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

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.

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."
'"/>

Source:Cold Spring Harbor Laboratory


Related biology news :

1. Novel technology detects human DNA mutations
2. Novel antiviral technology inhibits RSV infection in mice
3. The BIOS Initiative - open source biotechnology is born
4. Revolutionary nanotechnology illuminates brain cells at work
5. Study: homemade gene expression technology unreliable
6. First technology to remove prions that cause vCJD from blood launched
7. Integration of Agilents MS technology, Proteome Systems software to help scientists in proteomics research
8. Agilent Technologies new genome analysis technology set to accelerate Australia fight against mesothelioma
9. Recombinant DNA technology may enable oral, rather than injectable, delivery of protein drugs
10. First production of human monoclonal antibodies in chicken eggs published in Nature Biotechnology
11. Vietnam war technology could aid elephant conservation

Post Your Comments:
*Name:
*Comment:
*Email:


(Date:6/22/2016)... , June 22, 2016   Acuant ... and verification solutions, has partnered with RightCrowd ... solutions for Visitor Management, Self-Service Kiosks and ... products that add functional enhancements to existing ... corporations and venues with an automated ID ...
(Date:6/16/2016)... 16, 2016 The global ... to reach USD 1.83 billion by 2024, according ... Inc. Technological proliferation and increasing demand in commercial ... to drive the market growth.      ... The development of advanced multimodal techniques for biometric ...
(Date:6/7/2016)...  Syngrafii Inc. and San Antonio Credit Union ... integrating Syngrafii,s patented LongPen™ eSignature "Wet" solution into ... result in greater convenience for SACU members and ... existing document workflow and compliance requirements. ... Highlights: ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... June 27, 2016  Sequenom, Inc. (NASDAQ: ... healthier lives through the development of innovative products and ... the United States denied its petition ... claims of Sequenom,s U.S. Patent No. 6,258,540 (",540 Patent") ... established by the Supreme Court,s Mayo Collaborative Services v. ...
(Date:6/27/2016)...  Liquid Biotech USA , ... Sponsored Research Agreement with The University of Pennsylvania ... cancer patients.  The funding will be used to ... clinical outcomes in cancer patients undergoing a variety ... employed to support the design of a therapeutic, ...
(Date:6/24/2016)... ... 24, 2016 , ... Researchers at the Universita Politecnica delle Marche in Ancona ... or pleural mesothelioma. Their findings are the subject of a new article on the ... are signposts in the blood, lung fluid or tissue of mesothelioma patients that can ...
(Date:6/23/2016)... A person commits a crime, and the detective ... the criminal down. An outbreak of foodborne illness ... (FDA) uses DNA evidence to track down the bacteria that ... It,s not. The FDA has increasingly used a complex, cutting-edge ... illnesses. Put as simply as possible, whole genome sequencing is ...
Breaking Biology Technology: