Monthly Archives: March 2020

The genetic architecture of the human cerebral cortex

By Katrina L. Grasby, Neda Jahanshad, Jodie N. Painter, Luca Colodro-Conde, Janita Bralten, Derrek P. Hibar, Penelope A. Lind, Fabrizio Pizzagalli, Christopher R. K. Ching, Mary Agnes B. McMahon, Natalia Shatokhina, Leo C. P. Zsembik, Sophia I. Thomopoulos, Alyssa H. Zhu, Lachlan T. Strike, Ingrid Agartz, Saud Alhusaini, Marcio A. A. Almeida, Dag Alns, Inge K. Amlien, Micael Andersson, Tyler Ard, Nicola J. Armstrong, Allison Ashley-Koch, Joshua R. Atkins, Manon Bernard, Rachel M. Brouwer, Elizabeth E. L. Buimer, Robin Blow, Christian Brger, Dara M. Cannon, Mallar Chakravarty, Qiang Chen, Joshua W. Cheung, Baptiste Couvy-Duchesne, Anders M. Dale, Shareefa Dalvie, Tnia K. de Araujo, Greig I. de Zubicaray, Sonja M. C. de Zwarte, Anouk den Braber, Nhat Trung Doan, Katharina Dohm, Stefan Ehrlich, Hannah-Ruth Engelbrecht, Susanne Erk, Chun Chieh Fan, Iryna O. Fedko, Sonya F. Foley, Judith M. Ford, Masaki Fukunaga, Melanie E. Garrett, Tian Ge, Sudheer Giddaluru, Aaron L. Goldman, Melissa J. Green, Nynke A. Groenewold, Dominik Grotegerd, Tiril P. Gurholt, Boris A. Gutman, Narelle K. Hansell, Mathew A. Harris, Marc B. Harrison, Courtney C. Haswell, Michael Hauser, Stefan Herms, Dirk J. Heslenfeld, New Fei Ho, David Hoehn, Per Hoffmann, Laurena Holleran, Martine Hoogman, Jouke-Jan Hottenga, Masashi Ikeda, Deborah Janowitz, Iris E. Jansen, Tianye Jia, Christiane Jockwitz, Ryota Kanai, Sherif Karama, Dalia Kasperaviciute, Tobias Kaufmann, Sinead Kelly, Masataka Kikuchi, Marieke Klein, Michael Knapp, Annchen R. Knodt, Bernd Krmer, Max Lam, Thomas M. Lancaster, Phil H. Lee, Tristram A. Lett, Lindsay B. Lewis, Iscia Lopes-Cendes, Michelle Luciano, Fabio Macciardi, Andre F. Marquand, Samuel R. Mathias, Tracy R. Melzer, Yuri Milaneschi, Nazanin Mirza-Schreiber, Jose C. V. Moreira, Thomas W. Mhleisen, Bertram Mller-Myhsok, Pablo Najt, Soichiro Nakahara, Kwangsik Nho, Loes M. Olde Loohuis, Dimitri Papadopoulos Orfanos, John F. Pearson, Toni L. Pitcher, Benno Ptz, Yann Quid, Anjanibhargavi Ragothaman, Faisal M. Rashid, William R. Reay, Ronny Redlich, Cline S. Reinbold, Jonathan Repple, Genevive Richard, Brandalyn C. Riedel, Shannon L. Risacher, Cristiane S. Rocha, Nina Roth Mota, Lauren Salminen, Arvin Saremi, Andrew J. Saykin, Fenja Schlag, Lianne Schmaal, Peter R. Schofield, Rodrigo Secolin, Chin Yang Shapland, Li Shen, Jean Shin, Elena Shumskaya, Ida E. Snderby, Emma Sprooten, Katherine E. Tansey, Alexander Teumer, Anbupalam Thalamuthu, Diana Tordesillas-Gutirrez, Jessica A. Turner, Anne Uhlmann, Costanza Ludovica Vallerga, Dennis van der Meer, Marjolein M. J. van Donkelaar, Liza van Eijk, Theo G. M. van Erp, Neeltje E. M. van Haren, Daan van Rooij, Marie-Jos van Tol, Jan H. Veldink, Ellen Verhoef, Esther Walton, Mingyuan Wang, Yunpeng Wang, Joanna M. Wardlaw, Wei Wen, Lars T. Westlye, Christopher D. Whelan, Stephanie H. Witt, Katharina Wittfeld, Christiane Wolf, Thomas Wolfers, Jing Qin Wu, Clarissa L. Yasuda, Dario Zaremba, Zuo Zhang, Marcel P. Zwiers, Eric Artiges, Amelia A. Assareh, Rosa Ayesa-Arriola, Aysenil Belger, Christine L. Brandt, Gregory G. Brown, Sven Cichon, Joanne E. Curran, Gareth E. Davies, Franziska Degenhardt, Michelle F. Dennis, Bruno Dietsche, Srdjan Djurovic, Colin P. Doherty, Ryan