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Danaher Places Two Polonator Sequencers at Harvard Medical School
 
Danaher Motion has placed Polonator instruments, the new commercial version of George Church’s polony sequencing platform, in two Harvard Medical School research groups.
 
One instrument went to George Church’s lab, the other to Jonathan Seidman’s group. Both research groups are currently testing the performance of the instruments.
 
Earlier this year, Seidman and colleagues published an analysis of mRNA in heart muscle in Science, a study for which they made improvements to the first version of the platform (see In Sequence 6/12/2007).
 
Church disclosed at a conference last month that the Dover business of Danaher Motion, based in Salem, NH, will distribute the Polonator G.007 (see In Sequence 10/16/2007).
 

 
Consumer Genomics Startup Navigenics Raises $25M from VC Firms
 
Navigenics of Redwood Shores, Calif., said this week that it has raised a total of $25 million from venture capital firms to date. The direct-to-consumer genomics company, which officially launched this week, also named its advisers and investors.
 
The company recently completed a Series B financing round, led by new investor MDV-Mohr Davidow Ventures, with pro rata investments from existing investors Kleiner Perkins Caufield and Byers and Sequoia Capital.
 
Kleiner Perkins Caufield and Byers and Mohr Davidow Ventures have also invested in sequencing technology startup Pacific Biosciences (see In Sequence 4/24/2007).
 
Navigenics said it plans to “help people understand their genetic predisposition to disease and arm them with the information about what actions to take to help them stay healthy.”
 
The company will initially offer a saliva-based, whole-genome scan and analysis that will match an a person’s DNA against results from gene-disease correlation studies.
 
Navigenics said it is “developing relationships” with medical institutions, including Cleveland Clinic, Georgetown University, Mayo Clinic, Scripps Health, and Partners HealthCare, a health system founded by Brigham and Women's Hospital and Massachusetts General Hospital and a teaching affiliate of Harvard Medical School.
 
The company has also partnered with Mayo Clinic to provide health information on its website. Affymetrix will provide lab services via its CLIA-certified laboratory in Sacramento, Calif., and Medscape will develop continuing medical education materials for physicians.
 

 
Agilent, BioNanomatrix to Co-develop Genetic Analysis System
 
Agilent Technologies and BioNanomatrix are teaming up to develop an integrated genetic analysis system with applications in genotoxicity and cytogenetics assay development, as well as potentially DNA sequencing, the companies said this week.
 
Under the agreement, the companies plan to combine BioNanomatrix’s single-molecule imaging technology to develop chips and reagents with a measurement platform developed by Agilent.
 
Philadelphia-based BioNanomatrix is currently developing nanoscale single-molecule technology that will enable the identification and analysis of an entire genome, the company said.
 
The firm recently announced a partnership with Complete Genomics, under which the two companies will use a joint $8.8 million grant from the US National Institute of Standards and Technology to develop a platform aimed at sequencing a human genome in eight hours for under $100 (see In Sequence 10/2/2007).
 
Financial terms of the agreement were not released.
 

 
Baylor to Use $2.3M from NHGRI for Human Bacteria Metagenomics Study
 
Baylor College of Medicine will use $2.3 million from the National Human Genome Research Institute to study the genomics of bacteria that live in the human body, BCM said last week.
 
The funding, which is part of the first phase of the NIH’s Human Microbiome Project, adds to an ongoing NHGRI-funded Human Microbiome Pilot Project (see In Sequence 6/19/2007).
 
BCM's microbiome projects, taken together, aim to produce reference sequences for 150 bacteria and to sample microbial communities from the gut, vagina, skin, mouth, and nose, BCM said.
 
New sequencing platforms will play a role in these projects: "Next generation DNA sequencing technology, which enables us to produce genetic sequences quickly and accurately, has finally reached a state where such a large project is possible," said Richard Gibbs, director of the BCM Human Genome Sequencing Center, in a statement.
 
The researchers will start by determining the genetic sequence of various bacteria that colonize humans, he said, followed by studies of variation among individuals and populations.
 

