health Research (Grants 301538 and 232519), the Human Frontiers Science Program (CDA-00025/2012), and the Canada Research Chairs Program (950-228993). Y.N. received a grant from the Network of Applied Genetic Medicine Network (RMGA); A.P.S. received a grant from the Fonds de recherche du Québec-Nature et technologies (FRQNT); and G.B. received a grant from the Fonds de recherche du Québec-Santé (FRQS).


News Article | November 28, 2016
Site: www.eurekalert.org

Scientists have developed an easy-to-use software tool that can detect important genetic mutations that previously needed to be identified by a separate test. The software, called DECoN, accurately and quickly detects changes in copy number of blocks of DNA called exons, by analysing sequencing data already generated to identify smaller gene changes. It was developed by researchers at The Institute of Cancer Research, London, and the Wellcome Trust Centre for Human Genetics, Oxford. Most gene mutations are small DNA changes within an exon. These small changes are readily detected by DNA sequencing tests. But sometimes whole exons are deleted or duplicated. These are called exon copy number variants (exon CNVs), and they are not easily picked up by standard DNA sequencing tests. It is vital to be able to find these variants because they are an important cause of disease. For example, about 10 percent of the BRCA1 mutations that predispose women to breast and ovarian cancer are exon CNVs. In clinical testing laboratories a separate test has traditionally been used to detect exon CNVs, but this adds considerable time and cost, and is not available for all genes. Using DECoN (which stands for Detection of Exon Copy Number variants), the researchers took advantage of the high density of sequencing data available in new gene panels to accurately detect deletions or duplications of exons. DECoN does this automatically, adding only 30 minutes to the data analysis of up to 96 samples, and without costing any more. The team performed extensive evaluations of DECoN including in more than 1,900 clinical BRCA tests where it successfully detected all the exon CNVs. Study leader Professor Nazneen Rahman, Head of Cancer Genetics at The Institute of Cancer Research, London, and The Royal Marsden Hospital Foundation Trust, said "DECoN has transformed our gene testing pipeline, making it more efficient and more effective, whilst also making it much faster and cheaper. Previously we had to do an additional slow and expensive test to detect these tricky mutations. Now they are automatically detected by DECoN during the data analysis process." Professor Gerton Lunter at the Wellcome Trust Centre for Human Genetics in Oxford, who led the software development, said "This was an outstanding collaboration for us. It is hugely rewarding to see our work having a real impact for patients." DECoN was developed through the Wellcome-funded Mainstreaming Cancer Genetics programme and Transforming Genetic Medicine Initiative. A key element of these programmes is to develop tools that can be easily and freely used around the world. A paper detailing the development, evaluation and implementation of DECoN was published today in Wellcome Open Research, a newly launched publishing platform that promotes fast, open publication of any useful work by Wellcome researchers. Professor Rahman added: "It's very important to us that our work can be as impactful as possible. We have made an easy-to-use version of DECoN freely available from http://www. and the source code is also available." "We took advantage of the new Wellcome Open Research publication platform to publish our DECoN paper. The paper was freely available for anyone to read and download within two weeks of submitting it. If we had chosen the traditional publishing route it would have taken months. We plan to use Wellcome