Espiritu, Daniel Garijo, Yolanda Gil, Penny A. Gowland, Robert C. Green, Alexander N. Husler, Walter Heindel, Beng-Choon Ho, Wolfgang U. Hoffmann, Florian Holsboer, Georg Homuth, Norbert Hosten, Clifford R. Jack Jr., MiHyun Jang, Andreas Jansen, Nathan A. Kimbrel, Knut Kolskr, Sanne Koops, Axel Krug, Kelvin O. Lim, Jurjen J. Luykx, Daniel H. Mathalon, Karen A. Mather, Venkata S. Mattay, Sarah Matthews, Jaqueline Mayoral Van Son, Sarah C. McEwen, Ingrid Melle, Derek W. Morris, Bryon A. Mueller, Matthias Nauck, Jan E. Nordvik, Markus M. Nthen, Daniel S. OLeary, Nils Opel, Marie-Laure Paillre Martinot, G. Bruce Pike, Adrian Preda, Erin B. Quinlan, Paul E. Rasser, Varun Ratnakar, Simone Reppermund, Vidar M. Steen, Paul A. Tooney, Fbio R. Torres, Dick J. Veltman, James T. Voyvodic, Robert Whelan, Tonya White, Hidenaga Yamamori, Hieab H. H. Adams, Joshua C. Bis, Stephanie Debette, Charles Decarli, Myriam Fornage, Vilmundur Gudnason, Edith Hofer, M. Arfan Ikram, Lenore Launer, W. T. Longstreth, Oscar L. Lopez, Bernard Mazoyer, Thomas H. Mosley, Gennady V. Roshchupkin, Claudia L. Satizabal, Reinhold Schmidt, Sudha Seshadri, Qiong Yang, Alzheimers Disease Neuroimaging Initiative, CHARGE Consortium, EPIGEN Consortium, IMAGEN Consortium, SYS Consortium, Parkinsons Progression Markers Initiative, Marina K. M. Alvim, David Ames, Tim J. Anderson, Ole A. Andreassen, Alejandro Arias-Vasquez, Mark E. Bastin, Bernhard T. Baune, Jean C. Beckham, John Blangero, Dorret I. Boomsma, Henry Brodaty, Han G. Brunner, Randy L. Buckner, Jan K. Buitelaar, Juan R. Bustillo, Wiepke Cahn, Murray J. Cairns, Vince Calhoun, Vaughan J. Carr, Xavier Caseras, Svenja Caspers, Gianpiero L. Cavalleri, Fernando Cendes, Aiden Corvin, Benedicto Crespo-Facorro, John C. Dalrymple-Alford, Udo Dannlowski, Eco J. C. de Geus, Ian J. Deary, Norman Delanty, Chantal Depondt, Sylvane Desrivires, Gary Donohoe, Thomas Espeseth, Guilln Fernndez, Simon E. Fisher, Herta Flor, Andreas J. Forstner, Clyde Francks, Barbara Franke, David C. Glahn, Randy L. Gollub, Hans J. Grabe, Oliver Gruber, Asta K. Hberg, Ahmad R. Hariri, Catharina A. Hartman, Ryota Hashimoto, Andreas Heinz, Frans A. Henskens, Manon H. J. Hillegers, Pieter J. Hoekstra, Avram J. Holmes, L. Elliot Hong, William D. Hopkins, Hilleke E. Hulshoff Pol, Terry L. Jernigan, Erik G. Jnsson, Ren S. Kahn, Martin A. Kennedy, Tilo T. J. Kircher, Peter Kochunov, John B. J. Kwok, Stephanie Le Hellard, Carmel M. Loughland, Nicholas G. Martin, Jean-Luc Martinot, Colm McDonald, Katie L. McMahon, Andreas Meyer-Lindenberg, Patricia T. Michie, Rajendra A. Morey, Bryan Mowry, Lars Nyberg, Jaap Oosterlaan, Roel A. Ophoff, Christos Pantelis, Tomas Paus, Zdenka Pausova, Brenda W. J. H. Penninx, Tinca J. C. Polderman, Danielle Posthuma, Marcella Rietschel, Joshua L. Roffman, Laura M. Rowland, Perminder S. Sachdev, Philipp G. Smann, Ulrich Schall, Gunter Schumann, Rodney J. Scott, Kang Sim, Sanjay M. Sisodiya, Jordan W. Smoller, Iris E. Sommer, Beate St Pourcain, Dan J. Stein, Arthur W. Toga, Julian N. Trollor, Nic J. A. Van der Wee, Dennis van t Ent, Henry Vlzke, Henrik Walter, Bernd Weber, Daniel R. Weinberger, Margaret J. Wright, Juan Zhou, Jason L. Stein, Paul M. Thompson, Sarah E. Medland, Enhancing NeuroImaging Genetics through Meta-Analysis Consortium (ENIGMA)Genetics working group

