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Archive - Oct 9, 2015

Geneticists Reconstruct Population History of New York City; Findings Reported at ASHG 2015 Annual Meeting

By combining genetic data, ancestry information, and electronic health records, scientists have been able to identify neighborhood-level patterns of migration in the New York City area, according to research presented on Friday, October 9, at the American Society of Human Genetics (ASHG) 2015 Annual Meeting in Baltimore, Maryland. In addition to supplementing historical and census data, these sorts of findings can inform biomedical and public health efforts in New York and other locations, the study authors said. “New York City is an important point of entry and immigration, and has long been one of the major ‘melting pots’ of the world. The population structure there is complex and interesting from a variety of perspectives, including the genetic one,” said Gillian Belbin, M.S., a graduate student at the Icahn School of Medicine at Mount Sinai (ISMMS) in New York City and first author on the study. “These days, other cities such as London and Shanghai are reaching the same levels of diversity as New York, and many of our methods and findings can be applied to those cities’ populations as well,” added Eimear Kenny, Ph.D., Assistant Professor at ISMMS and senior author on the study. Ms. Belbin and her colleagues are investigating a variety of questions related to migration into New York City, population transitions among its ethnic enclaves, and effects of historical events and trends on recent generation,s as well as during the last few centuries. They are using the ISMMS BioMed Biobank (http://icahn.mssm.edu/departments-and-institutes/genomics/about/resource...), an anonymized database of electronic health record and genetic information from more than 32,000 ISMMS patients who have volunteered to share their medical data with researchers.

Researchers Study Costs of Integrating Whole Genome Sequencing into Clinical Care; Initial Findings from MedSeq Project Reported at ASHG 2015 Annual Meeting

Integrating whole genome sequencing into primary care and heart disease care is unlikely to substantially increase the costs of health care utilization and follow-up tests, according to research presented on Friday, October 9, at the American Society of Human Genetics (ASHG) 2015 Annual Meeting in Baltimore, Maryland. “This finding helps to allay the worry that patients whose genomes are sequenced will run out and spend thousands of dollars on follow-up tests and care, which may or may not improve their eventual health outcomes,” said Jason L. Vassy, M.D., M.P.H., a primary care physician and co-investigator on the study at Brigham and Women’s Hospital. The cost analysis was conducted as part of the MedSeq Project (http://www.genomes2people.org/the-medseq-project/), a broader study of the best ways to integrate genome sequencing into clinical medicine and how these might impact health systems and individuals. The project has enrolled a total of 200 patients: 100 healthy adults in primary care settings and 100 adults receiving care for complex cardiomyopathy, a type of heart disease. Half of the patients in each group were randomly assigned to receive the standard of care, which included a discussion of family history of disease, and the other half received the standard of care plus whole genome sequencing, a personalized Genome Report, and a discussion of the results. Results from 108 of the 200 patients, 70 in the primary care group and 38 in the cardiology group, were included in the preliminary cost analysis presented at the ASHG annual meeting. On average, patients whose genomes were sequenced incurred a cost of $719 in follow-up tests and care over the following year, including out-of-pocket expenses, while standard treatment and follow-up averaged $430 per patient.

Tumor Microbiome Analysis Allows Genetic Classification of Colorectal Tumors; First Study to Integrate Tumor Microbiome Characteristics & Colorectal Cancer Mutations; Results Reported at ASHG 2015 Annual Meeting

By analyzing the types of gut bacteria present around colorectal tumors, researchers have found a way to predict key genetic mutations in the tumors themselves, a method that could eventually inform the development of colorectal cancer diagnostics and therapeutics. Their findings were presented on Friday, October 9, at the American Society of Human Genetics (ASHG) 2015 Annual Meeting in Baltimore, Maryland. Led by Ran Blekhman, Ph.D., Assistant Professor of Genetics, Cell Biology, and Development at the University of Minnesota and senior author on the study, the researchers examined the genetic differences between colorectal tumor cells and healthy colon cells from 44 adults with colorectal cancer. They looked for correlations between specific mutations in the tumor cells and the composition of the tumor microbiome – the types of bacteria present in the tumor’s immediate environment and their relative abundance – and found relationships between the two. “Ours was the first study to analyze both of these factors together,” said Michael B. Burns, Ph.D., a postdoctoral researcher in Dr. Blekhman’s laboratory. “Previous studies have found associations between certain mutations and colorectal cancer, and between certain microbiome characteristics and cancer, but had not integrated the two,” he explained. The researchers found that in general, the more cancer-associated mutations a person’s tumor cells had, the more varied his or her tumor microbiome was. In fact, specific mutations in tumor cells were associated with the presence of specific types of bacteria in the microbiome. Together with Dan Knights, Ph.D., Assistant Professor of Computer Science and Biotechnology at the University of Minnesota, Dr.