 
P&G Beauty Sequences Fungus Responsible for Dandruff
 
Scientists from P&G Beauty have sequenced the genome of Malassezia globosa, a fungus that causes the onset of dandruff and other skin conditions, the company said this week.
 
The genome sequence, which appears in PNAS this week, may help scientists understand at the molecular level what role the fungus plays in the onset of dandruff and seborrheic dermatitis, eczema, atopic dermatitis, and psoriasis.
 
M. globosa lives on the skin of humans and feeds off sebum and other lipids on the scalp.
 
M. globosa is also very closely related to multiple common plant pathogenic fungi that cause disease on corn, wheat, and other important food source crops.
 

 
Newly Sequenced Cat Genome May Enhance Disease, Mammalian Evolution Research
 
A multi-center team of researchers led by the National Cancer Institute and the National Human Genome Research Institute has sequenced the genome of the domestic cat, the groups said last week.
 
The first assembly of the genome of Felis catus, performed under the Cat Genome Project, could have “immediate value in many aspects of biology, particularly in discovery of genetic basis of hereditary and infectious diseases,” according to an article published in last week’s Genome Research. Agencourt Bioscience generated the sequencing data for the project.
 
The genome suggests that it could not only help veterinary medicine, but also serve as a model for human disease because domestic cats have 250 genetic pathologies that are similar to many that occur in humans.
 
The 1.9X genome annotation estimates the genome to be around 2.7 gigabases, which the researchers guessed by extrapolating the length of the cat sequence to homologous stretches in dog and human genomes, which are around 2.4 gigabases and 2.8 gigabases, respectively.
 
The resulting data could help researchers better understand how this and other mammals evolved and reconstruct chromosome exchanges “that punctuate mammal evolution,” the report concludes.
 
The donor DNA for the project came from a 4-year old Abyssinian cat called Cinnamon that has documented ancestry going back several generations. The researchers compared Cinnamon’s sequence against other mammalian genomes, including dog, rat, mouse, human, and chimpanzee.
 

 
Flanders Institutes Purchase Roche/454 Sequencer
 
The Flanders Institute for Biotechnology and the Catholic University of Leuven said this week that they have jointly purchased a sequencer from Roche subsidiary 454 Life Sciences.
 
The sequencer will be housed in the genetic service facility of the Flanders Institute for Biotechnology’s department of molecular genetics at the University of Antwerp, but the organizations said the system will available to other Flemish researchers as well.
 
The new sequencing capacity will be used to sequence “new, full genomes of interesting organisms” and to trace genetic variations that cause illnesses.
 
Financial terms of the joint purchase were not released.
 

 
New Partner Joins Sorenson's Krygyzstan Genealogy Research Project
 
An international project aimed at studying the genealogy of the people of Krygyzstan has added a new partner and intends to expand its scope to include other Central Asian nations, the Sorenson Molecular Genealogy Foundation said this week.
 
The project, which began a year ago between SMGF and the International University of Krygyzstan, aims to study the genetic genealogies, migration, and demographic patterns of Kyrgyzstan's various populations. A new partner, the American University of Central Asia’s department of anthropology, will now join the collaboration by contributing field work in various populations, SMGF said.
 
Krygyszstan is a land-locked Central Asian nation that borders China to the east and has a population of around 5 million. The country contains a wide variety of ethnic groups: approximately 65 percent of the population is comprised of indigenous Kyrgyz residents, more than 13 percent of residents have Uzbek ancestry, and 12.5 percent of residents are of Russian descent. 
 
Kyrgyzstan’s demographic makeup “might contribute important clues to the unique Central Asian phenomenon of significant differentiation between geographically close populations combined with relative genetic homogeneity within some populations,” said SMGF’s executive director, Scott Woodward, in a statement.
 
Since the research got underway last year, SMGF said it has collected 364 DNA samples from three ethnic populations within the country, including the Kyrgyz, Dungan, and Uyghur peoples.
 
The partners aim to collect between 800 and 1,100 DNA samples in the country, and a total of as many as 5,000 samples in Central Asia, including those collected from further studies in Kazakhstan, Tajikistan, Turkmenistan, and Uzbekistan.
 