Science20 Mar 2020

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The genetic architecture of the human cerebral cortex - Science Magazine

SIOUX FALLS, S.D. Averas laboratory in Sioux Falls has been verified by the South Dakota Department of Health to perform COVID-19 testing, according to a news release.

The additional testing site will allow for the processing of up to 200 tests per day.

The Avera Institute for Human Genetics has worked closely with the governors office as well as the state health department to establish guidelines on how pending tests are processed, the release states.

The most critical and highly suspicious tests will receive priority. Result time will depend on volume, however, most test results will be able to be returned in a few days and inpatient tests that are considered urgent based on the patients condition can be returned more quickly.

So far, testing for COVID-19 has been conducted by the state health departments laboratory and Averas contract laboratory.

All test results will be sent to the state for reporting purposes. Patients with positive test results will be contacted with instructions on how to care for themselves at home, symptom management, and when to contact a health care provider if symptoms worsen.

As a public service, weve opened this article to everyone regardless of subscription status.

Link:
Avera announces ability to test for COVID-19 in South Dakota - The Dickinson Press

Editors note: The Salt Lake Tribune is providing readers free access to critical local stories about the coronavirus during this time of heightened concern. See more coverage here.

University of Utah experts are expressing concern about the hype surrounding two medications that President Donald Trump and state officials have held up as potential treatments for the coronavirus.

Andy Pavia, chief of pediatric infectious disease at the U., is also urging caution, noting that the nations top infectious disease expert has warned that there is no convincing evidence yet that these drugs work, only stories.

The drugs have been used for years for arthritis, psoriasis and malaria, and are available in Utah pharmacies through prescription by doctors. But Grunwald said casting the unproven medications as a potential treatment for coronavirus could incite panic buying and limit the availability of the drugs for sick patients who depend on them.

The geneticist said hes not asserting that the drugs are necessarily ineffective just that they are wholly unproved.

I am simply saying defying the principles of reviewed science has dangerous consequences, especially seen in a community that is fearful and in an environment that is susceptible to panicked behavior, said Grunwald, who is a scientist, but not a medical doctor.

The drugs have not been approved by the Food and Drug Administration for COVID-19 although Utah officials said Friday that doctors still may prescribe them for COVID-19 patients here and say evidence shows they should.

On the other hand, Pavia said medical experts dont yet have good data about whether the drugs are effective against the virus.

We need to be very cautious until we have better information. In fact, chloroquine worked in the test tube against other viruses but proved to be potentially harmful when properly studied, he said. "We hope it works, but hope is not the best way to choose safe and effective treatment.

The information that youre referring to specifically is anecdotal, Fauci told reporters. It was not done in a controlled clinical trial. So you really cant make any definitive statement about it.

Trump, standing next to Fauci, still said the federal government has ordered millions of doses. He also said the nation has nothing to lose by trying it.

During Fridays news conference, Utah officials and medical representatives were essentially saying the same things as the president.