Majority of Teens Value Results of Genetic Tests to Inform Future Life Decisions; Survey Conducted by Cincinnati Children’s Hospital; Findings Reported at ASHG 2015 Annual Meeting

The majority of adolescents in grades 7-12 would prefer to know the results of unanticipated findings found in whole exome sequencing genetic testing, even if the findings are not medically actionable until adulthood, according to survey data presented on October 9, 2015 at the American Society of Human Genetics (ASHG) 2015 Annual Meeting in Baltimore. The survey addressed secondary findings – genetic findings unrelated to the initial indication that prompted the test – gleaned from sequencing the protein-coding regions of a person’s genome. “Whole exome sequencing in minors can potentially reveal an elevated risk for a condition unrelated to the initial reason they underwent genetic testing, and there may be no medical intervention to mitigate that risk until adulthood,” said Sophia Bous Hufnagel, M.D., a pediatric geneticist at Cincinnati Children’s Hospital Medical Center and first author on the study. “Some people prefer to know about these secondary findings anyway, while others would rather not know,” she said. Clinical guidelines urge physicians to counsel adult patients through choosing which types of secondary findings, if any, are disclosed to them. For minors, however, the consensus has been to discourage disclosure, except in rare cases. “Some argue that disclosing such findings to teens would take away their right to decide later, as an adult, what they want to know. Many people also felt that disclosing results to children may cause psychological harm, especially when there are no prevention or treatment options available until adulthood – that you should just let a kid be a kid,” Dr. Hufnagel explained. “Others argue that a truly non-actionable finding does not exist and that knowledge of such results, despite available treatment options, has value and benefit in itself.

First Ancient African Human Genome Sequenced; Profound Influence of Mysterious “Eurasian Backflow” into Horn of Africa Revealed by Comparison of Ancient “Mota Man” Genome with DNA of Modern Africans

The first ancient human genome from Africa to be sequenced has revealed that a wave of migration back into Africa from Western Eurasia approximately 3,000 years ago was up to twice as significant as previously thought, and affected the genetic make-up of populations across the entire African continent. The genome that was sequenced was recovered from the skull of a man buried face-down 4,500 years ago in a cave called Mota (image) in the highlands of Ethiopia, a cave cool and dry enough to preserve his DNA for thousands of years. Previously, ancient genome analysis has been limited to samples from northern and arctic regions. The latest study is the first time an ancient human genome has been recovered and sequenced from Africa, the source of all human genetic diversity. The findings were published online on October 8, 2015 in Science. The article is titled “Ancient Ethiopian Genome Reveals Extensive Eurasian Admixture throughout the African Continent.” The ancient genome predates a mysterious migratory event that took place roughly 3,000 years ago, and is known as the “Eurasian backflow,” when people from regions of Western Eurasia such as the Near East and Anatolia suddenly flooded back into the Horn of Africa. The ancient genome enabled researchers to run a millennia-spanning genetic comparison and determine that these Western Eurasians were closely related to the Early Neolithic farmers who had brought agriculture to Europe 4,000 years earlier. By comparing the ancient African genome to DNA from modern Africans, the team has been able to show that, not only do East African populations today have as much as 25% Eurasian ancestry from this “backflow” event, but that African populations in all corners of the continent - from the far West to the South - have at least 5% of their genome traceable to the Eurasian migration.

Georgetown’s Experimental Ewing Sarcoma & Prostate Cancer Drug Turns Off Mutant Cancer Gene in Animals with Leukemia

A compound discovered and developed by a team of Georgetown Lombardi Comprehensive Cancer Center researchers that halts cancer in animals with Ewing sarcoma and prostate cancer appears to work against some forms of leukemia, too. The team's latest work, with Austrian colleagues and including this leukemia finding, was published online on October 8, 2015 in an open-access article in Oncotarget. The compound is YK-4-279, the first drug targeted at similar chromosomal translocations found in Ewing sarcoma, prostate cancer, and in some forms of leukemia. Translocations occur when two normal genes break off from a chromosome and fuse together in a new location. This fusion can produce new genes that code for proteins, which can then push cancer cells to become more aggressive and spread. One of those proteins is EWS-FLI1. YK-4-279 appears effective in controlling the cancer promoting functions of EWS-FLI1. The Oncotarget article is titled “YK-4-279 Effectively Antagonizes EWS-FLI1 Induced Leukemia in a Transgenic Mouse Model.” "EWS-FLI1 is already known to drive a rare, but deadly, bone cancer called Ewing sarcoma, which occurs predominantly in children, teens, and young adults," says Aykut Üren (photo), M.D., Professor of Molecular Oncology at Georgetown Lombardi. "It also appears to drive cancer cell growth in some prostate cancers." In this new study led by Dr. Üren and colleagues, mice with EWS-FLI1-driven leukemia were given injections of YK-4-279 five days per week for two weeks and compared with untreated mice. By the end of the first week, the mice receiving YK-4-279 had much lower numbers of leukemia cells.

Cancer Rare in Elephants: 38 Extra Copies of p53 Tumor Suppressor Gene May Be Why

Why elephants rarely get cancer is a mystery that has stumped scientists for decades. Now, a study led by researchers at Huntsman Cancer Institute (HCI) at the University of Utah and Arizona State University, and including researchers from the Ringling Bros. Center for Elephant Conservation, may have found the answer. According to the results, published online on October 8, 2015 in an open-access article in the Journal of the American Medical Association (JAMA), and determined over the course of several years and in a unique collaboration between HCI, Primary Children's Hospital, Utah's Hogle Zoo, and the Ringling Bros. Center for Elephant Conservation, elephants have 38 additional modified copies of a gene that encodes p53, a well-defined tumor suppressor, as compared to humans, who have only two. Further, elephants may have a more robust mechanism for killing damaged cells that are at risk for becoming cancerous. In isolated elephant cells, this activity is doubled compared to healthy human cells, and five times that of cells from patients with Li-Fraumeni Syndrome, who have only one working copy of p53 and more than a 90 percent lifetime cancer risk in children and adults. The results suggest extra p53 could explain elephants' enhanced resistance to cancer. The JAMA article is titled “Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans.” An JAMA open-access editorial accompanies the research report (see links to both articles below)."Nature has already figured out how to prevent cancer.