Open Research for much of our work. We are excited about the faster, broader impact we will have through using the platform." For more information please contact Sophia McCully on 020 7153 5136 or sophia.mccully@icr.ac.uk. For enquiries out of hours, please call 07595 963 613. DECoN was developed, validated and implemented by the Mainstreaming Cancer Genetics Programme and the Transforming Genetic Medicine Initiative. Both are funded by Wellcome. DECoN detects deletions and duplications of exons, which are termed exon CNVs, through analysis of next-generation sequencing (NGS) data. DECoN was first evaluated through testing 96 samples with known exon CNV status and achieved 100% sensitivity and 99% specificity. Extensive simulations were also performed which showed that DECoN performance is excellent, giving >98% sensitivity and specificity for all typical NGS run parameters. DECoN performance was also validated in a real-world setting in a clinical testing laboratory, and is now used routinely to detect exon CNVs in cancer predisposition gene testing in theTGLclinical laboratory. About The Institute of Cancer Research, London The Institute of Cancer Research, London, is one of the world's most influential cancer research institutes. Scientists and clinicians at The Institute of Cancer Research (ICR) are working every day to make a real impact on cancer patients' lives. Through its unique partnership with The Royal Marsden NHS Foundation Trust and 'bench-to-bedside' approach, the ICR is able to create and deliver results in a way that other institutions cannot. Together the two organisations are rated in the top four cancer centres globally. The ICR has an outstanding record of achievement dating back more than 100 years. It provided the first convincing evidence that DNA damage is the basic cause of cancer, laying the foundation for the now universally accepted idea that cancer is a genetic disease. Today it leads the world at isolating cancer-related genes and discovering new targeted drugs for personalised cancer treatment. As a college of the University of London, the ICR provides postgraduate higher education of international distinction. It has charitable status and relies on support from partner organisations, charities and the general public. The ICR's mission is to make the discoveries that defeat cancer http://www. About The Wellcome Trust Centre for Human Genetics The Wellcome Trust Centre for Human Genetics is one of the leading international centres for the study of the genetic basis of common human diseases. As well as hosting high-profile groups pursuing the genetic basis of diabetes, cardiovascular, and infectious disease, and neuropsychiatric phenotypes (amongst others), the WTCHG has led the efforts of the Wellcome Trust Case Control Consortium and been responsible for advancing the application of large-scale genetic analysis to the dissection of common human phenotypes. The Centre also houses leading research groups in statistical genetics and structural biology in a lively interdisciplinary environment. The Centre provides core facilities in genomics, bioinformatics and statistical genetics, imaging, and chromosome dynamics. Presently the WTCHG has around 470 scientists and support staff and had a £20.3M grant turnover in 2010/11. For more information please visit: http://www. Wellcome exists to improve health for everyone by helping great ideas to thrive. We're a global charitable foundation, both politically and financially independent. We support scientists and researchers, take on big problems, fuel imaginations and spark debate. Wellcome Open Research provides all Wellcome researchers with a place to rapidly publish any results they think are worth sharing. All articles benefit from immediate publication, transparent refereeing and the inclusion of all source data.