There are responses that are equivalent to Lazarus literally the biblical Lazarus people almost dead coming back, said physician Kurt Hegmann, director of the Rocky Mountain Center for Occupational and Environmental Health at the University of Utah, about hydroxychloroquine.

Officials said they are surveying Utah pharmacies to see how much of the drugs they now have on hand and are working with other states to develop plans for distributing the drugs to areas in need.

They also cautioned doctors and pharmacists to be judicious in how they dispense the drugs for now.

Utah Senate President Stuart Adams said the news conference about the drugs was called to give worried Utahns some hope.

We need some good news. We think this is good news, the Layton Republican said. We believe theres hope in America.

Utahs state epidemiologist, Angela Dunn, said last week that a lot of scientists internationally and in the U.S. are studying medications that could help treat COVID-19. Most have involved extremely small patient groups, she noted.

Current studies about the malaria drugs specifically have been very small sample sizes one in particular was only 40 people so its difficult to extrapolate that to large population," she said. So the next step is to do studies with bigger populations to see if its effective.

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University of Utah experts advise caution over drugs hyped as possible coronavirus treatments - Salt Lake Tribune

Clement Chow, an assistant professor of human genetics at The University of Utah, US, tweeted last week that he was in the ICU with coronavirus. And that's when researchers who had attended a meeting with him found out about it. At a time when experts are stressing on testing and contract tracing to check community transmission, this incident reveals serious and massive gaps in America's fight against COVID-19.

"Hi guys. Have you missed me? Ive been in the ICU fighting...wait for it...Coronavirus! I am the first case at the U of U ICU! Breaking the bamboo ceiling!," tweeted Chow on March 16. He further said, "Basically had a low-grade fever for a few days then a bad cough, that turned into respiratory failure. I came in and they had to put me on high flow oxygen (3 times normal)...hence ICU."

According to a March 20 report in Nature, two dozen geneticists who had attended a meeting with him nine days earlier subsequently saw the tweet and came to know that Chow had tested positive for COVID-19. While the researchers were worried for Chow, they were also upset that this was the first they had heard about it, says the report.

The fact that we learned about this from a tweet points to a failure of our department of health. But maybe we can come together with grass-root responses, Nels Elde, also an associate professor of human genetics at The University of Utah in Salt Lake City, told Nature. He had reportedly shared a dinner plate with Chow before he was diagnosed with COVID-19.

Elde tweeted to Chow on March 16 and said, "Was going through our text messages and your decision to self-quarantine early for cold-like symptoms that you were convinced was not SARS-CoV-2 was a good one and good example for us all. Get well soon @ClementYChow."

Chow further explained that his breathing was so compromised that he could not keep his oxygen levels up even with "10L of oxygen." He said while he was the first COVID19 patient in the ICU on March 19, there are more now. "Important point: we really dont know much about his virus. Im young and not high risk, yet I am in the ICU with a very severe case," said Chow.

Another researcher who had attended the meeting with Chow described how the group from 16 states "scrambled to work out who they had spent time with since returning home from the meeting." "They were upset that four days had passed between when their colleague was hospitalized with symptoms of COVID-19 and when they found out, through Twitter, that he had the disease. Another 24 hours would pass before an email from Utahs public-health departments made it their way. Every passing minute, the virus has a chance to move to someone else," reports Nature.

Meanwhile, the researchers who learned of their exposure through Twitter are taking precautionary measures by taking their temperatures and self-quarantining themselves.

Over 33,270 cases have been reported in the US so far, and 417 have died. New York state accounts for 117 deaths currently, passing Washington state, the initial epicenter of the pandemic in the US, in the number of fatal cases.

According to experts, contact tracing is important as people in close contact with someone who is infected with a virus, such as the COVID-19 virus are at higher risk of becoming infected themselves and of potentially further infecting others.

An analysis of Singapores containment measures that were implemented to minimize disease spread, for example, shows that contact tracing contributed to the primary detection of approximately half (53%) of COVID-19 patients. The study, based on a review of the first 100 cases in Singapore, shows that the mean interval from symptom onset to isolation was 5.6 days and declined after approximately 1 month.

