Emory University scientists have identified and created a map of more than 400,000 insertions and deletions (INDELs) in the human genome that signal a little-explored type of genetic difference among individuals. INDELS are an alternative form of natural genetic variation that differs from the much-studied single nucleotide polymorphisms (SNPs). Both types of variation are likely to have a major impact on humans, including their health and susceptibility to disease.
The INDEL research, led by Scott Devine, PhD, assistant professor of biochemistry at Emory University School of Medicine, has been posted online and will be published in the September issue of the journal Genome Research.
The human genome sequence in our DNA contains three billion base pairs of four chemical building blocks Ð adenine, thymine, cytosine, and guanine (A, T, C, G), strung together in different combinations in long chains within 23 pairs of chromosomes. When the first human genome was being sequenced, it became apparent that additional human genomes would have to be sequenced to identify the places in the genetic code that account for human variation. Scientists now know that humans share about 97-99 percent of the genetic code, and the remaining 1-3 percent dictates individual differences. These naturally occurring differences, called polymorphisms, help explain differences in appearance, susceptibility to diseases, and responses to the environment.
SNPs are differences in single chemical bases in the genome sequence, and INDELs result from the insertion and deletion of small pieces of DNA of varying sizes and types. If the human genome is viewed as a genetic instruction book, then SNPs are analogous to single letter changes in the book, whereas INDELs are equivalent to inserting and deleting words or paragraphs.
Most polymorphism discovery projects have focused on SNPs, resulting in the International HapMap Project Ð a catalog and map of more than 10 million SNPs derived from diverse individuals throughout the globe. Dr. Devine and postdoctoral researcher Ryan Mills, PhD, focused instead on INDELs, using a computational approach to examine DNA re-sequences that originally were generated for SNP discovery projects. Thus far they have identified and mapped 415,436 unique INDELs, but they expect to expand the map to between 1 and 2 million by continuing their efforts with additional human sequences.
Dr. Devine says INDELs can be grouped into five major categories, depending on their effect on the genome: (1) insertions or deletions of single base pairs; (2) expansions by only one base pair (monomeric base pair expansions); (3) multi-base pair expansions of 2 to 15 repeats; (4) transposon insertions (insertions of mobile elements); (5) and random DNA sequence insertions or deletions. INDELs already are known to cause human diseases. For example, cystic fibrosis is frequently caused by a three-base-pair deletion in the CFTR gene, and DNA insertions called triplet repeat expansions are implicated in fragile X syndrome and Huntington's disease. Transposon insertions have been identified in hemophilia, muscular dystrophy and cancer.
"Were entering an exciting new era of predictive health where an individuals personal genetic code will provide guidance on healthcare decisions says Dr. Devine. "Our maps of insertions and deletions will be used together with SNP maps to create one big unified map of variation that can identify specific patterns of genetic variation to help us predict the future health of an individual. The next phase of this work is to figure out which changes correspond to changes in human health and develop personalized health treatments. This could include specific drugs tailored to each individual, given their specific genetic code.
Ultimately, each person's genome could be re-sequenced in a doctor's office and his or her genetic code analyzed to make predictions about their future health. Dr. Devine believes the technology holds the promise of predicting whether a person will develop diabetes, mental disorders, cancer, heart disease and a range of other conditions.
Holly Korschun | EurekAlert!
Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory
How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.
Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.
The results will be published on March 22 in the journal „Astronomy & Astrophysics“.
Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...
Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.
Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...
In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.
Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.
Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...
20.03.2017 | Event News
14.03.2017 | Event News
07.03.2017 | Event News
24.03.2017 | Materials Sciences
24.03.2017 | Physics and Astronomy
24.03.2017 | Physics and Astronomy