News Article | February 3, 2016
Site: www.nature.com

Researchers at the body responsible for monitoring birth defects in Latin America are questioning the size of an apparent surge in the number of Brazilian children born with 'microcephaly' — abnormally small heads and brains. Alarm is growing about a reported rise in suspected cases of the rare condition, which has been tentatively linked to the rapid spread of the Zika virus through the Americas. But Jorge Lopez-Camelo and Ieda Maria Orioli, from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), say that the surge might largely be attributed to the intense search for cases of the birth defect, and misdiagnoses, because of heightened awareness in the wake of the possible link with Zika. This ‘awareness’ effect is well known and inevitable, they say, and must be revealing cases that would have gone unnoticed under normal circumstances. They also say that a high rate of misdiagnoses among reported cases is likely because the diagnostic criteria being used for microcephaly are broad. Lopez-Camelo and Orioli presented their analysis in Portuguese-language reports, and, after Nature’s enquiries, provided an English version of the summary (ECLAMC Report). They say that from the epidemiological data available, it is impossible to establish the true size of the surge in microcephaly, and whether there is any link with the Zika virus. In particular, large 'prospective' studies, in which pregnant women in areas of Brazil experiencing Zika outbreaks are monitored to see how many of their children develop microcephaly are needed, they say. Several research groups in and outside Brazil are already planning such studies, and some have begun. Specialists contacted by Nature emphasize that it is prudent for pregnant women to be cautious — for example, by protecting themselves against mosquito bites — until more is known. The experts agree that the reported size of the microcephaly increase so far is probably inflated — and this chimes with the latest figures from the Brazilian government. On 27 January, it said that of 4,180 suspected cases of microcephaly recorded since October, it has so far confirmed 270 and rejected 462 as false diagnoses. But some disagree with the ECLAMC team's conclusion that the reported surge in recent months can mostly be attributed to an increase in the intensity of the search for cases and misdiagnosis. Thomas Jaenisch, a tropical medicine specialist at the Heidelberg University Hospital in Germany, calls this an “extreme” position and says that it “might also create uncertainty in the media and public discussion in Brazil”. Previously confined to Africa and Asia, Zika virus reached the Americas in 2015, where it is currently causing an unprecedented epidemic in Brazil (see 'Zika in the Americas'). Most people infected with the virus — after being bitten by a mosquito — have no symptoms; the remainder have mild symptoms such as fever, skin rash and headache. But in October, Brazil's health ministry reported an unusual spike in reported cases of microcephaly in the northeastern state of Pernambuco, where the affected children's mothers had been in early pregnancy at around the same time as large Zika outbreaks occurred. The ministry subsequently raised the alarm of a possible link to Zika. This led the World Health Organization and its regional office, the Pan American Health Organization (PAHO), to issue an epidemiological alert on 17 November last year, which called on member states to look out for any similar increase in microcephaly among their populations. Earlier this month, the US Centers for Diseases Control and Prevention issued a travel notice, “out of an abundance of caution”, that advised pregnant women to consider postponing travel to places that have ongoing Zika outbreaks. To investigate the situation, the researchers at ECLAMC turned to its own databases dating back to 1967, as well as the country's Live Birth Information System (SINASC). According to ECLAMC, the average historical prevalence of microcephaly in Brazil is around 2 cases per 10,000 births, although rates in the country's north have typically been higher. The researchers calculate that the maximum number of cases that would have been expected in the northern state of Pernambuco in 2015 is around 45. Yet Pernambuco reported 26 times that number last year. Even if Zika is causing microcephaly, these huge numbers are simply too high to be credible, says the report. As well as the increased diagnoses owing to heightened awareness from the media and governments, Lopez-Camelo also highlights that the diagnostic criteria for microcephaly are relatively unspecific and are casting too wide a net. Brazilian health authorities are treating all fetuses with head circumferences that are more than two standard deviations below the average, and newborns with a head circumference of less than 32 centimetres, as suspected cases. But these criteria will inevitably capture many healthy children within the normal growth range who do not have microcephaly. But head circumference is only a proxy measure, note Lopez-Camelo and Orioli: confirming microcephaly requires a diagnosis of small brain size, and a decreased rate of brain growth. The pair are not alone in drawing attention to the broad diagnostic criteria — a risk assessment published on 21 January by the European Centre for Disease Prevention and Control (ECDC) also noted this and said: “It is expected that many of the suspected cases will be reclassified and discarded.” Helen Dolk, an epidemiologist at the University of Ulster near Belfast, UK, who works on the surveillance of congenital abnormalities, says that the ECLAMC’s conclusion — that the apparent surge could be largely an artefact — is possible in principle. But she stresses that it is impossible to confirm until more data becomes available — and that she is reserving judgement on the portion of the apparent increase that can be attributed to confounding factors. Lavinia Schüler-Faccini, a researcher at the Federal University of Rio Grande do Sul, Brazil, and president of the Brazilian Society of Genetic Medicine, says that she is certain that there has been a substantial increase in microcephaly cases. She notes that physicians began reporting a rise before the increased attention by health authorities, and the media began reporting a spike last November. “My personal impression is that there is an augmentation of cases of microcephaly in Brazil,” she says. “However it is not as huge as the suspected cases referred to the Ministry of Health.” Prospective studies have started and others are planned, she says. And she adds: “All our efforts now are to establish the real level of increase.” Establishing whether there is a link between microcephaly and Zika is particularly important because people living in the Americas lack immunity to the virus. This, combined with the fact that the Aedes mosquitoes that transmit the virus are widespread in the Americas, means that many people will be infected in future, including pregnant women. Zika virus has been found in amniotic fluid, placental or fetal tissues in several cases of nervous system malformations, including microcephaly, in Brazil. Following a World Health Organization press conference on Zika virus on 28 January, the agency said in a statement: “A causal relationship between Zika virus infection and birth defects and neurological syndromes has not been established, but is strongly suspected.” It also said: “The Organization is supporting the scaling up and strengthening of surveillance systems in countries that have reported cases of Zika and of microcephaly and other neurological conditions that may be associated with the virus.”


