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Archive - 2019

October 16th

Quantifying Hispanic and Latinx Populations' Interest in Genetic Research Participation

Researchers are increasingly prioritizing the need for diversity in genetics and genomics research. To help make such studies more inclusive, José G. Pérez-Ramos, MPH, and Timothy D.V. Dye, PhD, research scientists at the University of Rochester in New York. examined Hispanic and Latinx populations’ desire to participate in genomics research. Mr. Pérez-Ramos presented the findings on October 16 at the American Society of Human Genetics (ASHG) 2019 Annual Meeting in Houston, Texas (October 15-19). The presentation abstract is titled “Variation in Intention to Participate in Genetic Research Among Hispanic/Latinx Populations by Latin America Birth-Residency Concurrence: A Global Study. “We were interested in the determinants for people to participate in genetic research,” said Dr. Dye, principal investigator on the study. “Not only is representation in research important for accuracy of results, but it also helps improve distributional justice. If Hispanic and Latinx people are not represented, then there’s no possibility of them benefitting from all of the important genetics research that’s happening.” Mr. Pérez-Ramos and colleagues surveyed 1,718 individuals from 69 countries; among whom, 251 participants self-identified as Hispanic or Latin American and Caribbean (LAC). When measured as a single group, Hispanic and LAC people were as willing to participate in genomics research studies, and felt as positively about their impact, as other groups. However, when the participants of Hispanic and LAC ancestry were segmented further by country of birth and residence, there were noticeable differences in attitudes toward, and interest in, genetic research participation.

New Human Reference Genome Resources Help Capture Global Genetic Diversity

Scientists have assembled a set of genetic sequences that enable the reference genome to better reflect global genetic diversity. The new sequences improve the utility of the human reference genome, a touchstone resource for modern genetics and genomics research, and these sequences were presented at the American Society of Human Genetics (ASHG) 2019 Annual Meeting in Houston, Texas. The presentation was titled “Constructing a Reference Genome That Captures Global Genetic Diversity for Improved Interpretation of Whole Genome Sequencing Data,” and the abstract is available online at When the Human Genome Project was completed in 2003, its signature achievement was the human reference genome, a set of DNA sequences that serves as a structure and representative example of the complete set of human genes. For areas of the genome where there is little variation among different people, the reference genome is an important resource that has helped move forward efforts in gene sequencing, genome-wide association studies, and protein characterization. Because almost all genetic sequencing experiments rely on the human reference genome, there is a pressing need to improve the reference to better capture the diversity found in different human populations, explained Karen Wong (photo), BS, a graduate student in Professor Pui-Yan Kwok’s laboratory at the University of California, San Francisco (UCSF), who presented the research. A more representative reference would benefit scientists using the millions of existing sequencing datasets, as well as future sequencing studies.

October 15th

“Resurrection” of 50,000-Year-Old Gene Reveals How Malaria Parasite Jumped from Gorillas to Humans

For the first time, scientists have uncovered the likely series of events that led to the world’s deadliest malaria parasite being able to jump from gorillas to humans. Researchers at the Wellcome Sanger Institute in the UK and the University of Montpellier in France reconstructed an approximately 50,000-year-old gene sequence that was acquired by the ancestor of Plasmodium falciparum, giving it the ability to infect human red blood cells. The researchers found that this rh5 gene enabled the parasite to infect both gorillas and humans for a limited time, explaining how the jump was made at a molecular level. The team also identified the specific DNA mutation that subsequently restricted P. falciparum to humans. The study, published on October 15, 2019 in PLOS Biology, provides a plausible molecular explanation for how one of the world’s most deadly infectious diseases came to infect humans, and will be important more generally for understanding how pathogens are able to jump from one species to another. The open-access article is titled “Resurrection of the Ancestral RH5 Invasion Ligand Provides a Molecular Explanation for the Origin of P. Falciparum Malaria In Humans.” Malaria remains a major global health problem causing an estimated 435,000 deaths per year, with 61 per cent occurring in children under five years of age. P. falciparum is the species of parasite that is responsible for the most deadly form of malaria and is particularly prevalent in Africa, where it accounted for 99.7 per cent of malaria cases in 2017. P. falciparum is one of seven species of parasite that can cause malaria in a family known as the Laverania.

Researchers Glean New Insights into Biological Underpinnings of Schizophrenia; Ten Risk Genes Implicated

Researchers have implicated 10 risk genes in the development of schizophrenia using a method called whole exome sequencing, the analysis of the portion of DNA that codes for proteins. Working with a global consortium of schizophrenia research teams, Tarjinder Singh, PhD, a postdoctoral fellow affiliated with the Stanley Center for Psychiatric Research at Broad Institute of MIT and Harvard, Massachusetts General Hospital, and Harvard Medical School, and colleagues completed one of the largest of such studies so far, incorporating genetic data from over 125,000 people to gain deeper insights into the genetic underpinnings of schizophrenia. The research was presented on October 15 as a featured plenary presentation ( at the American Society of Human Genetics (ASHG) 2019 Annual Meeting in Houston, Texas (October 15-19). The presentation was titled “Exome Sequencing of 25,000 Schizophrenia Cases and 100,000 Controls Implicates 10 Risk Genes, and Provides Insight into Shared and Distinct Genetic Risk and Biology with Other Neurodevelopmental Disorders.” “The main aim of our research is to understand the genetic causes of schizophrenia and motivate the development of new therapeutics,” said Dr. Singh. “Drug development for schizophrenia has had limited progress in the last 50 years, but, in the last decade, we have started to make genetic discoveries that help us better understand the mechanisms underlying the disorder.”

