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Perlegen Sciences, 454 Life Sciences, Genome Corp., SeqWright, ABI, Affymetrix, Navigenics, Sorenson Molecular Genealogy Foundation, Sorenson Molecular Genealogy Foundation, Nexttec, Deltadot, SAE Consortium, Ceres, Newsham Genetics, ABI, GenomeQuest, Bio

Perlegen, 454 Partner in Drug Response Re-sequencing Study
Perlegen Sciences and 454 Life Sciences will collaborate on a project to re-sequence “hundreds” of human DNA samples with the goal of developing a test that will predict how patients respond to a certain class of drug, the companies said this week.
Perlegen said it has collected samples from individuals with specific responses to a “widely prescribed” class of drug. The partners intend to identify and validate genetic variations that could be developed into a clinical test that would predict response to the drug family.
Under the agreement, the companies will each re-sequence portions of genomes from each sample using 454 sequencing and Perlegen's sample-prep and amplification technologies.
The companies' data analysis groups will work together to determine to what extent certain genetic variations influence patient response to this class of drugs.
Perlegen did not divulge the name of the drug class involved in the study, but said the research "holds the promise to improve therapeutic outcomes for a vast number of patients."
Financial terms of the agreement were not released.

Sequencing Start-up Genome Corp. Gets $250K Seed Funding from Slater Fund
Genome Corp., a sequencing start-up based in Providence, RI, has received a $250,000 seed capital investment from the Slater Technology Fund, the companies said last week.
The company was founded earlier this year to develop and commercialize a sequencing method it calls “massively parallel Sanger sequencing.”
Company co-founder and CSO Kevin Ulmer founded single-molecule sequencing company SEQ in 1987. The firm was later purchased by Amersham Biosciences. Ulmer was also involved in forming Exact Sciences, and has served as a consultant at Helicos BioSciences.

SeqWright To Use ABI's SOLiD Next-Gen Sequencer for Services Offering
SeqWright will purchase a SOLiD genetic analyzer from Applied Biosystems for use in its sequencing services offering, the Houston-based company said last week.
The company said the next-generation sequencer will enhance its abilities to perform services such as whole-genome sequencing, re-sequencing, transcriptome analysis, small RNA discovery, SNP detection, and epigenomic and metagenomic studies.
“The agreement reflects a long-standing relationship between SeqWright and ABI that grows stronger with time,” SeqWright said in a statement.
Earlier this year, SeqWright’s CEO Fei Lu told In Sequence that the company “would like to introduce [a next-gen sequencer] as soon as possible,” but cautioned that in order for a technology to become suitable for her company’s business, read lengths would have to increase, and the cost of sequencing individual samples would have to come down (see In Sequence 2/27/2007).

Affymetrix Partners with Navigenics to Offer Personal Genetics Service
Affymetrix and personal genetics startup Navigenics are teaming up to provide consumers with information on genetic predispositions for certain medical conditions.
Under the pact, which Affymetrix President Kevin King disclosed last week at the UBS Global Life Sciences Conference in New York, consumers will be able to go to the Navigenics website and order a saliva collection kit. The customer will then send the kit to Affymetrix’s CLIA lab, which will run a whole-genome screen and send the analysis to Navigenics. Then, Navigenics will provide the genetic-predisposition analysis to the customer via a secure, private web portal and offer genetic counseling.
Neither Affymetrix nor Navigenics, which has been funded by venture capital firms Kleiner Perkins and Sequoia Capital, has disclosed the cost of the service or its launch date, but Affymetrix officials said the firm is “realistic” and does not expect the alliance to provide it any significant revenue in the near term.
King added that the potential of combining electronic health records with the personal genetics service could eventually help healthcare providers and researchers better understand the role that environmental factors play in disease.
Navigenics is offering a similar service to that of another consumer genotyping startup, 23andMe. In Sequence’s sister publication BioArray News reported last month that Illumina had inked a partnership with 23andMe under which it would provide the company customized SNP arrays.
Edward Winnick, editor, BioCommerce Week