Alanay Y.,Hacettepe University | Avaygan H.,University of California at Los Angeles | Camacho N.,University of California at Los Angeles | Utine G.E.,Hacettepe University | And 22 more authors.
American Journal of Human Genetics | Year: 2010

Osteogenesis imperfecta is a clinically and genetically heterogeneous brittle bone disorder that results from defects in the synthesis, structure, or posttranslational modification of type I procollagen. Dominant forms of OI result from mutations in COL1A1 or COL1A2, which encode the chains of the type I procollagen heterotrimer. The mildest form of OI typically results from diminished synthesis of structurally normal type I procollagen, whereas moderately severe to lethal forms of OI usually result from structural defects in one of the type I procollagen chains. Recessively inherited OI, usually phenotypically severe, has recently been shown to result from defects in the prolyl-3-hydroxylase complex that lead to the absence of a single 3-hydroxyproline at residue 986 of the α1(I) triple helical domain. We studied a cohort of five consanguineous Turkish families, originating from the Black Sea region of Turkey, with moderately severe recessively inherited OI and identified a novel locus for OI on chromosome 17. In these families, and in a Mexican-American family, homozygosity for mutations in FKBP10, which encodes FKBP65, a chaperone that participates in type I procollagen folding, was identified. Further, we determined that FKBP10 mutations affect type I procollagen secretion. These findings identify a previously unrecognized mechanism in the pathogenesis of OI. © 2010 The American Society of Human Genetics.


