Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New technology used to construct the first map of structural variation in the human genome

24.11.2006
Methods also applicable to disease diagnosis, drug response tests

Beyond the simple stream of one-letter characters in the human genome sequence lies a complex, higher-order code. In order to decipher this level of architecture, scientists have developed powerful new experimental and algorithmic methods to detect copy number variants (CNVs)--defined as large deletions and duplications of DNA segments. These technologies--reported today in the journal Genome Research--were used to create the first comprehensive map of CNVs in the human genome, concurrently published in Nature. A related article appears in Nature Genetics.

CNVs are responsible for genetic changes in Alzheimer's and Parkinson's, susceptibility to HIV-1, some forms of color blindness, and many other diseases. They lead to variation in gene expression levels and may account for a large amount of phenotypic variation among individuals and ethnic populations, including differential responses to drugs and environmental stimuli. Mechanisms underlying the formation of CNVs also provide insight into evolutionary processes and human origins.

Using microarray technology, scientists can scan for CNVs across the genome in a single experiment. While this is a cost-effective means of obtaining large amounts of data, scientists have struggled to accurately determine CNV copy number and to precisely define the boundaries of CNVs in the genome. Two papers published today in Genome Research present groundbreaking approaches to address these issues.

... more about:
»Array »CNV »Genome »algorithm

One paper describes a new whole-genome tiling path microarray, which was constructed from the same DNA used to sequence the human genome in 2001. The array covers 93.7% of the euchromatic (gene-containing) regions of the human genome and substantially improves resolution over previous arrays. The array was employed in a process known as comparative genomic hybridization (CGH), which involves tagging genomic DNA from two individuals and then co-hybridizing it to the array. Data from the array were assessed with a new algorithmic tool, called CNVfinder, which accurately and reliably identified CNVs in the human genome.

"This method helped us to develop the first comprehensive map of structural variation in the human genome," says Dr. Nigel Carter, one of the lead investigators on the project. "We used it to help identify 1,447 CNVs, which covered 12% of the human genome."

The other paper presents a new multi-step algorithm used with the Affymetrix GeneChip® Human Mapping 500K Early Access SNP arrays. The specificity of the algorithm, coupled with the increased probe density of these arrays, permitted the identification of approximately 1,000 CNVs, many of which were below the detection size limit of alternative methodologies. Furthermore, the algorithm more accurately estimated CNV boundaries, thereby permitting a detailed comparison with other genomic features.

"This new approach will be useful in understanding the role of CNVs in disease pathology--not only copy number changes in cancer cells, but also possible association of CNVs with common diseases," explains Dr. Hiroyuki Aburatani, one of the scientists who led the development of the algorithm. "We'll be able to develop diagnostic tests with sub-microscopic resolution, and because the analysis detects SNPs--single-nucleotide polymorphisms--in addition to CNVs, it will find widespread use among researchers performing disease-association studies."

Maria A. Smit | EurekAlert!
Further information:
http://www.genome.org

Further reports about: Array CNV Genome algorithm

More articles from Life Sciences:

nachricht Ion treatments for cardiac arrhythmia — Non-invasive alternative to catheter-based surgery
20.01.2017 | GSI Helmholtzzentrum für Schwerionenforschung GmbH

nachricht Seeking structure with metagenome sequences
20.01.2017 | DOE/Joint Genome Institute

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Traffic jam in empty space

New success for Konstanz physicists in studying the quantum vacuum

An important step towards a completely new experimental access to quantum physics has been made at University of Konstanz. The team of scientists headed by...

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...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Sustainable Water use in Agriculture in Eastern Europe and Central Asia

19.01.2017 | 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

 
Latest News

Helmholtz International Fellow Award for Sarah Amalia Teichmann

20.01.2017 | Awards Funding

An innovative high-performance material: biofibers made from green lacewing silk

20.01.2017 | Materials Sciences

Ion treatments for cardiac arrhythmia — Non-invasive alternative to catheter-based surgery

20.01.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>