Tracing the start of COVID-19 in GA

At a time when COVID-19 appears to be receding in much of Georgia, it’s worth revisiting the start of the pandemic in early 2020. Emory virologist Anne Piantadosi and colleagues have a paper in Viral Evolution on the earliest SARS-CoV-2 genetic sequences detected in Georgia. Analyzing relationships between those virus sequences and samples from other states and countries can give us an idea about where the first COVID-19 infections in Georgia came from. We can draw Read more

Reddit as window into opioid withdrawal strategies

Drug abuse researchers are using the social media site Reddit as a window into the experiences of people living with opioid addiction. Abeed Sarker in Emory's Department of Biomedical Informatics has a paper in Clinical Toxicology focusing on the phenomenon of “precipitated withdrawal,” in collaboration with emergency medicine specialists from Penn, Rutgers and Mt Sinai. Precipitated withdrawal is a more intense form of withdrawal that can occur when someone who was using opioids starts medication-assisted treatment Read more

CROI: HIV cure report and ongoing research

The big news out of CROI (Conference on Retroviruses and Opportunistic Infections) was a report of a third person being cured of HIV infection, this time using umbilical cord blood for a hematopoetic stem cell transplant. Emory’s Carlos del Rio gave a nice overview of the achievement for NPR this morning. As del Rio explains, the field of HIV cure research took off over the last decade after Timothy Brown, known as “the Berlin patient,” Read more

Simpler, more portable ECGs: Emory experts hosting computing challenge

An electrocardiogram or ECG is a basic non-invasive diagnostic tool for cardiologists, which conventionally uses 12 electrodes to gather information about electrical signals in the heart and its rhythms. Emory biomedical informatics specialists are hosting an international computing contest aimed at reducing that number as low as possible, so that future portable or wearable ECG devices can be smaller, more convenient and lower in cost.

“We are challenging the research community and industry to design algorithms that classify a large range of cardiac abnormalities using ECGs with varying numbers of channels,” says co-organizer Gari Clifford, PhD, chair of biomedical informatics at Emory University School of Medicine. “The aim is to determine how low we can go — that is, how many channels of data do we need to make an accurate diagnosis?”

The devices could aid in diagnosing common conditions such as atrial fibrillation or supraventricular tachycardia.

“Reduced-lead ECGs are more accessible than standard twelve-lead ECGs in many parts of the world, and the development of effective open-source algorithms for reading reduced-lead ECGs is key for tackling the growing problem of cardiac events internationally,” says co-organizer Matthew Reyna, PhD, assistant professor of biomedical informatics and pharmacology and chemical biology.

The 2021 PhysioNet/Computing in Cardiology Challenge is titled “Will Two Do? Varying Dimensions in Electrocardiography” and calls for designers to build an algorithm that can classify cardiac abnormalities based on 12, 6, 3 and 2-lead ECGs.

So that participants can try out their algorithms, contest organizers are sharing the world’s largest and most diverse set of publicly available ECG data: over 45,000 recordings from China, Europe, Russia and the USA. A similar amount of data has been hidden for the organizers to test the competitors’ algorithms, and a separate evaluation metric will reflects errors of misdiagnosis.

This year’s contest builds upon previous years; in 2017, the challenge was to classify atrial fibrillation based on a single lead, and last year’s was a challenge to diagnose a variety of cardiac problems using standard 12 leads. Contest participants are invited to submit an abstract describing their algorithm, open-source code for their algorithm and a paper on their work.

The contest culminates in the Computing in Cardiology conference, scheduled for September 12-15 in Brno, Czech Republic. More information about the contest is available at PhysioNet.org and requirements for entry and the schedule are detailed at the PhysioNet/Computing in Cardiology Challenge 2021 site. The initial deadline for applying to enter the contest is April 9, 2021.

The contest is part of PhysioNet, an archive of biomedical computing resources supported by the National Institute of Biomedical Imaging and Bioengineering (R01EB030362). It is being co-sponsored by the Gordon and Betty Moore Foundation, Google and MathWorks. Complementary MATLAB licenses and Google Cloud Platform credits are being made available for this year’s challenge. The sponsors are also making it possible to offer several prizes worth several thousand dollars.