News Article | March 9, 2016
Site: www.nature.com

Researchers have found Colombia's first cases of birth defects linked to the Zika virus, Nature has learned — which are likely forerunners of a widely anticipated wave of Zika-related birth defects in the country. The discovery is perhaps no surprise: the virus arrived in Colombia last September, and the country is second only to Brazil in terms of the number of people infected with Zika. But Colombian researchers hope that plans put in place to closely monitor pregnant women can help to better establish the magnitude of the threat posed to fetuses by Zika. That is a crucial question that scientists have not so far been able to answer with the data from Brazil. Researchers have diagnosed one newborn with microcephaly — an abnormally small head — and two others with congenital brain abnormalities, says Alfonso Rodriguez-Morales, who chairs the Colombian Collaborative Network on Zika (RECOLZIKA), which made the diagnoses. All three tested positive for the presence of Zika virus. The researchers have submitted a report of their detections to a scientific journal. Rodriguez-Morales, an infectious-diseases epidemiologist at the Technological University of Pereira in western Colombia, says that he expects to see a rise in cases of Zika-linked birth defects starting in two or three months' time. The RECOLZIKA group — a network of researchers and public-health institutions across Colombia — are already investigating a handful of other suspected cases of microcephaly, which have a possible link to Zika. Brazil is the only country so far to report a large surge in newborns with microcephaly that coincides with outbreaks of Zika virus. By the time the alarm over a possible microcephaly link was raised there (in October 2015), Zika infections had already peaked in many parts of the country, because the virus first reached Brazil at the beginning of last year. In Colombia, by contrast, researchers detected the first Zika cases in September, and by December had set up national tracking programmes to monitor pregnant women for signs of infection, and to spot early signs of birth defects in fetuses. Since then, researchers have been waiting attentively to see whether their country might experience a similar rise in birth defects. The true size of Brazil's surge in microcephaly cases is unknown. The country's health ministry says that 5,909 suspected microcephaly cases have been registered since early November, but only 1,687 of them have been investigated so far. Of those, 1,046 have been discarded as false positives, and 641 have been confirmed. (A link with the Zika virus has been confirmed by molecular-lab tests in 82 cases.) Given that Brazil reported only 147 cases of microcephaly in 2014, the reported increase in cases since November suggests a marked rise in the number of babies born with the condition. But the 2014 figure is a “huge underestimate”, says Lavinia Schüler-Faccini, a geneticist who specialises in birth defects at the Federal University of Rio Grande do Sul, Brazil, and president of the Brazilian Society of Genetic Medicine. She says that according to the frequency of microcephaly typically observed in regions around the world, one would expect to see 300–600 cases of severe microcephaly in any given year in Brazil, and around 1,500 less-severe ones. The search for cases of microcephaly in Brazil since October is probably turning up many mild cases that previously went unnoticed — so that the reported surge looks higher than it really is. Still, Schüler-Faccini and other clinicians say there is a real problem. They have observed first-hand a marked increase in the number of unusually severe cases of microcephaly, they say. To be prepared to better interpret any imminent peak in birth defects in Colombia, RECOLZIKA plans to look at historical cases to establish a baseline for the annual numbers of birth defects in different regions. It is also setting up a study to analyse patterns in the distribution of head-circumference measurements recorded in obstetrics units regionally throughout the country, to get a better idea of the local range of normal values. It has also not been possible so far from Brazilian data to quantify the extent to which Zika virus is linked to the rise in microcephaly. The latest data from Brazil's ministry of health show that increased cases of microcephaly and/or congenital malformations of the central nervous system are still concentrated in the northeast — raising questions as to whether other factors, perhaps specific to this region, might also be in play. Clinical evidence leaves little doubt that a link between Zika and microcephaly exists: the virus has been detected in amniotic fluid, in the cerebrospinal fluid of affected babies and in the brains of stillborn fetuses and those aborted after the detection of severe malformations during pregnancy. But there are also many other possible causes of microcephaly, including a group of infections that are collectively called STORCH (syphilis, toxoplasmosis, other infections, rubella, cytomegalovirus infection and herpes simplex), which are known to cause birth defects. Exposure to toxic chemicals and the consumption of alcohol during pregnancy can also cause the condition. “There is a clear need for a full assessment of other detailed causes of microcephaly, such as STORCH, and even non-infectious causes,” says Rodriguez-Morales. Brazil’s health ministry has stated that it is carrying out tests for such causes, but it has not made public how many of the confirmed microcephaly cases are attributable to these. A key question in assessing the scale of the threat that Zika may pose to fetuses is how many pregnant women infected with Zika — in particular during the first trimester, when the fetus is most vulnerable — nonetheless give birth to healthy babies. RECOLZIKA researchers hope to help to answer this through their monitoring programme. The risk posed by Zika may well be lower than that of other diseases that are known to cause microcephaly such as toxoplasmosis and rubella, says Rodriguez-Morales. That is a preliminary estimate, he says, based on back-of-the-envelope calculations of the reported numbers of confirmed cases of microcephaly and congenital disorders, compared to the number of pregnant women in regions experiencing Zika epidemics. But even if its risk does turn out to be low, Zika could still lead to many cases because a large number of pregnant women in the Americas are likely to become infected with the virus. The biggest risk to pregnant women is right now, rather than in the long term. The epidemic is sweeping so quickly through the Americas that much of the population, including young women, will become naturally vaccinated by their exposure to the virus. As population immunity increases, the Zika epidemic is likely to fade quickly, and it will become endemic with only occasional flare ups. In a modelling study posted to the preprint server bioRxiv1 on 29 February, US researchers noted that the risk of prenatal Zika virus exposure “should decrease dramatically following the initial wave of disease, reaching almost undetectable levels”.


