 |
|
New technology used to construct the first map of structural variation in the human genome
November 27, 2006Beyond the simple stream of one-letter characters in the human genome sequence lies a complex, higher-order code. In order to decipher this level of architecture, scientists have developed powerful new experimental and algorithmic methods to detect copy number variants (CNVs)-defined as large deletions and duplications of DNA segments. These technologies-reported today in the journal Genome Research-were used to create the first comprehensive map of CNVs in the human genome, concurrently published in Nature. A related article appears in Nature Genetics.
CNVs are responsible for genetic changes in Alzheimer's and Parkinson's, susceptibility to HIV-1, some forms of color blindness, and many other diseases. They lead to variation in gene expression levels and may account for a large amount of phenotypic variation among individuals and ethnic populations, including differential responses to drugs and environmental stimuli. Mechanisms underlying the formation of CNVs also provide insight into evolutionary processes and human origins.
Using microarray technology, scientists can scan for CNVs across the genome in a single experiment. While this is a cost-effective means of obtaining large amounts of data, scientists have struggled to accurately determine CNV copy number and to precisely define the boundaries of CNVs in the genome. Two papers published today in Genome Research present groundbreaking approaches to address these issues.
One paper describes a new whole-genome tiling path microarray, which was constructed from the same DNA used to sequence the human genome in 2001. The array covers 93.7% of the euchromatic (gene-containing) regions of the human genome and substantially improves resolution over previous arrays. The array was employed in a process known as comparative genomic hybridization (CGH), which involves tagging genomic DNA from two individuals and then co-hybridizing it to the array. Data from the array were assessed with a new algorithmic tool, called CNVfinder, which accurately and reliably identified CNVs in the human genome.
"This method helped us to develop the first comprehensive map of structural variation in the human genome," says Dr. Nigel Carter, one of the lead investigators on the project. "We used it to help identify 1,447 CNVs, which covered 12% of the human genome."
The other paper presents a new multi-step algorithm used with the Affymetrix GeneChip® Human Mapping 500K Early Access SNP arrays. The specificity of the algorithm, coupled with the increased probe density of these arrays, permitted the identification of approximately 1,000 CNVs, many of which were below the detection size limit of alternative methodologies. Furthermore, the algorithm more accurately estimated CNV boundaries, thereby permitting a detailed comparison with other genomic features.
"This new approach will be useful in understanding the role of CNVs in disease pathology-not only copy number changes in cancer cells, but also possible association of CNVs with common diseases," explains Dr. Hiroyuki Aburatani, one of the scientists who led the development of the algorithm. "We'll be able to develop diagnostic tests with sub-microscopic resolution, and because the analysis detects SNPs-single-nucleotide polymorphisms-in addition to CNVs, it will find widespread use among researchers performing disease-association studies."
Cold Spring Harbor Laboratory
One paper describes a new whole-genome tiling path microarray, which was constructed from the same DNA used to sequence the human genome in 2001. The array covers 93.7% of the euchromatic (gene-containing) regions of the human genome and substantially improves resolution over previous arrays. The array was employed in a process known as comparative genomic hybridization (CGH), which involves tagging genomic DNA from two individuals and then co-hybridizing it to the array. Data from the array were assessed with a new algorithmic tool, called CNVfinder, which accurately and reliably identified CNVs in the human genome.
"This method helped us to develop the first comprehensive map of structural variation in the human genome," says Dr. Nigel Carter, one of the lead investigators on the project. "We used it to help identify 1,447 CNVs, which covered 12% of the human genome."
The other paper presents a new multi-step algorithm used with the Affymetrix GeneChip® Human Mapping 500K Early Access SNP arrays. The specificity of the algorithm, coupled with the increased probe density of these arrays, permitted the identification of approximately 1,000 CNVs, many of which were below the detection size limit of alternative methodologies. Furthermore, the algorithm more accurately estimated CNV boundaries, thereby permitting a detailed comparison with other genomic features.
"This new approach will be useful in understanding the role of CNVs in disease pathology-not only copy number changes in cancer cells, but also possible association of CNVs with common diseases," explains Dr. Hiroyuki Aburatani, one of the scientists who led the development of the algorithm. "We'll be able to develop diagnostic tests with sub-microscopic resolution, and because the analysis detects SNPs-single-nucleotide polymorphisms-in addition to CNVs, it will find widespread use among researchers performing disease-association studies."