Overall, the researchers will study genomic data in different groups based on demographic, socio-anthropological, and cultural characteristics. The researchers plan to document and preserve oral histories, connect families and individuals through genealogies, increase genetic data from Central Asia in SMGF’s public database, and to compare these results with other studies.
 

 
UCSC Tailors Genome Browser for Public Use in Malaria Studies
 
A group of students at the University of California, Santa Cruz, has worked with faculty at the Hughes Undergraduate Research Lab to tailor UCSC's Genome Browser for use in malaria genomics research, UCSC said last week.
 
The Malaria Genome Browser, which is a free resource aimed at the malaria research community, has been linked to an upcoming version of PlasmoDB, an international repository of genomic information about the Plasmodium parasite.
 
UCSC said the browser "brings together on a single screen the full DNA sequences of eight species of the malaria parasite (Plasmodium), alongside experimental results and previously discovered genes culled from the literature."
 
The university said the program allows researchers to search through the 26 million bases in the parasite's 14 chromosomes, and to enter sequence data and notes in order to compare information about different species.
 
The Hughes Undergraduate Research Lab was funded in part by the Howard Hughes Medical Institute.
 
Other projects at the lab include bioinformatics work on the SARS virus, malaria, and yeast biology. UCSC's Malaria Genome Browser can be found here.
 

 
Sequenom's Q3 Revenues Jump 51 Percent on MassArray Sales, Service Business
 
Sequenom said last week that third-quarter revenue surged 51 percent as R&D spending declined 6.6 percent and its net loss widened 20 percent.
 
Total receipts for the three months ended Sept. 30 rose to $9.8 million, from $6.5 million year over year. CEO Harry Stylli said in a statement that the increase was driven by “strong contributions from MassArray system placements and consumables as well as our contract research services business.” Sequenom said sales of consumables rose 25 percent, to $4 million, while other product-related sales increased 63 percent, to $4.9 million. Meantime, receipts from services more than doubled, to $885,000.
 
R&D spending decreased to $2.8 million, from $3 million year over year, Sequenom said. The company said its net loss grew to $5.5 million, from $4.6 million in the year-ago quarter.
 
Sequenom said it expects to raise around $28.1 million in a private stock placement it recently completed to help it launch a non-invasive fetal genetic test and other products “designed to support additional growth in our core MassArray systems and services businesses," Stylli added.
 
The company had $29.1 million in cash, cash equivalents, and short-term investments as of Sept. 30.
 
In September, Sequenom said it plans to develop a third-generation nanopore-based single molecule sequencing technology licensed from Harvard University (see In Sequence 10/2/2007).
 

 
Biomatrica and Cal State, LA, to Study DNA Storage Method for Forensics Under Federal Grant
 
Biomatrica of San Diego and researchers in the department of criminal justice and criminalistics at the California State University, Los Angeles, will jointly test the company’s SampleMatrix DNA storage product in forensics under a grant from the National Institutes of Justice, Biomatrica said last week.
 
“Since crime scene samples tend to be sparse, preserving every spec is crucial to DNA analysis,” the company said in a statement, claiming that its storage method “ensures 100 percent sample recovery allowing for picogram amounts of DNA to be preserved.” Biomatrica did not mention the amount of the grant.
 
The scientists will study how well SampleMatrix preserves blood, semen, and saliva that have been exposed to environmental and storage conditions similar conditions that crime scene evidence is exposed to. The technology is based on anhydrobiosis — life without water — that allows multicellular organisms to survive in extreme conditions.
 

Biomatrica said that storing samples with its method at room temperature costs 15 times less than storing them in freezers.

The Scan

Response Too Slow, Cautious

A new report criticizes the global response to the threat of the COVID-19 pandemic, Nature News reports.

Pushed a Bit Later

Novavax has pushed back its timeline for filing for authorization for its SARS-CoV-2 vaccine, according to Bloomberg.

AMA Announces Anti-Racism Effort

The Associated Press reports that the American Medical Association has released a plan to address systemic racism in healthcare.

Nucleic Acids Research Papers on miRMaster 2.0, MutationTaster2021, LipidSuite

In Nucleic Acids Research this week: tool to examine small non-coding RNAs, approach to predict ramifications of DNA variants, and more.