News Article | February 21, 2017
Site: www.businesswire.com

ALISO VIEJO, Calif.--(BUSINESS WIRE)--Ambry Genetics (Ambry) has created an online portal to enable more patients and families to participate in research through the AmbryShare program. With this simplified portal, Ambry has streamlined the research consent process to make cohort recruitment easier for clinicians at the time of sample collection for clinical testing. Patients now have the flexibility to e-consent from home, or a mobile device during their office visits. An individual can also enroll themselves and submit a sample to the program independently, whether or not their clinician orders a clinical test at Ambry. The new e-consent portal is one more example of the company’s mission to use AmbryShare to remove the red-tape that has been slowing down scientific progress. The data-sharing program is currently focused on the genomics of autism and prostate cancer, and Ambry is actively seeking research partners for those initiatives. “We've created a simple way for patients to participate in crowd-sourced research,” said Brigette Tippin Davis, PhD, Ambry’s Director of Emerging Genetic Medicine. “If your family is impacted by disease, we are empowering you to make a real difference. AmbryShare freely enables researchers worldwide to put your de-identified genomic DNA to work to find treatments, keeping your privacy protected at the same time.” Since March 2016, Ambry has provided researchers with de-identified aggregated data from whole exome sequencing on a large cohort of affected patients with the intention of aiding and accelerating scientific research at no cost to the public. This data will ultimately help clinicians create more tailored treatments through enhanced understanding of human disease. For more information and to enroll in AmbryShare, visit the AmbryShare portal here. Ambry Genetics is both College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified. Ambry leads in clinical genetic diagnostics and genetics software solutions, combining both to offer the most comprehensive testing menu in the industry. Ambry has established a reputation for sharing data while safeguarding patient privacy, unparalleled service, and responsibly applying new technologies to the clinical molecular diagnostics market. For more information about Ambry Genetics, visit www.ambrygen.com.


News Article | February 17, 2017
Site: www.eurekalert.org

When a child is conceived, he or she receives DNA from both parents. The child's own genome thus consists of a maternal and a paternal genome. However, some genes -- about 100 out of the 20,000 encoded genes-- are exclusively expressed either from the maternal or from the paternal genome, with the other copy of the gene remaining silent. We know that these imprinted genes are more likely to lead to serious genetic diseases, such as Prader-Willi or Angelman syndrome. Researchers at the University of Geneva (UNIGE), Switzerland, have devised a new technique, based on a combination of biology and bioinformatics, to quickly and accurately detect the imprinted genes expressed in each of the cell types that constitute the human organs. This major breakthrough will improve our understanding and diagnosis of genetic diseases. The study can be read in full in the American Journal of Human Genetics. The research team, led by Professor Stylianos Antonarakis from the Department of Genetic Medicine and Development in the Faculty of Medicine at UNIGE, focused on genomic imprinting. This is a set of genes exclusively expressed from the genetic code inherited either from the father (the paternal allele) or from the mother (maternal allele). Why is there so much interest in the identification of the imprinted genes? Because if a deleterious mutation affects the functional allele, it cannot be compensated by the expression of the second silent allele, likely causing a serious genetic disease. The goal, therefore, is to determine the imprinted genes in all cell types of human body tissues that are liable to cause these kind of diseases. Until recently, millions of cells were analysed together without distinction. «We have now developed a new technique with a better resolution, known as Human Single-Cell Allele-Specific Gene Expression," explains Christelle Borel, UNIGE researcher. "The process can be used to simultaneously examine the expression of the two alleles, paternal and maternal, of all known genes in each individual cell. The method is fast and can be carried out on thousands of single cells with the utmost precision using next-generation sequencing technology." The heterogeneity of each tissue of the body is thus analysed in detail while searching for imprinted genes in disease-relevant tissue. The individual's genome is sequenced, as is the genome of both parents, in order to identify the parental origin of the alleles transcribed in the person's single cell. Federico Santoni, first author of the study and researcher at UNIGE and HUG (Geneva University Hospitals) further explains, "We establish the profile of the allelic expression for thousands of genes in each single cell. We then process this data with a novel computational and statistical framework to identify the specific signature of each imprinted gene, enabling us to accurately record them." This new technique redefines the landscape of imprinted genes by examining all cell types, and can be applied to all tissues affected by diseases, such as cardiac and brain tissue. Moreover, the scientists have discovered novel imprinted genes and demonstrated that some were restricted to certain tissues or cell types. This technique focuses on the specific characteristics of each individual by treating each cell as a single entity. This concept, called Single-cell Genomics, is part of an emerging field that is assuming an all-important role at UNIGE, which sees it as the future of medicine that will be personalised rather than generalised. Thanks to the technique pioneered by UNIGE researchers, it will be possible to identify new disease causing genes and to adapt a specific and targeted treatment for individual patients.


