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Forsyth Institute, Kings College, Helicos, UBS, Cantor Fitzgerald, USDA, Trilobium Genome Sequencing Consortium, GeneTree, Sorenson Molecular Genealogy Foundation, Manchester BRC, EuroGentest

Forsyth, Kings College Scientists Kick Off Human Oral Microbiome Database
Scientists from the Forsyth Institute and Kings College, London launched the Human Oral Microbiome Database this week.
The online database will be a resource for those interested in understanding the role of oral microbes in human health and disease.
In addition to descriptions of the bacteria, such as their taxonomy, phenotypic characteristics, prevalence, and disease associations, it categorizes each microbe by its 16S rRNA sequence. For those organisms whose DNA has been sequenced, HOMD provides online tools to view and analyze all of their genes and proteins. More genomic information will be added as it becomes available through the NIH’s Human Microbiome Project, which began last December.
HOMD also introduces the first comprehensive nomenclature system for naming uncultured or previously unnamed oral microbes.
Taxonomic descriptions of the 600 or so species currently known to live in the mouth should be complete sometime around the end of next year, according to the site, though the database itself is expected to continue expanding for at least three years. The project is supported by the US National Institute for Dental and Craniofacial Research.
The Human Oral Microbiome Database is available here.

UBS Upgrades Helicos' Stock, Lowers Revenue Forecast; Cantor Fitzgerald Initiates Coverage
Investment bank UBS last week upgraded its rating on Helicos BioSciences’ stock from “sell” to “neutral" and lowered its revenue forecast for the firm. Also last week, Cantor Fitzgerald started covering Helicos with a “buy” rating.
Following Helicos’ 2007 third-quarter results in November, UBS had downgraded the stock to “sell.” Despite that downgrade, Helicos’ shares had hit a high of $18.60 on Jan. 16. Since then, the stock has fallen sharply, closing at $6.15 on Monday, down 32 percent from its $9 opening bid when the company went public May 24, 2007.
“Although we still have lingering concerns regarding [Helicos’] ability to execute and have lowered our sales forecasts, we upgrade to Neutral from Sell chiefly on valuation following the recent pull back” of the stock price, UBS analysts wrote in a research note.
“While we expect the company to ship more units to early-access customers during 2008, we also believe that, given the HeliScope’s $1.35 million price tag, significant customer validation will be needed to spur broad uptake, and these third-party data may not be available until late ’08 or early ’09,” according to the note.
UBS lowered its price target on Helicos’ stock to $6.50 per share from $10. It also lowered its 2008 revenue forecast for Helicos down to $8.4 million from an earlier estimate of $21.7 million, and its 2009 revenue forecast to $35.4 million from $80.2 million. The firm said it expects Helicos to ship 11 next-generation sequencing systems in 2008, versus its prior expectation of 20 systems.
Helicos did not provide revenue guidance during its recent fiscal-year 2007 and fourth-quarter conference call.

USDA Scientists Will Use $3M to Create Soy SNP Library
Researchers with the US Department of Agriculture plan to create a library of 50,000 SNPs from the soybean genome that could be used to develop soybeans with improved yield, greater resistance to pests, and improved protein and oil quality, the USDA’s Agricultural Research Service said late last week.
Scientists at the ARS’ Soybean and Genomics Improvement Research Unit in Beltsville, Md., will be working with $2.9 million in funding from the United Soybean Board.
The researchers will use the SNPs in conjunction with data from the draft soybean genome that the US Department of Energy’s Joint Genome Institute completed in January.
The USDA said it is particularly interested in using this data to identify plants carrying traits such as resistance to pests and production of high-quality oil.
“Our overall goal is to harness the remarkable recent developments in rapid genome analysis to construct a new, highly detailed, high-resolution description of the genetic diversity contained within soybean and its close wild relatives,” ARS administrator Edward Knipling said in a statement.

