Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

CSHL scientists develop new method to detect copy number variants using DNA sequencing technologies

26.08.2009
The new technique can detect key genetic variations overlooked by current methods

Cold Spring Harbor, N.Y. – A research team led by Associate Professor Jonathan Sebat, Ph.D., of Cold Spring Harbor Laboratory (CSHL) has developed a sensitive and accurate way of identifying gene copy number variations (CNVs).

The method, which is described in a paper published online ahead of print in Genome Research, uses new DNA sequencing technologies to look for regions of the genome that vary in copy number between individuals in the population. Capable of detecting a wide range of different classes of CNVs, large and small, this method allows researchers to extract more genetic information from the complete genome sequence of an individual.

CNVs are regions of the genome that vary in the number of copies between individuals. These variants were once considered to be anomalies that occurred rarely among healthy individuals. As the result of a discovery by CSHL Professor Michael Wigler and Dr. Sebat in 2004, CNVs are now recognized as a major source of human genetic variation and methods for detecting CNVs have proven to be an effective approach for identifying genetic risk factors for disease.

Genome sequencing technologies are improving at a rapid pace. The current challenge is to find ways to extract all of the genetic information from the data. One of the biggest challenges has been the detection of CNVs. Sebat, in collaboration with Seungtai Yoon of CSHL and Kenny Ye, Ph.D., at the Albert Einstein College of Medicine, developed a statistical method to estimate DNA copy number of a genomic region based on the number of sequences that map to that location (or "read depth"). When the genomes of multiple individuals are compared, regions that differ in copy number between individuals can be identified.

The new method allows the detection of small structural variants that could not be detected using earlier microarray-based methods. This is significant because most of the CNVs the genome are less than 5000 nucleotides in length. The new method is also able to detect certain classes of CNVs that other sequencing-based approaches struggle with, particularly those located in complex genomic regions where rearrangements occur frequently.

The development of this novel method is timely. The 1000 Genomes Project was launched in 2008, as an international effort to sequence the genomes of 2000 individuals across geographic and ethnic regions to catalog human genetic variation. Sebat's team along with many other groups has contributed to the production and analysis of these data.

This innovation improves the detection of structural variants from whole genome sequence data, which will lead to improved sensitivity to detect disease-causing CNVs.

"Sensitive and accurate detection of copy number variants using read depth of coverage" can be found online at http://genome.cshlp.org/content/early/2009/08/05/gr.092981.109.long. The full citation is: Seungtai Yoon, Zhenyu Xuan, Vladimir Makarov, Kenny Ye and Jonathan Sebat. Support for this work was provided by the National Human Genome Research Institute, part of the National Institutes of Health.

Cold Spring Harbor Laboratory (CSHL) is a private, not-for-profit research and education institution at the forefront of efforts in molecular biology and genetics to generate knowledge that will yield better diagnostics and treatments for cancer, neurological diseases and other major causes of human suffering.

Peter Tarr | EurekAlert!
Further information:
http://www.cshl.edu

More articles from Life Sciences:

nachricht Toward a 'smart' patch that automatically delivers insulin when needed
18.01.2017 | American Chemical Society

nachricht 127 at one blow...
18.01.2017 | Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut für Biodiversität der Tiere

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: How gut bacteria can make us ill

HZI researchers decipher infection mechanisms of Yersinia and immune responses of the host

Yersiniae cause severe intestinal infections. Studies using Yersinia pseudotuberculosis as a model organism aim to elucidate the infection mechanisms of these...

Im Focus: Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

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...

Im Focus: Studying fundamental particles in materials

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...

Im Focus: Designing Architecture with Solar Building Envelopes

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...

Im Focus: How to inflate a hardened concrete shell with a weight of 80 t

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...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

12V, 48V, high-voltage – trends in E/E automotive architecture

10.01.2017 | Event News

2nd Conference on Non-Textual Information on 10 and 11 May 2017 in Hannover

09.01.2017 | Event News

Nothing will happen without batteries making it happen!

05.01.2017 | Event News

 
Latest News

A big nano boost for solar cells

18.01.2017 | Power and Electrical Engineering

Glass's off-kilter harmonies

18.01.2017 | Materials Sciences

Toward a 'smart' patch that automatically delivers insulin when needed

18.01.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>