Cold Spring Harbor Laboratory
Human Genome Current Events and Human Genome News RSSGenetic analysis helps dissect molecular basis of cardiovascular disease
Using highly precise measurements of plasma lipoprotein concentrations determined by nuclear magnetic resonance spectroscopy (NMR), researchers led by Daniel Chasman at Brigham and Women's Hospital and Harvard Medical School in Boston, MA, the Framingham Heart Study in Framingham, and the PROCARDIS consortium in Stockholm, Sweden and Oxford, England performed genetic association analysis across the whole genome among 17,296 women of European ancestry from the Women's Genome Health Study.
New Maize Map to Aid Plant Breeding Efforts
In a massive survey of genetic diversity in maize, also known as corn, researchers across the United States, have developed a gene map that should pave the way to significant improvements in a plant that is a major source of food, fuel, animal feed and fiber around the world.
Largest gene study of childhood IBD identifies 5 new genes
In the largest, most comprehensive genetic analysis of childhood-onset inflammatory bowel disease (IBD), an international research team has identified five new gene regions, including one involved in a biological pathway that helps drive the painful inflammation of the digestive tract that characterizes the disease.
No-entry zones for AIDS virus
The AIDS virus inserts its genetic material into the genome of the infected cell. Scientists of the German Cancer Research Center have now shown for the first time that the virus almost entirely spares particular sites in the human genetic material in this process. This finding may be useful for developing new, specific AIDS drugs.
Aileron collaborates study in Nature: Stapled peptides inhibit Notch1 transcription factor
This research validates the potential for Stapled Peptides to modulate key intracellular biological targets, such as transcription factors, that have not been addressable with current small molecule or biologic drug modalities.
UCSD discovery allows scientists for the first time to experimentally annotate genomes
Over the last 20 years, the sequencing of the human genome, along with related organisms, has represented one of the largest scientific endeavors in the history of mankind.
Study sheds light on evolution of human complexity
A painstaking analysis of thousands of genes and the proteins they encode shows that human beings are biologically complex, at least in part, because of the way humans evolved to cope with redundancies arising from duplicate genes.
Hunting for the Prozac Gene
Prozac works wonders for some depressed people, but not for others. In some cases, patients derive little benefit and at worst, it can lead to bizarre hallucinations and fits of rage.
Will genomics help prevent the next pandemic?
This week, the Public Library of Science, an open-access publisher, presents the "Genomics of Emerging Infectious Disease," a collection of essays, perspectives, and reviews that explores how genomics-with all its associated tools and techniques-can provide insights into our understanding of emerging infectious disease.
UCR researchers develop genetic map for cowpea, accelerating development of new varieties
Cowpea, a protein-rich legume crop, is immensely important in many parts of the world, particularly drought-prone regions of Africa and Asia, where it plays a central role in the diet and economy of hundreds of millions of people.
More Human Genome Current Events and Human Genome News Articles
 |
A Short Guide to the Human Genome by Stewart Scherer (Author) How many genes are in the human genome? Which genes are commonly associated with genetic diseases? How many mobile elements, simple sequence repeats, or protein kinases are encoded in the genome? What are the largest genes and proteins? How similar are human proteins to those of mouse, yeast, or bacteria? Although the human genome has been sequenced, it often can be surprisingly difficult to find answers to seemingly simple questions about its characteristics. This convenient handbook, written in question-and-answer format, allows researchers and teachers alike access to basic facts about the human genome. Using a recent assembly of the human genome sequence, Stewart Scherer has compiled answers to a broad range of questions about the structure and function of the human... |
 |
Genome: The Autobiography of a Species in 23 Chapters (P.S.) by Matt Ridley (Author) The genome's been mapped. Arguably the most significant scientific discovery of the new century, the mapping of the twenty-three pairs of chromosomes that make up the human genome raises almost as many questions as it answers. Questions that will profoundly impact the way we think about disease, about longevity, and about free will. Questions that will affect the rest of your life. Genome offers extraordinary insight into the ramifications of this incredible breakthrough. By picking one newly discovered gene from each pair of chromosomes and telling its story, Matt Ridley recounts the history of our species and its ancestors from the dawn of life to the brink of future medicine. From Huntington's disease to cancer, from the applications... |
 |
