Comparing the DNA from patients at the best and worst extremes of a health condition can reveal genes for resistance and susceptibly. This approach discovered rare variations in the DCTN4 gene among cystic fibrosis patients most prone to early, chronic airway infections.
The DCTN4 gene codes for dynactin 4. This protein is a component of a molecular motor that moves trouble-making microbes along a cellular conveyer belt into miniscule chemical vats, called lysosomes, for annihilation.
This study, led by the University of Washington, is part of the National Heart Lung and Blood Institute GO Exome Sequencing Project and its Lung GO, both major National Institutes of Health chronic disease research efforts.
Similar "testing the extremes" strategies may have important applications in uncovering genetic factors behind other more common, traits, such as healthy and unhealthy hearts.
The results of the cystic fibrosis infection susceptibility study appear this Sunday, July 8, in Nature Genetics.
The infection in question was Pseudomonas aeruginosa, an opportunistic soil bacterium that commonly infects the lungs of people with cystic fibrosis and other airway-clogging disorders. The bacteria can unite into a slithery, hard-to-treat biofilm that hampers breathing and harms lung tissue. Chronic infections are linked to poor lung function and shorter lives among cystic fibrosis patients. These bacteria rarely attack people with normal lungs and well-functioning immune systems.
In the study, these rare variations in DCTN4 did not appear in any of the cystic fibrosis patients who were the most resistant to Pseudomonas infection. The study subjects most susceptible to early, chronic infection had at least one DCTN4 missense variant. A missense variant produces a protein that likely can't function properly.
The lead author of the report published July 8 in Nature Genetics is Mary J. Emond, research associate professor of biostatistics at the University of Washington School of Public Health in Seattle. The senior author is medical geneticist Michael Bamshad, UW professor of pediatrics in the Division of Genetic Medicine.
To the extent of their knowledge, the researchers think that this might be the first time that genetic variants underlying complex trait were discovered by sequencing all the protein-coding portions of the genomes of people at each extreme of a disease spectrum.
"We did not have a candidate gene in mind when we did this study," said Emond. Statistical analysis of the DNA of 91 patients led the research team to this particular gene. Of the initial study group, 43 children had their first onset of chronic lung infection with Pseudomonas as when they were very young, and the 48 oldest individuals had not yet reached a state of chronic infection. The patients selected for sequencing were from the Early Pseudomonas Control (EPIC) Observational Study, a project at the Seattle Children's Research Institute, and the North American Cystic Fibrosis Genetic Modifiers Study. Exome sequencing was done by UW researchers in the laboratory of Deborah Nickerson, UW professor of genome sciences.
Comparisons of the protein coding portions of the study subjects' DNA called the researchers attention to missense variations of the DCTN4 gene. The researchers went on to screen a selected group of 1,322 other EPIC participants to check their findings.
Exome Sequencing Project scientists are using an approach similar to the one in this study to examine the genetics behind resistance and susceptibility to other chronic conditions like obesity, heart attacks and hypertension. They plumb for gene variations linked to heart disease, for example by putting DNA maps from people with ideal cholesterol levels up against those from people with exceptionally poor levels.
Adapting a similar strategy to determine the genetics underlying other complex human traits may require exome sequencing of a much larger sample sizes, the researchers noted.
"As the costs of exome sequencing are dropping rapidly and more efficient statistical analysis is becoming available, we think medical researchers' enthusiasm for this approach will continue," Bamshad predicted.
In addition to National Heart Lung and Blood Institute funding, the study released today was supported by grants from the National Human Genome Research Institute, the Cystic Fibrosis Foundation, and the Life Sciences Discovery Fund.
Leila Gray | EurekAlert!
New study finds distinct microbes living next to corals
22.05.2019 | Woods Hole Oceanographic Institution
Summit charts a course to uncover the origins of genetic diseases
22.05.2019 | DOE/Oak Ridge National Laboratory
Engineers at the University of Tokyo continually pioneer new ways to improve battery technology. Professor Atsuo Yamada and his team recently developed a...
With a quantum coprocessor in the cloud, physicists from Innsbruck, Austria, open the door to the simulation of previously unsolvable problems in chemistry, materials research or high-energy physics. The research groups led by Rainer Blatt and Peter Zoller report in the journal Nature how they simulated particle physics phenomena on 20 quantum bits and how the quantum simulator self-verified the result for the first time.
Many scientists are currently working on investigating how quantum advantage can be exploited on hardware already available today. Three years ago, physicists...
'Quantum technologies' utilise the unique phenomena of quantum superposition and entanglement to encode and process information, with potentially profound benefits to a wide range of information technologies from communications to sensing and computing.
However a major challenge in developing these technologies is that the quantum phenomena are very fragile, and only a handful of physical systems have been...
Working group led by physicist Professor Ulrich Nowak at the University of Konstanz, in collaboration with a team of physicists from Johannes Gutenberg University Mainz, demonstrates how skyrmions can be used for the computer concepts of the future
When it comes to performing a calculation destined to arrive at an exact result, humans are hopelessly inferior to the computer. In other areas, humans are...
Scientists develop a molecular recording tool that enables in vivo lineage tracing of embryonic cells
The beginning of new life starts with a fascinating process: A single cell gives rise to progenitor cells that eventually differentiate into the three germ...
29.04.2019 | Event News
17.04.2019 | Event News
15.04.2019 | Event News
22.05.2019 | Life Sciences
22.05.2019 | Life Sciences
22.05.2019 | Physics and Astronomy