News Article | March 18, 2016
More evidence reveal that our prehistoric human ancestors had interbred with Neanderthals and another archaic line of ancient humans called Denisovans hundreds of thousands of years ago. A previous study conducted by scientists from the Max Planck Institute for Evolutionary Anthropology says that Neanderthals and Denisovans may have only split 430,000 years ago. If the findings of this study are correct, it would mean that the species Homo antecessor could be the common ancestor of modern humans, Neanderthals and Denisovans, scientists said. Now, a new study found that the genes of the Denisovans and Neanderthals who had interbred with our prehistoric ancestors actually live on today among modern Asians, Europeans, and in the Melanesians of Papua New Guinea. Led by scientist Svante Paabo who is also from the Max Planck Institute, the international team of researchers focused on the genetic code of Melanesians in particular, comparing the DNA sequences of 35 modern humans on islands off the New Guinea coast with DNA from Neanderthals and Denisovans. Their findings confirm theories that our human ancestors did not interbreed with other hominin species until after they left Africa. Even today, there is barely a trace of Neanderthal DNA in modern Africans. When our ancient human ancestors started traveling across Eurasia, they lived side-by-side and had a few run-ins with other species. Paabo said diverse populations of modern humans have various levels of Neanderthal DNA, and this means that ancient humans often ran into Neanderthals as they moved across Europe. "Substantial amounts of Neanderthal and Denisovan DNA can now be robustly identified in the genomes of present-day Melanesians," the researchers say. Molecular anthropologist Andrew Merriwether of Binghamton University said this is the first time that full genomes from blood samples collected 15 years ago in Melanesia have been sequenced. He said he was surprised that Denisovan and Neanderthal DNA even made it out as far as Papua New Guinea. They know that people have been on the island at least 48,000 years, especially because they have found human remains whose age go back that far. However, no one has ever been able to connect the remains to any other place, he said. "When you compare most of their genome sequences, they don't cluster with any other group," said Merriwether. "They've been there and been isolated for a very, very long time." In fact, researchers found that the genetic connection between ancient hominins and modern Melanesians were between 1.9 to 3.4 percent. This meant that modern human ancestors and early humans have interbred on at least three separate occasions. Benjamin Vernot of the University of Washington, who is also part of the study, said he believes that Denisovans and Neanderthals liked to wander. "And yes, studies like this can help us track where they wandered," added Vernot. The question now is this: how did the Denosivans make their way to the island of Melanesia? "Most people know back a few generations, maybe five generations, but where did we come from before that? That's what we want to find out," added Merriwether. The findings of the study are featured in the journal Science. The authors were from the Max Planck Institute, Binghamton University, Italy's University of Ferrara, the University of Washington, Temple University, the Coriell Institute for Medical Research, the University of Cincinnati, and the Institute for Medical Research in Papua New Guinea.
