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 Study shines light on brain cells that coordinate movement
26.06.2017 | University of Washington Health Sciences/UW Medicine

nachricht New insight into a central biological dogma on ion transport
26.06.2017 | Aarhus University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Study shines light on brain cells that coordinate movement

26.06.2017 | Life Sciences

Smooth propagation of spin waves using gold

26.06.2017 | Physics and Astronomy

Switchable DNA mini-machines store information

26.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>