Posted on by Quinn Eastman in Heart Leave a comment

First (and massive) whole-genome study of IBD in African Americans

In African Americans, the genetic risk landscape for inflammatory bowel disease (IBD) is very different from that of people with European ancestry, according to results of the first whole-genome study of IBD in African Americans. The authors say that future clinical research on IBD needs to take ancestry into account.

Findings of the multi-center study, which analyzed the whole genomes of more than 1,700 affected individuals with Crohn’s disease and ulcerative colitis and more than 1,600 controls, were published on February 17 in the American Journal of Human Genetics.

As part of their analysis, the researchers developed an algorithm that corrects for ancestry when calculating an IBD polygenic risk score. Polygenic risk scores are tools for calculating gene-based risk for a disease, which are used for IBD as well as other complex conditions such as coronary artery disease.

“Even though the disease destination looks the same, the populations look very different, in terms of what specific genes contribute to risk for IBD,” says lead author Subra Kugathasan, MD. “It shows that you can’t develop a polygenic risk score based on one population and apply it to another.”

Kugathasan is scientific director of the pediatric IBD program and director of the Children’s Center for Transplantation and Immune-mediated Disorders at Children’s Healthcare of Atlanta, as well as Marcus professor of pediatrics and human genetics at Emory University School of Medicine.

The first author of the paper is geneticist Hari Somineni, PhD, who earned his doctorate working with Kugathasan at Emory, and is now working at Goldfinch Bio in Massachusetts.

The primary sites to recruit study participants were Emory, Cedars-Sinai and Rutgers, along with Johns Hopkins and Washington University at Saint Louis. Along with Kugathasan, the co-senior authors and co-organizers of the study were Steven Brant, MD from Rutgers and Dermot McGovern, MD, PhD from Cedars-Sinai.

“One of our goals in treating IBD is to move toward a more personalized approach,” says McGovern, the Joshua L. and Lisa Z. Greer Chair in Inflammatory Bowel Disease Genetics at Cedars-Sinai. “Deciphering the genetic architecture is an important part of this effort. Studies such as this one are vital to ensure that diverse populations, including African-Americans, benefit from the tremendous advances promised by genomic medicine.”

Read more

Posted on by Quinn Eastman in Immunology, Uncategorized Leave a comment

Emory researchers SNARE new Alzheimer’s targets

Diving deep into Alzheimer’s data sets, a recent Emory Brain Health Center paper in Nature Genetics spots several new potential therapeutic targets, only one of which had been previous linked to Alzheimer’s. The Emory analysis was highlighted by the Alzheimer’s site Alzforum, gathering several positive comments from other researchers.

Thomas Wingo, MD

Lead author Thomas Wingo and his team — wife Aliza Wingo is first author – identified the targets by taking a new approach: tracing connections between proteins that are altered in abundance in patients’ brains and risk genes identified through genome-wide association studies.

The list of 11 genes/proteins named as “consistent with being causal” may be contributing to AD pathogenesis through various mechanisms: vesicular trafficking, inflammation, lipid metabolism and hypertension. We asked Wingo which ones he wanted to highlight, and he provided this comment:

“The most interesting genes, to me, are the ones involved in the SNARE complex (in the paper, STX4 and STX6) and the others involved in vesicular trafficking. There is already a deep body of literature that describe a role for some of these components in AD, and I’m hopeful providing specific targets might be useful to those studies.”

A simplistic way to look at the mechanism of Alzheimer’s disease is: proteins build up in the brain, in the form of amyloid plaques and neurofibrillary tangles. The functions of neurons and other brain cells are thought to be impaired by bits of beta-amyloid floating around.

Inside neurons, the SNARE complex is the core of the machinery that pushes vesicles to fuse with the cell membrane. Neurons communicate with each other by having vesicles inside the cell – bags full of neurotransmitters – release their contents. They’re like tiny packets of pepper or other spices that make the neuron next door sneeze. In Alzheimer’s, amyloid oligomers have been reported to block SNARE complex assembly, which may explain aspects of impaired cognition.

Posted on by Quinn Eastman in Neuro Leave a comment

Strengthening SARS-CoV-2 genomic surveillance: support from CDC, private foundations

As part of an effort to strengthen genomic surveillance for emerging strains of SARS-CoV-2, the Centers for Disease Control and Prevention (CDC) has awarded a contract to Emory University researchers to characterize viral variants circulating in Georgia.

The two-year contract is part of the SPHERES (SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance) initiative, with roughly $620,000 in total costs. The prin