Investigators from six countries have completed the second phase of the International HapMap Project, an effort to identify and catalog genetic similarities and differences among populations around the world. Information provided in the first phase of the HapMap, completed in 2005, has led to the development of techniques facilitating the search for genes associated with common diseases – such as schizophrenia and heart disease – and the identification of more than 50 such disease-associated genes.
In the past year, using data and methods based on the HapMap, MGH researchers have published new genetic contributors to conditions such as type 2 diabetes, Crohn’s disease, elevated blood cholesterol, rheumatoid arthritis, multiple sclerosis, and prostate cancer. These studies and many others used a suite of analytical methods developed at MGH and its partner institutions.
“The original HapMap provided the backbone for genome-wide association studies that have uncovered previously unsuspected genetic components of many diseases, leading to new areas of research,” says Mark Daly, PhD, of the Massachusetts General Hospital (MGH) Center for Human Genetic Research, co-senior author of the report in the Oct. 18 issue of Nature. “The second phase has tripled the amount of genetic variation assessed and describes up to 95 percent of common single-letter variations in the human genetic code.”
While the Human Genome Project confirmed that the more than 3 billion “letters” of DNA in each human were 99.9 percent identical, analyzing the small fraction that differ – including about 10 million distinct, single-letter variations, also called SNPs – remained a daunting task. In 2001 Daly and colleagues showed that adjacent DNA variations are inherited together in segments called haplotypes, with the boundaries between adjacent segments defined by locations of enhanced recombination – the shuffling of DNA segments between the chromosomes inherited from each parent. Based in part on those findings, the HapMap project was started to create a map of SNPs and haplotypes across the genomes of 270 individuals from Nigeria, China, Japan and the U.S. While the first phase identified and cataloged about 1.3 million SNPs, the second phase has brought the total to more than 3.1 million SNPs catalogued in the same population.
“The increased density of identified SNPs in the second phase has allowed us to much more specifically understand the nature of these recombination ‘hotspots.’ ” says Daly. “Another interesting finding is that we can identify, among apparently unrelated individuals, chromosome segments that clearly have been inherited without change from common ancestors who lived hundreds to a thousand years ago. The ability to detect these more recently inherited segments of DNA may hold the key to rare disease-associated variations that have been hard to detect with current tools.” Daly is an assistant professor of Medicine at Harvard Medical School and a senior associate member of the Broad Institute of Harvard and Massachusetts Institute of Technology.
The information in the HapMap is freely accessible to researchers around the world. The data assembled in the second phase was added to the public database as it became available and already has been used in a number of research studies. As the project continues, it will use new sequencing techniques to further analyze genetic variations in the same study group and in a larger population.
“While the completion of Phase 2 of the HapMap Project makes possible comprehensive studies of common SNPs in the sampled populations, there remains much work to be done,” says David Altshuler, of the MGH Center for Human Genetic Research. “Current efforts aim to catalogue genetic variation in more diverse samples from around the world, to define larger chromosomal alterations that might be missed by SNPs-based approaches and to find rare genetic variations that might have potent effects on individual patients. Only by combining all these approaches can we hope to have a complete understanding of the genetic root causes of common human diseases.” Altshuler is also an associate professor of Genetics and Medicine at HMS, director of the Program in Medical and Population Genetics at the Broad Institute, and co-chair for Analysis of the International HapMap Project.
Sue McGreevey | EurekAlert!
Nanoparticle Exposure Can Awaken Dormant Viruses in the Lungs
16.01.2017 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt
Cholera bacteria infect more effectively with a simple twist of shape
13.01.2017 | Princeton University
Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.
While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...
Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales
Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...
Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.
As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...
At TU Wien, an alternative for resource intensive formwork for the construction of concrete domes was developed. It is now used in a test dome for the Austrian Federal Railways Infrastructure (ÖBB Infrastruktur).
Concrete shells are efficient structures, but not very resource efficient. The formwork for the construction of concrete domes alone requires a high amount of...
Many pathogens use certain sugar compounds from their host to help conceal themselves against the immune system. Scientists at the University of Bonn have now, in cooperation with researchers at the University of York in the United Kingdom, analyzed the dynamics of a bacterial molecule that is involved in this process. They demonstrate that the protein grabs onto the sugar molecule with a Pac Man-like chewing motion and holds it until it can be used. Their results could help design therapeutics that could make the protein poorer at grabbing and holding and hence compromise the pathogen in the host. The study has now been published in “Biophysical Journal”.
The cells of the mouth, nose and intestinal mucosa produce large quantities of a chemical called sialic acid. Many bacteria possess a special transport system...
10.01.2017 | Event News
09.01.2017 | Event News
05.01.2017 | Event News
17.01.2017 | Earth Sciences
17.01.2017 | Materials Sciences
17.01.2017 | Architecture and Construction