Sorenson Molecular Genealogy Foundation Says DNA Collections and Analysis Are Growing
The Sorenson Molecular Genealogy Foundation said this week that it plans to collect more than 30,000 DNA samples this year and expects to have more than 100,000 samples and corresponding genealogical records by year end.
Regarding DNA sample processing and analysis, the foundation said that growth has been most pronounced in mitochondrial DNA, and predicted that it will have collected more than 70,000 samples by the end of the year.
The company said it is also experiencing “strong growth” in the number of Y-chromosome DNA samples and samples containing autosomal information, though it did not provide further details.
SMGF's database currently contains information about more than six million ancestors through linked DNA samples and pedigree charts from 172 countries. This expansion is enabled by an increase in funding from the Foundation's founder, billionaire inventor and philanthropist James LeVoy Sorenson.
The foundation did not reveal the size of the funding increase.

Bio&Sell to Distribute Nexttec’s DNA Purification Kits
Nexttec said this week that Bio&Sell will sell and distribute its one-step DNA isolation kits in Germany, Austria, and Switzerland.
The Leverkusen, Germany-based firm said it chose Bio&Sell because of its “proven expertise in molecular and cellular biology” and its “market access to the life sciences industry.”
Nexttec said its DNA-isolation system allows users to purify DNA with a single centrifugation step within four minutes following cell lysis. The DNA is can be used for applications such as PCR, RT-PCR, sequencing, and Southern blots.

Deltadot Raises $6M Private Equity for R&D, Marketing
Deltadot said this week it has received £3 million ($6.1 million) to close a round of private equity funding that it will use to support R&D and marketing.
The company originally announced the funding round in March 2006. The financing announced this week is the fourth and final tranche for the round and brings the total funds raised to £6 million ($12.2 million).
The round was led by Fleming Family & Partners Private Equity, and included investments from Imperial Innovations, NPI Ventures, Sitka Health Fund VCT, and London Technology Fund.
Deltadot’s CEO, Anthony Baxter, said the molecular imaging company will use the capital to ramp up production of its Peregrine high-performance capillary electrophoresis system, to develop capillary and microfluidic technologies such as its Osprey system, and to develop international sales and marketing programs, particularly in the US.

SAE Consortium Kicks Off; Begins Two Projects to ID Genetic Markers Linked to Adverse Events
Several large pharmaceutical firms and academic research groups kicked off a collaborative effort last week that will use genomics to study adverse drug reactions.
The initiative, called the Severe Adverse Events Consortium, plans to identify genetic markers that may help predict which individuals are at risk for serious drug-related adverse events. Last week, consortium members officially launched the initiative and identified two specific studies they plan to conduct: One will address drug-related liver toxicity and the other will study a rare but serious drug-related skin condition called Stevens-Johnson Syndrome.
Member organizations include Abbott; GlaxoSmithKline; Johnson & Johnson Pharmaceutical Research & Development; Pfizer; Roche; Sanofi-Aventis; Wyeth; Newcastle University; Diligen, a UK program that is developing a test to identify patients at high risk of developing drug-induced liver disease; Eudragene, a European academic consortium conducting research on drug-related liver toxicity; Illumina; and Columbia University.
In addition, the US Food and Drug Administration is providing “scientific and strategic input” regarding the design and conduct of SAEC studies. The consortium said it also plans to consult the European Agency for the Evaluation of Medicinal Products and other national regulatory bodies for guidance.
SAEC chairman Arthur Holden said in a conference call last week that the consortium plans to make all of the information it gains from these studies public so it may be developed into tests.
Holden, who will soon resign as senior vice president of corporate and market development at Illumina (see Paired Ends in this issue), said the SAEC expects to release the data from its first two studies in around a year in order to “create a knowledgebase to be available to future researchers.”
The SAEC is funding liver toxicity and SJS studies at Columbia University and at the University of North Carolina at Chapel Hill, which will perform analysis and genotyping studies on samples collected largely from Europe.
The consortium’s corporate partners will “provide needed financial contributions and define strategy and organize and manage research,” Holden said.