Sequencing African Genomes Yields New Data Resource with Broad Applicability

By collaborating globally in a new, large-scale effort, researchers have made strong progress in sequencing genomes from regions and countries across Africa. These findings will enable more broadly representative and relevant studies ranging from basic through clinical genetics. The researchers' new data and preliminary observations were presented as a featured plenary abstract at the American Society of Human Genetics (ASHG) 2019 Annual Meeting in Houston. The abstract is titled “High-Depth Genome Sequencing in Diverse African Populations Reveals the Impact of Ancestral Migration, Cultural Demography, and Infectious Disease on the Human Genome.” "There is a dearth of baseline genetic data for African populations," said Neil Hanchard, MD, DPhil, Assistant Professor at the Baylor College of Medicine, who presented the work. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, a collaborative effort supported by the National Institutes of Health to conduct genomic research in Africa, Dr. Hanchard and his colleagues sequenced the whole genomes of 426 individuals from 13 African countries, whose ancestries represented 50 ethnolinguistic groups from across the continent. Of the 426 genomes sequenced, 320 were analyzed at high depth. This allowed the researchers to examine rare genetic variants in an accurate and quantifiable way, in addition to the common variants that have been the focus of most of the previous genetic studies in Africans, Dr. Hanchard explained.

Genomenon’s Mastermind to be Integrated into SOPHiA Platform; Genomic Search Engine to Provide Direct Links to Genomic Evidence in SOPHiA’s Solutions; Combination Should Enable Much Faster, More Thorough, More Democratized Genomic Analysis

On October 15, 2019, at the American Society of Human Genetics Annual Meeting (ASHG) 2019 annual meeting, Genomenon® announced a partnership with SOPHiA GENETICS that includes incorporating the Genomenon’s Mastermind® Genomic Search Engine into the SOPHiA Platform and the Alamut Suite. The partnership puts the most up-to-date genomic research at the fingertips of clinical researchers performing genomic analysis worldwide. The SOPHiA Platform is the technology of choice for streamlined Data-Driven Medicine, including clinical-grade genomic analysis, interpretation, and reporting. SOPHiA has been adopted by 1,000 healthcare institutions to date, and has analyzed over 420,000 genomic profiles, with 16,000 new profiles processed each month. The Alamut Suite, which is powered by SOPHiA, is a decision-support software designed to explore and investigate variations of the human genome. Alamut helps clinical researchers in the complex tasks of genomic variants annotations, filtration, and exploration. With the addition of Mastermind, users of both technologies will be able to quickly access the genomic evidence associated with human variants, shortening the search time required to interpret a variant and assess its pathogenicity. This partnership will allow SOPHiA’s users to see a wider picture of the detected variants. A key driver in the decision is the breadth and depth of Mastermind’s coverage of genomic variants and published literature. Mastermind has indexed over 7 million full-text articles and 600,000 supplemental data sets and covers over 5.7 million variants found in the medical literature. “This partnership will help experts better and more quickly assess the impact of accurately detected genomic variants in a clinical context.

American Society of Human Genetics (ASHG) Annual Meeting Opens in Houston, Texas; Meeting Highlights Discoveries in Genetic Research & Progress to Improve Health &Treat Disease; Thousands Attend from Around the World

Thousands of genomics and genetics researchers, professors, doctors, genetic counselors, nurses, and others from around the world will gather in Houston, Texas, October 15-19, for ASHG 2019, to share their latest research about the benefits of human genetics and genomics research, one of the fastest-growing fields of modern health care development. ASHG 2019, the annual meeting of the American Society of Human Genetics (ASHG), is the world’s largest source of emerging news and cutting-edge science across the rapidly expanding fields of human genetics and genomics. Scientists from nearly 80 countries will take part in more than 3,400 scientific presentations, workshops, and collaborative events. This will be the first time that Houston has hosted ASHG’s annual meeting since the organization was founded in 1948. Hosting ASHG 2019 in Houston, a major epicenter of biomedical and life sciences, offers ASHG and its members an outstanding venue to inform the general public of new scientific knowledge that is changing the way we diagnose and treat disease, understand human history, and unravel fundamental biologic mysteries. It comes at a time when Houston’s position as an international leader in biomedical research is growing rapidly and will expand with the construction of a collaborative 30-acre biomedical research campus downtown. “The remarkable research that we will see at this meeting is transforming our knowledge about the role of genetics in human health and, increasingly, our ability to improve treatments and outcomes,” ASHG President Dr. Leslie G. Biesecker said. “This scientific progress will be on display in Bayou City and will demonstrate the essential role of robust funding for biomedical research to further revolutionize health care and successful treatments.