NOVA - Cracking the Code of Life Starring: Robert Krulwich Directed By: Betsey Arledge; Elizabeth Arledge Does it amaze you that yeast is your very close relative? That you possess roughly the same number of genes as a mouse? That you are 99.9% genetically identical to every other human? ABC Nightline correspondent Robert Krulwich lends a lighthearted touch to genetic science in this provocative two-hour NOVA special that takes you inside the amazing, complex and contentious race to decode the human genome. The Human Genome Project was born in 1990, when an international consortium of labs set out to sequence all 3 billion letters of our DNA, predicting they’d finish by 2005. Halfway through their schedule, controversial scientist and entrepreneur J. Craig Venter threw the genome world into turmoil, when he announced his for-profit company Celera could finish the job in just two years.... |
 |
The Human Genome, Second Edition: A User's Guide (Elsevier Science in Society) by Julia E. Richards (Author), R. Scott SH Hawley (Author) This second edition of a very successful text reflects the tremendous pace of human genetics research and the demands that it places on society to understand and absorb its basic implications. The human genome has now been officially mapped and the cloning of animals is becoming a commonplace scientific discussion on the evening news. Join authors Julia Richards and Scott Hawley as they examine the biological foundations of humanity, looking at the science behind the sensation and the current and potential impact of the study of the genome on our society. The Human Genome, Second Edition is ideal for students and non-professionals, but will also serve as a fitting guide for the novice geneticist by providing a scientific, humanistic, and ethical frame of reference for a more... |
 |
The Human Genome by Carina Dennis (Editor), Richard Gallagher (Editor) The sequencing of the human genome is being hailed as history's most important scientific discovery. This unprecedented project attempts to map our complete DNA sequence-the key to human history and identity, and to an extraordinary future of scientific and medical progress. Now the editors of Nature, the world's leading scientific publication help everyone understand the human genome. Lavishly illustrated throughout, this full-color guide covers everything from genetics and the basic biology and landmark events, the key players, and its political, social, and scientific impact. It also includes the full text of Nature's papers that unveil the human genome. From the frontline of science reporting, and with a foreword by James Watson, the man who discovered the double helix structure of... |
 |
SciEd Sequencing the Human Genome; Dna Map Using Restcn Enzymes by Edvotek DNA Map Using Restcn Enzymes |
 |
The Human Genome Project Completed in 2003, the Human Genome Project (HGP) was a 13-year project coordinated by the U.S. Department of Energy and the National Institutes of Health. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner; additional contributions came from Japan, France, Germany, China, and others. See our history page for more information. Project goals were to identify all the approximately 20,000-25,000 genes in human DNA, determine the sequences of the 3 billion chemical base pairs that make up human DNA, store this information in databases, improve tools for data analysis, transfer related technologies to the private sector, and address the ethical, legal, and social issues (ELSI) that may arise from the project. Though the HGP is finished, analyses of... |
 |
Londons Times Funny Science Cartoons - Fruit-Human Genome Experiment Gone Bad - Light Switch Covers - 2 plug outlet cover by 3dRose LLC Fruit-Human Genome Experiment Gone Bad Light Switch Cover is new and handcrafted utilizing unique process resulting in a stunning high gloss ceramic-like finish. SET OF MATCHING SCREWS IS INCLUDED giving it a perfect finishing touch. Made of durable metal material. |
 |
Fruit Human Genome Experiment Gone Bad - Youth SweatShirt Small(6-8) by 3dRose Fruit Human Genome Experiment Gone Bad Sweatshirt is commercial quality 9.3-ounce high resolution heat transfers garment. 50-50 cotton-poly NuBlend fleece, fully coverseamed, ribbed collar, cuffs and waistband with spandex, set-in sleeves. Our image transfer produces professional matte finish with Premium Quality and Superior image resolution. Colors do not bleed and the image is sharp and crisp. |
 |
Fruit Human Genome Experiment Gone Bad - Toddler Light-Blue-T-Shirt (3T) by 3dRose Fruit Human Genome Experiment Gone Bad T-Shirt is commercial quality high resolution heat transfers garment. 5.6-ounce, 50-50 cotton-poly; taped shoulder to shoulder, coverseamed ribbed collar, double-needle sleeve and bottom hem. Todler and infant t-shirts are 4.1-ounce. 100% ring spun combed cotton. Our image transfer produces professional matte finish with Premium Quality and Superior image resolution. Colors do not bleed and the image is sharp and crisp. Available in white, gray, blue and pink. Washing Instructions: 1. Turn Garment inside-out and machine wash in cold water. 2. Do not use Bleach or Fabric Softener. 3. Detergents with bleach additives are not recommended. 4. Tumble Dry on Warm. 5. Do not Iron. Do not Dry clean. |
| © 2009 BrightSurf.com |