Ceres Nets $75M in Private Stock Offering for Biofuel Plant R&D
Plant genomics company Ceres has raised $75 million through a private offering of convertible stock led by the private equity firm Warburg Pincus, Ceres said last week.
Ceres plans to use the funds for capital expenditures, corporate purposes and to support development of crops bred to maximize biomass that may be used for biofuels.
Ceres said its development efforts include biofuel crops such as switchgrass, sorghum, miscanthus, energycane, and woody species.
The Thousand Oaks, Calif.-based company said its switchgrass cultivar is scheduled for commercial launch in 2009.

Newsham Genetics Acquires Monsanto Choice Genetics
Swine genetics company Newsham Genetics said last week that it will acquire its competitor, Monsanto Choice Genetics.
Through the acquisition of Monsanto Choice Genetics, Newsham will be able to “add new products and lines that complement our current offerings, accessing new genetic combinations that provide the most value to our customers, providing even more product choices,” said Newsham Genetics Co-CEO Brent Mitchell in a company statement.
Newsham Genetics said MCG made a “significant investment” over the past 10 years in its genomics platform, developing “the most extensive swine genomic map in the industry, with over 6,000 genomic marker associations for swine performance.”
As part of the agreement, the companies signed a three-year research alliance to focus on technology and the genomics platform to “maximize the value created in the industry from these tools.”
The acquisition will be completed “as soon as practical.” Terms of the agreement were not disclosed.
Newsham Genetics is the largest privately owned swine genetics company in the U.S. Monsanto Choice Genetics is a wholly owned subsidiary of Dekalb Genetics, itself a wholly owned subsidiary of Monsanto.

ABI Helps Forensic Labs Validate Its Technology
Applied Biosystems said last week that it has launched a service program for forensic DNA laboratories that will help these labs comply with quality assurance standards and validation guidelines.
Forensic application experts from Applied Biosystems will help conduct validation studies
using Applied Biosystems' new Valid software. Data from the validation process is used with national quality assurance guidelines and accreditation standards.
The Tennessee Bureau of Investigation participated as an early-access site in the validation support and training program to implement multiple instrument platforms, the AmpFlSTR kits, and software at its crime laboratories in Nashville, Knoxville, and Memphis.
"The major support provided by Applied Biosystems' validation program has allowed our crime laboratory scientists to spend more time processing casework samples," said Joe Minor, DNA technical manager at TBI, in a statement. "The final result has been the rapid implementation of new DNA equipment and typing kits without sacrificing valuable time in the crime laboratory."

GenomeQuest Raises $4M in Venture Funding
GenomeQuest has received $4 million in venture capital funding from new and existing investors, the company said last week.
The genomic information search company said it plans to use the Series B cash infusion to expand its organization to support sales of the GenomeQuest software and to introduce new product features.
This round of funding was led by Mosaix Ventures. Previous investors Cross Atlantic Partners, Milestone Venture Partners, and Société Générale Asset Management Alternative Investments also participated.
The company, formerly known as Gene-IT, received $4.1 million in Series A funding in November 2005.
GenomeQuest CEO and president Ronald Ranauro said in a statement that the company expects the market for its software to grow as the cost of genomic sequencing drops, and that this round of financing will help the company prepare for that anticipated growth.

Biobase to Curate Integrated Genomics' Ergo Database
Biobase will curate and expand Integrated Genomics' Ergo database of microbial genomics information under a collaboration agreement, the companies said last week.
Biobase staffers based in Bangalore, India, will add manually curated functional gene annotations and pathways to the Ergo database, which currently holds more than 3.1 million non-redundant gene sequences from more than 1,200 microbial genomes and around 6,300 biological pathways.
Biobase is based in Wolffenbuttel, Germany, and has offices in Beverly, Mass., as well as in Bangalore.
Financial terms of the agreement were not released.

The Scan

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.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.