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SeqWright, ENCODE, Duke University, NIH Roadmap Initiative, CDC, DNAStar

SeqWright Enters Personal Genome Analysis Business
DNA sequencing and genomic services provider SeqWright of Houston said last week that it will offer a genomic profiling service to private individuals.
The company will use Affymetrix’s Human Genome-Wide SNP Array 6.0 to analyze customers’ genomes at a cost of $998. All analyses will be performed at its GLP-compliant and CLIA-certified facility.
The results “may be used by the customer to infer the risk of developing specific diseases, relatedness to various world populations and ethnic groups, and genetic traits they share with participating family members,” according to a company statement.
SeqWright will provide customers with “tools which can compare their SNP genotype results to the most well-established common disease associations” and will keep customers updated about new disease association study results.
The company will also compare a customer’s genetic markers to European, East Asian, and West African populations in order to provide a “measure of relatedness” to these.
SeqWright CEO Fei Lu told In Sequence last week that the company will initially only report approximately 100 SNPs to customers, while it will “stay away” from SNPs that are associated with a high risk for birth defects.
Long term, when the cost of sequencing drops, SeqWright plans to offer genome-sequencing services to individuals as well. “I think a lot of individuals would be willing to pay $10,000 to get their genome done,” Lu said.
The company recently installed a SOLiD sequencer, but that instrument, “at the current cost, [is] kind of expensive for sequencing a whole genome,” Lu said.
SeqWright shares a building with VisiGen Biotechnologies and has invested an undisclosed amount in the startup company, which is developing a real-time single-molecule sequencing-by-synthesis technology (see In Sequence 5/8/2007).
VisiGen has said that it plans to offer sequencing services by the end of 2009. “Definitely, when they launch, we will use them” for the personal genomics service, Lu said.

Researchers Use Microarrays, Next-Gen Sequencers to Map Potential Gene Regulatory Regions
Scientists last week published a new, genome-wide approach for mapping open chromatin that involves next-generation sequencing.
The researchers, who are members of the ENCODE Consortium (see In Sequence 11/27/2007) and based at Duke and Boston Universities, the National Cancer Institute, and the National Human Genome Research Institute, used a novel combination of targeted DNA digestion, microarray analysis, and sequencing to identify 94,925 regions that are likely involved in some form of gene regulation. Their findings were published online last week in the journal Cell.
Most nuclear DNA is packaged and wrapped around protein complexes. But gene regulatory regions tend to be on open chromatin that is not assembled on these complexes, and these stretches of DNA are more easily chopped up by the enzyme DNase I.
Researchers have already exploited this DNase I hypersensitivity to identify regulatory for particular genes of interest. Terrence Furey, a biostatistician at Duke University, and his colleagues took this approach several steps further, scaling up the process to look for DNase I sensitive, regulatory regions across the entire genome.
After slicing and dicing the DNA from a primary blood cell line with DNase I, the team used size selection to pick up the smaller DNA fragments that had originated in hypersensitive, regulatory zones. Then they hybridized the fragments to whole-genome NimbleGen arrays or sequenced them using next-generation sequencing platforms from Illumina and 454.
Finally, they created what they call “a comprehensive and accurate genome-wide open chromatin map” based on the 94,925 DNase I hyper-sensitive sites they identified. They also assessed which potential regulatory regions fell in transcription sites, between transcription sites, or even within genes.
Although these experiments were done in normal cell lines, Furey and his colleagues hope to apply these studies to disease conditions as well. As such, their next step is using similar techniques to map DNase I sensitive regions for 15 to 20 additional cell lines — both normal and cancerous — looking for patterns that are linked to disease states.
Abridged version of a GenomeWeb Daily News article by Andrea Anderson.

NIH's $190M Epigenome Project to Link Genome to Living World
The National Institutes of Health last week officially launched its Epigenome Project, which will start as a five-year, $190 million trans-NIH effort aimed at understanding gene regulation.
The NIH called the epigenomics funding a priority research goal that will be funded through its Roadmap Initiative (see In Sequence 7/3/2007).
“Although there has been a lot of progress in the epigenome, new technologies are needed,” Alan Krensky, who directs the NIH Office of Portfolio Analysis and Strategic Initiatives, told In Sequence’s sister publication GenomeWeb Daily News in an interview last month. “We need comprehensive maps for different cell types, standardized platforms, and definitions, so that people can talk to each other about epigenetics and about how stable the epigenome is.”
“Epigenomics will build upon our new knowledge of the human genome and help us better understand the role of the environment in regulating genes that protect our health or make us more susceptible to disease,” NIH Director Elias Zerhouni said in a statement.
Like other Roadmap endeavors, the Epigenomics Project will be coordinated by OPASI, but will include leadership efforts from the National Institute of Environmental Health Sciences, the National Institute on Drug Abuse, the National Institute on Deafness and Other Communication Disorders, the National Institute of Diabetes and Digestive and Kidney Diseases, the National Institute of Neurological Disorders and Stroke, and the National Center for Biotechnology Information.
OPASI hopes to work with the other centers and with investigators to develop a series of reference epigenome maps that would be publicly available and would be analogous to genome maps.
The research will study epigenetic mechanisms involved in aging, development, and environmental exposure, and scientists will seek to develop new tools to analyze single cells and develop images of epigenetic activity in living organisms. The NIH also expects to work with the international scientific community to develop new tools and define standard practices and platforms.

CDC's Infectious Disease Centers to Use DNAStar's Sequence Analysis Software
The US Centers for Disease Control and Prevention has licensed DNAStar’s sequence analysis software for use at several of its facilities, the bioinformatics company said this week.
The multi-site license agreement allows the CDC’s Coordinating Center for Infectious Disease to use the company’s Lasergene software at its Atlanta base and at its campuses in Colorado, Alaska, and Puerto Rico.
The Lasergene software includes assembly, visualization, and analysis tools for traditional and next-generation sequencing data, DNAStar said.
The CCID includes the National Center for Immunization and Respiratory Disease; the National Center for Zoonotic, Vector Borne, and Enteric Disease; the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention; and the National Center for Preparedness, Control, and Prevention of Infectious Diseases.

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.