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Singapore Genomics Institute, Illumina, Invitrogen, Applied Biosystems, European Bioinformatics Institute, Max Planck Institute for Molecular Genetics, NIH, Rubicon Genomics, J. Craig Venter Institute, CLC Bio, Scripps Translational Science Institute, Nav

Singapore Genomics Institute Picks up Four Illumina Sequencers
Illumina said last week that the Genome Institute of Singapore has added four Genome Analyzers to its sequencing tool shed, tripling its stock to a total of six.
GIS plans to use the new sequencing power for a variety of research projects including the study of transcriptional networks that may be linked to cancer and stem cells.
The Singapore institute will use the analyzers “across a broad array of applications,” GIS Associate Director of Genome Technology Yijun Ruan said in a statement. These include building transcriptional networks by “identifying transcription factor interactions and chromatin modifications in stem cells and cancer cells,” Ruan said, as well as characterizing genome and transcriptome variations in healthy patients and discovering new pathogens through metagenomic sequencing.
Ruan said the expansion of sequencing power is necessary for the institute to continue advancing its Paired-End-diTag technology, which GIS developed in part through grants from the National Human Genome Research Institute and the National Cancer Institute. The aim of that research was to develop the technology for human genome annotation and to identify fusion genes that can cause cancer in humans.
Less than a month ago, Illumina competitor Applied Biosystems said that GIS had acquired three of its SOLiD sequencing systems.

Invitrogen Expects Greater Cost Savings Post-Merger; ABI Reaffirms Q1 Forecast
Invitrogen said last week that it expects gains from its pending $6.7 billion merger with Applied Biosystems to be at least $80 million in the first year after close, instead of the $60 million initially forecasted by the firm. It said these synergies are mostly attributable to cost savings.
Carlsbad, Calif.-based Invitrogen said that the combination of greater cost savings and a lower-than-expected share count of 179 million shares will lead to the combined firm posting higher earnings-per-share growth than initially expected. However, that benefit will be partially offset by recent fluctuations in currency exchange and an increase in the expected interest rate on new debt.
Last month, Invitrogen secured $2.65 million in financing lines to help fund the acquisition of ABI.
Invitrogen now expects the combined firm to report fiscal 2009 EPS of at least $2.65, up from its previous forecast of at least $2.60.
Invitrogen also said that it expects to report third-quarter revenue growth in the mid-teens, including several points of growth due to currency benefits, when it reports results on Oct. 21.
Its merger partner, ABI, also said last week that it expects its fiscal 2009 first-quarter results to be in line with the guidance it provided in late July. ABI expects its Q1 revenue to increase in line with the growth rate for the first quarter of 2008, with higher gross and operating margins compared to Q1 2008. ABI’s fiscal 2008 year ended on June 30, 2008.

1000 Genomes Project Nears 3 Terabases of Sequence Data; Berlin's MPI Joins Effort
The 1000 Genomes Project has almost tripled the amount of sequence data it has produced during its pilot phase since this spring, to 2.8 terabases, or approximately 100 terabytes.
The project has also added another production center, the Max Planck Institute for Molecular Genetics in Berlin, that has recently begun to generate data for the effort.
Paul Flicek, head of the vertebrate genomics group at the European Bioinformatics Institute in Hinxton, UK, and co-leader of the 1000 Genomes Project's data flow group, gave an update on the project's progress at the Personal Genomes meeting at Cold Spring Harbor Laboratory last week.
Raw sequence data generated by the production centers is amassed at the EBI, where researchers, in collaboration with colleagues from the Wellcome Trust Sanger Institute, recalibrate it in order to obtain accurate and uniform quality scores that allow data from different centers and sequencing platforms to be compared.
It is then uploaded to both the EBI’s and the National Center for Biotechnology Information's FTP sites for public access. Long term, the data will be stored in the NCBI’s Short Read Archive and the EBI’s European Read Archive.
The next batch of data — resulting from a data freeze in August — will be ready for download this week, according to Flicek. As a result of the increased data production, data transfer between the production centers and the data storage centers is becoming increasingly difficult, he added.
The next data freeze, which is planned for Oct. 24, is expected to complete data production for the first two of the three pilot projects.
Under the first pilot project, researchers are sequencing 60 HapMap samples from three different populations at low coverage. The second pilot involves sequencing two trios – parents and child – of European and African descent at high coverage. The third pilot project aims to sequence 1,000 genes in 1,000 individuals at high coverage.
Later this year, following a meeting in November, the scientists are planning to release a first genetic variation map, according to Flicek.
Following the pilot phase, the entire project, he said, will probably generate about 20 terabases of sequence data. Sequencing production worldwide, he estimated, will soon be just an order of magnitude smaller than data generation by the Large Hadron Collider that recently opened in Geneva, which is expected to produce 15 petabytes of data per year.
The 1,000 Genomes project, a three-year project, was launched in January (see In Sequence 1/22/2008). The goal of the project is to produce a detailed catalog of genetic variants in the human genome.
In May, the projects organizers announced they had generated 300 gigabases of sequence data, more than the amount of data stored in GenBank.
The following month, Illumina, Roche/454, and Applied Biosystems joined the project as data producers (see In Sequence 6/17/2008), which already included the Sanger Institute, BGI Shenzhen, the Broad Institute of MIT and Harvard, Washington University School of Medicine’s Genome Center, and Baylor College of Medicine’s Human Genome Sequencing Center.
The MPI in Berlin is the latest production center to join the effort, according to Flicek.