News Article | November 30, 2016
First five cell lines in Allen Cell Collection empower the cell science community to explore the dynamic organization of the cell and to better understand health and disease The Allen Institute for Cell Science has released the Allen Cell Collection: the first publicly available collection of gene edited, fluorescently tagged human induced pluripotent stem cells that target key cellular structures with unprecedented clarity. Distributed through the Coriell Institute for Medical Research, these powerful tools are a crucial first step toward visualizing the dynamic organization of cells to better understand what makes human cells healthy and what goes wrong in disease. "Each of our cells -- the fundamental units of life -- are like a city, with people and resources that move around and factories that generate those resources and carry out important functions," says Rick Horwitz, Ph.D., Executive Director of the Allen Institute for Cell Science. "With these cell lines, we aim to give the cell science community a kind of live traffic map to see when and where the parts of the cell are with the clarity and consistency they need to make progress toward understanding human health and tackling disease." Scientists at the Allen Institute for Cell Science used CRISPR/Cas9 technology to insert fluorescent tags for major cellular structures into human induced pluripotent stem cells. Unlike typical methods which flood the cell with fluorescent protein, these highly precise tags show exactly when and where the structures are at various stages in the cell's lifecycle. "By lowering the barrier to entry for cell biologists wishing to work on iPS cells, the availability of these lines will usher in a new era in cell biology," says Anthony Hyman, Ph.D., Director and Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics. This first collection of five cell lines targets a set of major cellular structures that help to orient the cell. These include the nucleus (tagged by the protein lamin B1), mitochondria (Tom20), microtubules (alpha-tubulin), cell-to-cell junctions (desmoplakin) and adhesion (paxillin). Subsequent collections will be released throughout 2017. "This kind of precise fluorescent tagging of structures in human stem cells is valuable for a variety of reasons, not least of which is that the pluripotent stem cells can be turned into a large number of cell types, like heart, brain or skin," says Ruwanthi Gunawardane, Ph.D., Director of Stem Cells and Gene Editing at the Allen Institute for Cell Science. "Our cells are healthy and as close to normal human cells as we can study in the lab, making these cell lines a powerful platform to identify the functions of genes, screen drugs, determine differentiation state and much more." "With these tagged cell lines, we get to 'spy' on the organization of healthy, normal human cells in a way that scientists never could before," says Susanne Rafelski, Ph.D., Director of Assay Development at the Allen Institute for Cell Science. "The images and movies we can generate from these lines show the cell's major structures with astonishing clarity and empower a broad, multi-structure view of how cells change as they execute their various activities and turn into different kinds of cells." The cell lines will be available for scientists around the world to use not just to understand the fundamentals of the cell, but also to investigate disease. Key mutations can be introduced to the cells in order to study how disease progresses in a dish, with broad potential impacts on the fields of biomedical science and personalized medicine. For more information about the Allen Cell Collection at the Coriell Institute for Medical Research, visit catalog.coriell.org/AllenCellCollection. About the Allen Institute for Cell Science The Allen Institute for Cell Science is a division of the Allen Institute (alleninstitute.org), an independent, 501(c)(3) nonprofit medical research organization, and is a research organization dedicated to understanding and modeling cells: the fundamental units of life. By integrating technologies, approaches, models and data into a common standardized framework, the Allen Institute for Cell Science is creating dynamic, visual models of how genetic information is transformed into cellular behavior, and how the molecules and organelles within each cell interact and function as systems. These predictive models will enable the cell science community to better understand the role of cells in both health and disease. The Allen Institute for Cell Science was launched in 2014 with a contribution from founder and philanthropist Paul G. Allen. The data, tools and models from the Allen Institute for Cell Science will be publicly available online. About the Coriell Institute for Medical Research Coriell Institute for Medical Research is recognized as one of the world's leading biobanks, distributing biological samples and offering research and biobanking services to scientists around the globe. A pioneer in genomics, Coriell is examining the utility of genetic information in clinical care through the Coriell Personalized Medicine Collaborative (CPMC) research study. The Institute is also unlocking the promise of induced pluripotent stem cells and their role in disease research and drug discovery.
Scheinfeldt L.B.,University of Pennsylvania |
Scheinfeldt L.B.,Coriell Institute for Medical Research |
Tishkoff S.A.,University of Pennsylvania
Nature Reviews Genetics | Year: 2013
The recent availability of genomic data has spurred many genome-wide studies of human adaptation in different populations worldwide. Such studies have provided insights into novel candidate genes and pathways that are putatively involved in adaptation to different environments, diets and disease prevalence. However, much work is needed to translate these results into candidate adaptive variants that are biologically interpretable. In this Review, we discuss methods that may help to identify true biological signals of selection and studies that incorporate complementary phenotypic and functional data. We conclude with recommendations for future studies that focus on opportunities to use integrative genomics methodologies in human adaptation studies. © 2013 Macmillan Publishers Limited. All rights reserved.
Budina-Kolomets A.,Wistar Institute |
Balaburski G.M.,Wistar Institute |
Balaburski G.M.,Coriell Institute for Medical Research |
Bondar A.,Wistar Institute |
And 3 more authors.