Singapore implemented strong surveillance and containment measures, which appear to have slowed the growth of the outbreak. The study estimated that if other countries had similar detection capacities as Singapore, the global number of imported cases detected would be 2.8 times higher than the observed current number, said the report. It added, The surveillance methods in Singapore complemented one another to identify infected persons, with the overlapping components constituting safety nets; none of the methods alone would have detected all patients.

During a media briefing on March 16, the World Health Organization (WHO) Director-general Dr Tedros Adhanom Ghebreyesus had said that while there has been a rapid escalation in social distancing measures across countries, they have not seen an urgent enough escalation in testing, isolation and contact tracing which, he said, was the backbone of the COVID-19 response. "We have a simple message for all countries: test, test, test, he had emphasized.

Dr Ghebreyesus explained that while social distancing measures can help to reduce transmission and enable health systems to cope, such measures alone would not be enough to "extinguish this pandemic." "Its the combination that makes the difference. As I keep saying, all countries must take a comprehensive approach, he said.

More here:
Coronavirus: Massive gap in US response revealed after scientists learn colleague tested positive through twee - MEAWW

Dr. Segun Fatumo is a computer scientist with specialization in bioinformatics with keen interest in the genetic impact of non-communicable diseases in Africa and bioinformatics capacity building in Africa. He has been involved in various genetic projects including analysing a large-scale genomic dataset from Ugandan population. During his PhD, he was able to identified twenty-two (22) potential novel drug targets against malaria. Currently, he is an Assistant Professor at the London School of Hygiene and Tropical Medicine (University of London). Genetic Literacy Project (GLP) interviewed him to shed more light on the importance, challenges and future direction of a recent genetic research that he was a leading author.

As one of the lead authors of your recently published paper, what motivated this research project?

Precision medicine is fundamentally going to change healthcare. Genomic medicines is a key component of precision medicine with enormous potential to inform clinical medicine. One potential limitation to genomic medicine is the underrepresentation of African and other populations in genomics research. Previous studies have warned that a much broader range of populations should be investigated to avoid genomic medicine being of benefit merely to a privileged few. This is especially problematic, as previous studies have shown that Africa studies contribute an outsized number of associations relative to studies of similar sizes in Europeans. To demonstrate the potential of African genomes as a great resource for genomic medicine, we collected and analyzed genome-wide data from 6,407 individuals from Uganda.

What is the value of collecting more genomic data from African populations which are badly underrepresented in genomic databases.

Our findings from even modest side studies highlight the importance and usefulness of examining genetically diverse populations within Africa. Findings from large-scale studies from Africa may foster the development of new treatments that will benefit people living in Africa as well as people of African descent around the world.

What sort of challenges did you face in the study, and how did you overcame them?

So many challenges including community engagement, ethics, recruitment, etc. Globally, genomics research and specifically recruitment of participants regardless of the continent is always challenging. However, 60% of Africans live in rural areas. Prospective participants are more likely to be poor and to have limited access to healthcare and education. This means that the carrying out of research in these settings invariably presents challenges of a different order to those in higher income countries. Researchers should not exploit these challenges.

Is the value of this research project beyond Uganda and why?

Yes. Findings from our study may foster the development of new treatments that will benefit people living in Africa as well as people of African descent around the world.

What were the responses that you have received so far about the findings?

Enormous responses. I find it difficult to attend to all media requests.

What is the future direction of the research?

While there is an urgent need to perform large-scale genomic research in Africa, several ongoing initiatives such as H3Africa and the Nigerian 100K Non-Communicable Diseases Genetic Heritage Study (NCD-GHS) could provide the data to improve the evidence base and make genome medicine useful to diverse populations.

How do you see the future of genetics and bioinformatics in Africa?

I think we are now on the right track. We have established the Nigerian Bioinformatics and Genomics Network (NBGN). There are also other initiatives. We are now focusing on building capacity in Africa.

Olumide Odeyemi is a research scientist with a doctoral degree from the University of Tasmania, Australia. His areas of expertise and interest include food microbiology, microbial food safety and quality, aquaculture microbiology and research communication. Follow him on Twitter @olumide_odeyemi

Dr. Segun Fatumo is an assistant professor of genetic epidemiology and bioinformatics at the London School of Hygiene & Tropical Medicine. Follow him on Twitter @SFatumo

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Studying the African genome could yield new medical treatments for everyone - Genetic Literacy Project