International Consortium Sequences Red Flour Beetle Genome
An international team of researchers has sequenced and started to analyze the genome of the red flour beetle, an agricultural pest that lives in and snacks on stored grains and dried foods.
More than 100 scientists from 14 countries pitched in to sequence the genome of the red flour beetle, Tribolium castaneum. The Trilobium Genome Sequencing Consortium reported the achievement in the advanced online publication of Nature this week.
T. castaneum can survive extremely dry environments, as well as every class of insecticides humans have devised against it. But because it is amenable to genetic crosses and grows easily in the lab, with a short life cycle and high reproduction rates, T. castaneum is a good model organism, especially for developmental studies.
The researchers generated about 1.5 million sequence reads at 7.3-fold coverage. They assembled these into contigs totaling 152 megabases, coding for 16,404 genes, thousands of which seem to be species-specific.
Compared to the genetic code of other insects, the red flour beetle genome has a “major expansion” of genes coding for smell- and taste-related proteins and receptors.
The genome also houses an expanded roster of cytochrome P450 genes, which are involved in metabolic detoxification, insecticide resistance, and environmental response. Overall, the authors report, the red flour beetle genome confirms the bug’s adaptation to a “dry, chemically diverse and toxin-rich microenvironment.”
The consortium suggests that identifying and understanding genes related to the flour beetle’s pesticide resistance, vision, smell, and taste could eventually help researchers trying to control these and similar pests.
The work was funded by the National Institutes of Health and the US Department of Agriculture and was led by Baylor College of Medicine’s Stephen Richards, who is at that institution’s Human Genome Sequencing Center.

GeneTree Offers DNA Donors Discounts Through Sorenson Foundation
The family history-sharing website GeneTree will offer discounted DNA profiles to individuals who have contributed DNA samples and genealogical charts to the Sorenson Molecular Genealogy Foundation’s database through a joint agreement, GeneTree said this week.
The company said the agreement with SMGF will give those individuals who donated materials to the database before the end of 2007 access to mitochondrial DNA profiles that they can use to seek potential genetic relatives and to learn more on the GeneTree website about how their profiles fit into the “greater human genetic story.”
The discount price for the service is $19.50 compared with the $99 or $149 the company generally charges for the service. GeneTree launched its web service in October 2007.
The SMGF started the database in 2000, and it currently contains DNA samples from nearly 100,000 people and has more than 6 million corresponding genealogical records from over 170 countries.
Both the company and the foundation are based in Salt Lake City. The GeneTree website was developed by the Sorenson family of companies.

UK Center to Use $69M for Genetics and Translational Research
A new government-funded research center in Manchester, UK, plans to perform genetic and translational research with the aim of creating predictive tests for fetal problems and pregnancy complications, government and media sources in the UK said last week.
The Biomedical Research Center will include research from Central Manchester and Manchester Children’s University Hospitals, NHS Trust, and the University of Manchester, according to the British Secretary of Health.
The Manchester BRC will receive £7.4 million ($14.7 million) per year over four years for a total of around £35 million from the Department of Health, and it has applied for as much as £10 million per year in external grants from the North West Developmental Agency, the Manchester Evening News reported last week.
The Manchester BRC joins similar Biomedical Research Centers in London, Oxford, Cambridge, Liverpool, and Newcastle.
The UK has allocated £50 million for all of the BRCs during the first year of operation and £100 million per year over the next four years. The amount allocated to each center is determined by the scale and nature of the research that it conducts and the anticipated impact of that activity, according to the UK’s National Institute for Health Research.
In addition to developing a predictive test for pregnancy complications, the Manchester BRC will use genetic technologies to improve diagnosis and treatment in other areas, including sudden cardiac death, developmental disease, disadvantaged populations, and inflammatory bowel disease.

Seeking ‘Confidence,’ EuroGentest Discloses Genetic Testing Lab Credentials
The European Union is making information about genetic testing labs available to individuals who are taking genetic tests, according to the EU-funded EuroGentest project.
“As genetic testing increases across the EU, it is essential that patients and their families have upmost confidence in the laboratories performing tests,” said Jean-Jacques Cassiman, a professor at the Center for Human Genetics and a coordinator for EuroGentest, in a statement.
The project has collated data on the majority of the more than 1,500 labs involved in member and associated EU states, according to EuroGentest. The group has made that data available free via a new version of Orphanet, a public portal for rare disease information.
The search tool lists the tests that labs perform, accreditation status, staff qualifications, and research interests.

Giving patients the ability to search a particular lab on Orphanet “gives confidence in the validity of the results of genetic tests, and means that families are able to make better, more informed decisions,” said Alastair Kent, director of the Genetic Interest Group.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.