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Ontario Cancer Institute, Geospiza, State of California, Consumer Genetic Testing Companies, 454 Life Sciences, University of Bielefeld, Pennsylvania State University

Ontario Cancer Institute Taps Geospiza for Genetic Analysis Software

The Ontario Institute for Cancer Research will use Geospiza’s genetic analysis software in its sequencing programs for cancer research, the company said this week.

Under the agreement, Toronto-based OICR will use Geospiza’s FinchLab software in its cancer studies. The not-for-profit institute is funded by the Ontario government under the Ministry of Research and Innovation.

In April, OICR said it received CA$60 million ($58.8 million), which it plans to spend on building up its cancer research program, starting new initiatives, and stocking up on new equipment.

The FinchLab platform will support analysis projects for data from OICR’s next-generation sequencing instruments, including Illumina’s Genome Analyzer and Applied Biosystems’ SOLiD platform, the Seattle-based company said.


California Says 13 Consumer Genetic Testing Firms Violating Law
The State of California is trying to keep consumer genetic testing companies from offering their services to the state’s residents and last week sent letters to 13 firms saying they are violating state law, California Department of Health spokesperson Lea Brooks told In Sequence’s sister publication GenomeWeb Daily News this week.
The state will not disclose the firms or which laws their services allegedly violate until the companies verify with the state that they have received the warnings, Brooks said.
With the move to begin regulating consumer genomics companies in the state, California follows New York, which less than two months ago warned 23 companies that they must have permits to offer their services to state residents.
New York’s warning letter was a shot across the bow of companies like Navigenics and 23andMe that last year entered into the fledgling field of consumer genomics, as well as technology suppliers Affymetrix and Illumina, which make the tools the testing companies use.
Whether California is focusing on consumer genomic testing companies or if it has broadened its authority to include technology suppliers will not be known until the companies’ identities are disclosed.
California authorities have not said whether information has been referred to the state’s Attorney General for further action.
One offense that genetic testing companies could commit would be to sell their products to California citizens over the internet without the request or counsel of a doctor, California Department of Public Health official Karen Nickel told last week. Another problem, Nickel said, could be that the companies’ tests have not been validated for accuracy or for clinical utility, which is required under California law.
Concerns over marketing genomic data to consumers and assertions about the ability of tests to predict disease risk were sharply rendered in January by Muin Khoury, director of the National Office of Public Health Genomics at the US Centers for Disease Control and Prevention.
After publishing a critical op-ed in the New England Journal of Medicine with two other authors, Khoury told GenomeWeb Daily News that consumer genomics as it is today should be considered “recreational genomics,” and that the field was premature and consumers were not ready to receive the “alphabet soup” of genomic information they were buying.
To Khoury and his fellow NEJM writers, the problem of how to show the clinical usefulness of these genomics offerings would prove to be the most critical.
“The bottom line here is that people are beginning to be concerned that there may be more harm than benefit,” Khoury said.

German Researchers Publish Bacterial Genome Based on Single 454 Run
Researchers from Bielefeld University in Germany have published the genome of Corynebacterium kroppenstedtii using data from a single run on a Genome Sequencer FLX, 454 Life Sciences said last week.
Their study appeared online in the Journal of Biotechnology last month.
The run yielded approximately 110 megabases of DNA, which the researchers assembled into the 2.4-megabase bacterial genome.
Based on an automatic annotation of the genome sequence, the researchers predicted 2,122 coding sequences, of which almost a third appear to be specific for C. kroppenstedtii, compared to other pathogenic corynebacteria.
Further analysis of the genome revealed a large repertoire of genes involved in sugar uptake and central carbohydrate metabolism.
The scientists also found that lipophilism is the dominant feature involved in C. kroppenstedtii’s pathogenicity.

Hair Holds Key to Woolly Mammoth History
Mitochondrial DNA harvested from ancient mammoth hair indicates that animals from two very different woolly mammoth clades roamed Siberia.
In a paper appearing in the Proceedings of the National Academy of Sciences last week, an international team of researchers delved into the history and population structure of Siberian woolly mammoths using a combination of comparative mitochondrial genomics and carbon dating.
The research indicates that the two woolly mammoth clades overlapped temporally, but had different geographical ranges and extinction patterns — with one clade disappearing before they had the opportunity to interact with humans.
“This discovery is particularly interesting because it rules out human hunting as a contributing factor, leaving climate change and disease as the most probable cause of extinction,” co-senior author Stephan Schuster, a biochemist and molecular biologist at Pennsylvania State University, said in a statement.
In a paper published last September in Science (see In Sequence 10/9/2007), Schuster and his team shotgun-sequenced 10 mitochondrial genomes collected from mtDNA in wooly mammoth hair shafts. For their latest paper, the researchers sequenced the mitochondrial genomes of five more woolly mammoths that died between 13,000 and 60,000 years ago with up to 73-fold coverage using a 454 GS FLX sequencer as well as standard PCR.
Based on the 300,000 nucleotides of sequence obtained, the researchers constructed five new woolly mammoth mitochondrial genomes and compared them with 13 that had been deciphered previously. Their results suggest that Siberian woolly mammoths consisted of two very different clades.
Clade I included animals that lived some 14,000 to 18,500 years ago and spanned sites more than 3,700 miles east to west. Animals belonging to clade II, on the other hand, lived much earlier and so far appear to be limited to sites just 700 miles or so across northern Siberia.
For example, the researchers noted that the two clade II animals assessed in this study lived more than 58,000 years ago, making them “the oldest of the 18 mammoth mitochondrial genomes that have so far been reconstructed.”
Based on their Bayesian phylogenetic analysis of mammoth, elephant (African and Asian), and mastodon mtDNA, the researchers estimated that the woolly mammoth clades diverged about 1 million or 2 million years ago. That’s roughly a quarter of the genetic distance between woolly mammoths and each of their living relatives, the African elephants (about 7.8 million years) and Asian elephants (about 6.5 million years).
In general, the researchers found that, although many mammoths lived over a much larger geographical region than elephants, their genetic diversity was comparatively very low.
“This low genetic divergence is surprising because the woolly mammoth had an extraordinarily wide range: from Western Europe, to the Bering Strait in Siberia, to Northern America,” co-senior author Webb Miller, a Penn State biologist and computer scientist, said in a statement. “The low genetic divergence of mammoth, which we discovered, may have degraded the biological fitness of these animals in a time of changing environments and other challenges.”
The study also highlights the value of hair samples. The team noted that hair samples —particularly hair shafts — contain copious amounts of mitochondrial DNA that is ideal for analysis and easily decontaminated. In a paper published in May, some members of the same research team used mitochondrial DNA from ancient human hair to better understand human population patterns in the far North.
“We plan to continue using our techniques to untangle the secrets of populations that lived long ago and to learn what it might have taken for them to survive,” Schuster said. “Many of us also have a personal interest in learning as much as we can about how any species of large mammal can go extinct.”
The mammoth mtDNA sequences have been added to GenBank.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.