Cancer Biology and Therapy | Year: 2014
The chaperone HSP70 promotes the survival of cells exposed to many different types of stresses, and is also potently anti-apoptotic. The major stress-induced form of this protein, HSP70-1, is overexpressed in a number of human cancers, yet is negligibly expressed in normal cells. Silencing of the gene encoding HSP70-1 (HSPA1A) is cytotoxic to transformed but not normal cells. Therefore, HSP70 is considered to be a promising cancer drug target, and there has been active interest in the identification and characterization of HSP70 inhibitors for cancer therapy. Because HSP70 behaves in a relatively non-specific manner in the control of protein folding, to date there are no reliably-identified "clients" of this protein, nor is there consensus as to what the phenotypic effects of HSP70 inhibitors are on a cancer cell. Here for the first time we compare three recently-identified HSP70 inhibitors, PES -Cl, MKT-077, and Ver-155008, for their ability to impact some of the known and reported functions of this chaperone; specifically, the ability to inhibit autophagy, to influence the level of HSP90 client proteins, to induce cell cycle arrest, and to inhibit the enzymatic activity of the anaphase-promoting complex/cyclosome (APC/C). We report that all three of these compounds can inhibit autophagy and cause reduced levels of HSP90 client proteins; however, only PES -Cl can inhibit the APC/C and induce G2/M arrest. Possible reasons for these differences, and the implications for the further development of these prototype compounds as anti-cancer agents, are discussed. © 2014 Landes Bioscience.
Delaney S.K.,Coriell Institute for Medical Research |
Christman M.F.,Coriell Institute for Medical Research
Clinical Pharmacology and Therapeutics | Year: 2016
The direct-to-consumer genetic testing debate reached a fever pitch in November 2013 when the US Food and Drug Administration (FDA) instructed 23andMe to discontinue marketing and sale of their Personal Genome Service. In 2015, 23andMe emerged with FDA approval to market a carrier test for Bloom syndrome only, and plans to release additional reports. The dust has settled and it is time to ask: What have we learned, and where do we go from here? © 2015 ASCPT.
Kronenthal C.,Coriell Institute for Medical Research |
Delaney S.K.,Coriell Institute for Medical Research |
Christman M.F.,Coriell Institute for Medical Research
Genetics in Medicine | Year: 2012
Genetic variant associations and advances in research technologies are generating an unprecedented volume of genomic data. Whole-genome sequencing will introduce even greater depth to current data sets and will propel medical research and development. Yet as one area of biomedical research evolves, another stagnates: informed consent. As presently employed, informed consent is not entirely attuned to the era of whole-genome sequencing. The greatest value of genomic data lays in its accessibility over time; the current model of informed consent restricts the use of data and does not readily accommodate prospective basic and clinical research, a priori research, or opportunities to act upon incidental findings. It also disengages the research participant from the discovery process, discouraging the provision of research results that may have clinical value to that individual. A revisited informed consent approach - the Informed Cohort Oversight Board (ICOB) - has been proven successful at consenting individuals to a model which facilitates the simultaneous construction of longitudinal data with the return of results to participants as scientific knowledge and technology allows. The opportunity to sequence once and consult often is cost-effective, encourages scientific innovation, and provides the opportunity to quickly translate genomics into better clinical care. ©American College of Medical Genetics and Genomics.
Stack C.B.,Coriell Institute for Medical Research |
Gharani N.,Coriell Institute for Medical Research |
Gordon E.S.,Coriell Institute for Medical Research |
Schmidlen T.,Coriell Institute for Medical Research |
And 2 more authors.
