The method, developed in cooperation with RainDance Technologies, is described in the Oct. 2011 issue of Genomics. Senior author Michael Zwick, PhD, assistant professor of human genetics at Emory University School of Medicine, is using the method to identify genetic variants that contribute to autism spectrum disorders.
Because the X chromosome is a hotspot for genes that are suspected of contributing to autism and intellectual disability, the Emory team’s finding could speed new discoveries and eventually make routine clinical diagnosis of autism and intellectual disability easier.
“This technology has the potential to be a valuable tool for genetic researchers across a wide variety of applications,” Zwick says. “Our data shows that it can support the routine sequencing of the exons of the human X chromosome in a uniform, accurate and comprehensive way.”
The team’s sequencing method does not read all the letters of the genetic code in the X chromosome from beginning to end. Instead, it targets more than 800 “exons”: all the genes that get read out and made into RNA.
A direct comparison with another method of target selection called oligonucleotide capture showed that the team’s technique needed between three and seven times fewer sequence reads to achieve high levels of accuracy and completeness, potentially meaning lower costs.
The Emory team’s experiments showed that their technique could read 97 percent of targeted sequences at high depth with an accuracy of 99.5 percent. The team used data from the HapMap Project, a partnership coordinated by the Human Genome Research Institute, as a reference standard for genetic sequence variation.Sex is determined by having two X chromosomes (female) or an X and a Y chromosome (male). Because males have only a single X chromosome, a mutation in a gene on the X chromosome is more likely to affect a male than a female because males lack another copy of the same gene to compensate. This pattern of inheritance can contribute to disorders that disproportionately affect males, such as autism spectrum disorder or intellectual disability.
Modern DNA sequencing techniques use the polymerase chain reaction (PCR) to isolate and “amplify” the target DNA scientists want to read. RainDance Technologies has developed a single molecule microdroplet-based technology that enables scientists to target up to 20,000 genomic loci in a single sample, saving time, space and cost while increasing reliability and ease of use. The reactions take place in millions of self-contained droplets, allowing each to amplify a different piece of DNA within an emulsion.
K. Mondal, A.C. Shetty, V. Patel, D.J. Cutler and M.E. Zwick. Targeted sequencing of the human X chromosome exome. Genomics Vol. 98, Issue 4, pp. 260-265 (Oct. 2011).
Writer: Quinn Eastman
The Robert W. Woodruff Health Sciences Center of Emory University is an academic health science and service center focused on missions of teaching, research, health care and public service.Learn more about Emory’s health sciences:
Holly Korschun | EurekAlert!
Barium ruthenate: A high-yield, easy-to-handle perovskite catalyst for the oxidation of sulfides
16.07.2018 | Tokyo Institute of Technology
The secret sulfate code that lets the bad Tau in
16.07.2018 | American Society for Biochemistry and Molecular Biology
For the first time ever, scientists have determined the cosmic origin of highest-energy neutrinos. A research group led by IceCube scientist Elisa Resconi, spokesperson of the Collaborative Research Center SFB1258 at the Technical University of Munich (TUM), provides an important piece of evidence that the particles detected by the IceCube neutrino telescope at the South Pole originate from a galaxy four billion light-years away from Earth.
To rule out other origins with certainty, the team led by neutrino physicist Elisa Resconi from the Technical University of Munich and multi-wavelength...
For the first time a team of researchers have discovered two different phases of magnetic skyrmions in a single material. Physicists of the Technical Universities of Munich and Dresden and the University of Cologne can now better study and understand the properties of these magnetic structures, which are important for both basic research and applications.
Whirlpools are an everyday experience in a bath tub: When the water is drained a circular vortex is formed. Typically, such whirls are rather stable. Similar...
Physicists working with Roland Wester at the University of Innsbruck have investigated if and how chemical reactions can be influenced by targeted vibrational excitation of the reactants. They were able to demonstrate that excitation with a laser beam does not affect the efficiency of a chemical exchange reaction and that the excited molecular group acts only as a spectator in the reaction.
A frequently used reaction in organic chemistry is nucleophilic substitution. It plays, for example, an important role in in the synthesis of new chemical...
Optical spectroscopy allows investigating the energy structure and dynamic properties of complex quantum systems. Researchers from the University of Würzburg present two new approaches of coherent two-dimensional spectroscopy.
"Put an excitation into the system and observe how it evolves." According to physicist Professor Tobias Brixner, this is the credo of optical spectroscopy....
Ultra-short, high-intensity X-ray flashes open the door to the foundations of chemical reactions. Free-electron lasers generate these kinds of pulses, but there is a catch: the pulses vary in duration and energy. An international research team has now presented a solution: Using a ring of 16 detectors and a circularly polarized laser beam, they can determine both factors with attosecond accuracy.
Free-electron lasers (FELs) generate extremely short and intense X-ray flashes. Researchers can use these flashes to resolve structures with diameters on the...
13.07.2018 | Event News
12.07.2018 | Event News
03.07.2018 | Event News
16.07.2018 | Physics and Astronomy
16.07.2018 | Life Sciences
16.07.2018 | Earth Sciences