INGELHEIM, Germany--(BUSINESS WIRE)--Boehringer Ingelheim today announced a collaboration with Weill Cornell Medicine to identify new treatment approaches for chronic obstructive pulmonary disease (COPD) in order to develop novel treatments that could possibly halt or even reverse the progression of the disease process. The new, three-year collaboration combines Weill Cornell Medicine’s Department of Genetic Medicine’s unique understanding of chronic airway diseases and experience in the investigation of novel therapeutic concepts for airway repair with Boehringer Ingelheim’s expertise in the discovery and development of new therapies for respiratory diseases. This collaboration is the second collaboration between Boehringer Ingelheim and Weill Cornell Medicine, following prior work in inflammatory bowel disease (IBD). Chronic lower respiratory diseases, which include COPD, are the third leading cause of death in the United States, and approximately 15 million Americans have been told by a healthcare provider that they have COPD. It cannot be cured and current treatment approaches focus on bronchodilation, reducing symptoms and preventing exacerbations to decelerate the downward spiral of the disease. The goal is to help patients keep as active as possible and overall, improve their quality of life. “Our continuous search for molecular drivers of chronic obstructive airway diseases has revealed novel repair mechanisms that warrant further investigation of their potential as therapeutic approaches,” said Dr. Ronald G. Crystal, Chairman of Genetic Medicine at Weill Cornell Medicine and lead investigator in the new collaboration. “We will look to further expand our knowledge about progressive airway destruction in close collaboration with Boehringer Ingelheim and focus on promising therapeutic concepts with the potential to slow down or halt progressive airway damage in patients with COPD.” “We are delighted to work with Dr. Crystal at Weill Cornell Medicine, who is one of the leading scientists in severe progressive airway diseases worldwide,” said Dr. Clive R. Wood, Senior Corporate Vice President, Discovery Research at Boehringer Ingelheim. “The scientists at Weill Cornell Medicine and Boehringer Ingelheim will work hand in hand to translate new discoveries into drug discovery and development programs at Boehringer Ingelheim. The new collaboration is an excellent example of our unique partnering approach and our focus on early innovation, underscoring our ambition to develop the next generation of medical treatments for patients with COPD.” Boehringer Ingelheim is combining a focus on cutting-edge science with a long-term view enabling the company to create a stable environment for the development of the next generation of medical breakthroughs. This new project adds another building block in this long-term strategy to improve the lives of patients with high unmet medical needs. Weill Cornell's Office of BioPharma Alliances and Research Collaborations negotiated the three-year collaboration. The office’s mission is to proactively generate, structure and market translational research alliances with industry in order to advance promising research projects that have commercial potential. For more information, contact Larry Schlossman at las2041@med.cornell.edu or at 212-746-6909. For references and notes to editors, please visit:

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