Genetics in Medicine | Year: 2011
Purpose: Recent genome wide-association studies have identified hundreds of single nucleotide polymorphisms associated with common complex diseases. With the momentum of these discoveries comes a need to communicate this information to individuals. Methods: The Coriell Personalized Medicine Collaborative is an observational research study designed to evaluate the utility of personalized genomic information in health care. Participants provide saliva samples for genotyping and complete extensive on-line medical history, family history, and lifestyle questionnaires. Only results for diseases deemed potentially actionable by an independent advisory board are reported. Results: We present our methodology for developing personalized reports containing risks for both genetic and nongenetic factors. Risk estimates are given as relative risk, derived or reported from representative peer-reviewed publications. Estimates of disease prevalence are also provided. Presenting risk as relative risk allows for consistent reporting across multiple diseases and across genetic and nongenetic factors. Using this approach eliminates the need for assumptions regarding population lifetime risk estimates. Publications used for risk reporting are selected based on the strength of the design and study quality. CONCLUSION:: Coriell Personalized Medicine Collaborative risk reports demonstrate an approach to communicating risk of complex disease via the web that encompasses risks due to genetic variants along with risks caused by family history and lifestyle factors. © 2011 Lippincott Williams & Wilkins.
Stark A.L.,University of Chicago |
Zhang W.,University of Illinois at Chicago |
Zhou T.,University of Illinois at Chicago |
O'Donnell P.H.,University of Chicago |
And 4 more authors.
American Journal of Human Genetics | Year: 2010
The International HapMap Project is a resource for researchers containing genotype, sequencing, and expression information for EBV-transformed lymphoblastoid cell lines derived from populations across the world. The expansion of the HapMap beyond the four initial populations of Phase 2, referred to as Phase 3, has increased the sample number and ethnic diversity available for investigation. However, differences in the rate of cellular proliferation between the populations can serve as confounders in phenotype-genotype studies using these cell lines. Within the Phase 2 populations, the JPT and CHB cell lines grow faster (p < 0.0001) than the CEU or YRI cell lines. Phase 3 YRI cell lines grow significantly slower than Phase 2 YRI lines (p < 0.0001), with no widespread genetic differences based on common SNPs. In addition, we found significant growth differences between the cell lines in the Phase 2 ASN populations and the Han Chinese from the Denver metropolitan area panel in Phase 3 (p < 0.0001). Therefore, studies that separate HapMap panels into discovery and replication sets must take this into consideration. © 2010 by The American Society of Human Genetics. All rights reserved.
News Article | November 30, 2016
Glowing Human Cells May Shed Light On Sickness And Health A nonprofit research group is giving scientists a new way to study the secret lives of human cells. On Wednesday, the Allen Institute for Cell Science provided access to a collection of living stem cells that have been genetically altered to make internal structures like the nucleus and mitochondria glow. "What makes these cells special is that they are normal, healthy cells that we can spy on and see what the cell does when it's left alone," says Susanne Rafelski, director of assay development at the institute. Under a microscope, "they are a wonder to behold," she says. The cells originally came from skin. But they have the potential to become many different types of cells, including those found in the heart and brain. And they could help scientists answer basic questions about how cells specialize as they develop, how disease changes a cell and how experimental drugs affect certain types of cells. "We're creating a powerful resource and a tool that any biologist can use," says Ruwanthi Gunawardane, director of stem cells and gene editing at the Allen institute. Initially, the institute is releasing five cell lines through the Coriell Institute for Medical Research. Each line has a different internal structure that glows, allowing researchers to see how that structure moves and changes during a cell's life. "What's really cool about this is that we can watch the cell as it divides," Gunawardane says. Any scientist can order the cells online for a price that reflects only the distribution cost. "Our goal was to make this absolutely accessible to any person working on stem cells," Gunawardane says. Until now, many scientists have had to rely on cells that grow abnormally or have mutations, Gunawardane says. And there has been no good way to see a living cell's internal structures without disrupting its normal operation. The new cell lines are the product of cutting-edge technology found in just a few labs, Gunawardane says. "We would not have been able to do this two years ago," she says.
News Article | November 30, 2016
The Allen Institute for Cell Science has released the Allen Cell Collection: the first publicly available collection of gene edited, fluorescently tagged human induced pluripotent stem cells that target key cellular structures with unprecedented clarity. Distributed through the Coriell Institute for Medical Research, these powerful tools are a crucial first step toward visualizing the dynamic organization of cells to better understand what makes human cells healthy and what goes wrong in disease.