October 14th

Koala Epidemic Provides Lesson on How DNA Protects Itself from Viruses

In animals, infections are fought by the immune system. Studies on an unusual virus infecting wild koalas, by a team of researchers from the University of Massachusetts Medical School and the University of Queensland, reveal a new form of "genome immunity." The study was published online on October 10, 2019 in Cell. The open-access article is titled “The piRNA Response to Retroviral Invasion of the Koala Genome.” Retroviruses, including pathogens like HIV, incorporate into the chromosomes of host cells as part of their infectious lifecycle. Retroviruses don't usually infect the germ cells that produce sperm and eggs and, therefore, are not usually passed from generation to generation, but this has happened several times during evolution. Of the entire 3 billion nucleotides of the human genome, only 1.5% of the sequence forms the 20,000 genes that code for proteins - and 8% of the human genome comes from fragments of viruses. These pathogen invasions of the genome have sometimes been beneficial. For example, a gene "co-opted" from a virus is required for formation of the placenta in all mammals, including humans. Retroviral infection of germ cells has been a rare, but important, driving force in human evolution. But how the germ cells in mammals respond to pathogen invasion has not been previously described and might be quite different than what happens in other cells of the body. KoRV-A is a retrovirus sweeping through the wild koala population of Australia and it is associated with susceptibility to infection and cancer. KoRV-A spreads between individual animals, like most viruses. Surprisingly, KoRV-A also infects the germline cells, and most wild koalas are born with this pathogen as part of the genetic material of every cell in the body. The team used this system to see how germ cells respond to a retrovirus.

Sleep Apnea May Be Risk Factor for Diabetic Macular Edema

New research from Taiwan shows that severe sleep apnea is a risk factor for developing diabetic macular edema, a complication of diabetes that can cause vision loss or blindness. Diabetic macular edema was also more difficult to treat in patients with severe sleep apnea. While earlier research showed a weak connection between the two conditions, evidence is mounting that sleep apnea exacerbates underlying eye disease. The researchers presented their study on October 14 at AAO 2019, the 123rd Annual Meeting of the American Academy of Ophthalmology (AAO) (, held October 12-15 in San Francisco. When people with diabetes have poor control over their blood sugar levels, the tiny blood vessels at the back of the eye can become damaged. This condition is called diabetic retinopathy and it's a leading cause of blindness in the United States. Sometimes, tiny bulges protrude from the blood vessels, leaking fluid and blood into the retina. This fluid can cause swelling or edema in an area of the retina that allows us to see clearly. Sleep apnea is a sleep disorder in which breathing repeatedly stops and starts, disrupting sleep and causing blood oxygen levels to drop. This drop in oxygen appears to unleash a host of changes in the body that may play a role in injuring blood vessels. People with sleep apnea are at risk of developing hypertension, heart attacks, stroke, and type 2 diabetes.nBut what about the eyes? Researchers believe that sleep apnea may contribute to the development and worsening of diabetic retinopathy by increasing insulin resistance, elevating inflammation and raising blood pressure, all of which can damage the blood vessels at the back of the eye.

Researchers Rediscover Fast-Acting German Insecticide Lost in Aftermath of WWII; Relative of DDT Permits Faster Killing of Insects with Lower Doses and May Have Less Environmental Impact

A new study, published online on October 11, 2019, in the Journal of the American Chemical Society, explores the chemistry as well as the complicated and alarming history of DFDT (image), a fast-acting insecticide. The open-access article is titled “Manipulating Solid Forms of Contact Insecticides for Infectious Disease Prevention.” "We set out to study the growth of crystals in a little-known insecticide and uncovered its surprising history, including the impact of World War II on the choice of DDT--and not DFDT--as a primary insecticide in the 20th century," said Bart Kahr, PhD, Professor of Chemistry at New York University (NYU) and one of the study's senior authors. Dr. Kahr and fellow NYU Chemistry Professor Michael Ward, PhD, study the growth of crystals, which two years ago led them to discover a new crystal form of the notorious insecticide DDT. DDT is known for its detrimental effect on the environment and wildlife. But the new form developed by Dr. Kahr and Dr. Ward was found to be more effective against insects--and in smaller amounts, potentially minimizing its environmental impact. In continuing to explore the crystal structure of insecticides, the research team began studying fluorinated forms of DDT, swapping out chlorine atoms for fluorine. They prepared two solid forms of the compound--a monofluoro and a difluoro analog--and tested them on fruit flies and mosquitoes, including mosquito species that carry malaria, yellow fever, Dengue, and Zika. The solid forms of fluorinated DDT killed insects more quickly than did DDT; the difluoro analog, known as DFDT, killed mosquitoes two to four times faster. "Speed thwarts the development of resistance," said Dr. Ward, a senior author on the study. "Insecticide crystals kill mosquitoes when they are absorbed through the pads of their feet.