NIH Awards $21.2M in Grants for Human Microbiome Project
The National Institutes of Health named the first awards for its Human Microbiome Project last week, which aims to create a foundation for understanding the microbes that interact with humans and affect health. The awards total up to $21.2 million.
This phase of the HMP, a five-year effort launched last year under the NIH’s Roadmap for Medical Research, will support the development of technologies, computational tools, coordination and data analysis, and examination of the ethical, legal, and social implications of human microbiome studies.
Researchers in the HMP first plan to sequence 600 microbial genomes, which will complete a collection totaling 1,000 genomes. This information will be used to characterize human microbial communities from five areas of the human body: the digestive tract, the mouth, the skin, the nose, and the vagina.
“The development of new tools and technologies is central to our ability to meet the goals of the Human Microbiome Project,” said Alan Krensky, director of the Office of Portfolio Analysis and Strategic Initiatives at NIH. “An exceptional amount of information will be generated by this project and we need robust technologies and analytical tools that are equal to the task.”
Much of the work funded in the HMP’s first round will focus on improving and refining the identification of microbes that constitute the microbiome, and computational tools will be developed to optimize assembly of sequence data to infer the location and function of genes and to classify microbial species.
Grantees supported under this round of funding include Eugene Chang of the University of Chicago Medical Center, who will receive $410,000 over two years; Andre Marziali of Boreal Genomics, who will get $770,000 over two years; David Relman of Stanford University, who receives $1.6 million over three years; Thomas Schmidt of Michigan State University and Vincent Young of the University of Michigan, who receive $1.3 million over three years; Kun Zhang and Yu-Hwa Lo of the University of California, San Diego, who will get $1.8 million over three years; Daniel Haft of the J. Craig Venter Institute, who will receive $1.6 million over three years; Robin Knight of the University of Colorado at Boulder, who was granted $1.1 million over three years; Mihai Pop of the University of Maryland, who will receive $780,000 over three years; and Yuzhen Ye of Indiana University, who will receive $770,000 over three years.
NIH also granted $9.9 million over five years to establish the Human Microbiome Project Data Analysis and Coordination Center, which will be run by Owen White of the University of Maryland’s School of Medicine, Baltimore.
HMP data will be deposited in the Data Analysis and Coordination Center and in other public databases, including those supported by the National Center for Biotechnology Information.
The HMP also has awarded $1.2 million over three years to Richard Sharp and Ruth Farrell of the Cleveland Clinic, who will examine the ethical, social, and legal implications of human microbiome research.

TCGA Taps Rubicon for Cancer Sample Amplification
Rubicon Genomics will amplify and standardize DNA samples from cancer patients for the Cancer Genome Atlas, the Ann Arbor, Mich.-based company said this week.
Under an agreement with SAIC-Frederick, Rubicon will use its GenomePlex whole-genome amplification technology on more than 3,000 blood and tissue samples. The DNA libraries will be deposited in the International Genomics Consortium’s Biospecimen Research Core, where they will be shared among international researchers taking part in the TCGA project.
Rubicon’s vice president of commercial development, John Langmore, said in a statement that IGC collaborators showed “that pre-amplification of patient DNA can increase the sensitivity, reproducibility, and robustness of analysis of patient samples using major analytical instruments."

Venter Institute Taps CLC Bio for Enterprise Bioinformatics Platform
CLC Bio said last week that the J. Craig Venter Institute has signed a multi-year site license for its full suite of bioinformatics products.
CLC said that JCVI will deploy its software across all of its research sites as an enterprise solution that will provide “a coherent integration layer and a standardized way of developing custom software and specialized algorithms.”
The client/server platform will support “all major database formats,” and will serve as a “technological gateway” for researchers to access proprietary algorithms and solutions developed at JCVI, CLC said.

Scripps, Navigenics, Affy, and Microsoft Launch Long-term Study on Behavioral Effects of Personal Genetic Testing
Scripps Translational Science Institute, Navigenics, Affymetrix, and Microsoft are embarking on a decades-long study to determine the long-term behavioral effects of personal genetic testing, Scripps said last week.
Collaborators plan to offer genetic scans to up to 10,000 Scripps Health system employees, family members, and friends in the study, the first of its kind, said STSI. Ultimately, researchers are hoping to determine whether participating in personal genomic testing spurs individuals to make beneficial lifestyle changes such as improving their diet and exercise regimes.
“Genome scans give people considerable information about their DNA and risk of disease, yet questions have been raised if these tests are ready for widespread public use,” principal investigator Eric Topol, director of the Scripps Translational Science Institute, said in a statement.
The team plans to track participants’ lifestyle changes using self-reported health questionnaires. Participants will complete the questionnaires at baseline and again three and six months after receiving the personal genetic test, which is designed to assess each individuals’ genetic propensity for more than 20 health conditions, including diabetes, hearts disease, and some cancers.
Those enrolled will also be asked to participate in surveys periodically over the next 20 years. The results will be compiled in a database hosted by the Scripps Genomic Medicine program. To maintain participants’ genetic privacy, researchers will de-identify both saliva samples and health assessment questionnaires, encrypt the data, and store it in a secure database.
In addition, researchers plan to use genetic variations identified in the study to improve their understanding of the genetics underlying diseases and the application of this genetic information for preventing, diagnosing, and treating diseases.
“This collaboration is a significant step forward in empowering people to proactively address their specific individual health needs, as well as give clinical researchers access to a broader pool of genetic data to develop new disease researchers,” Peter Neupert, corporate vice president of Microsoft’s Health Solutions Groups, said in a statement.
The study will be sponsored by Navigenics, Affymetrix, and Microsoft. Affymetrix will perform the genome scans, while Navigenics will interpret the results and offer guidance on steps individuals can take to try to decrease health risks based on their personal genetic information.
Participants will be able to access this information through Navigenics’ website and to enter and store their health and lifestyle information in a Microsoft HealthVault account, which they can share with their health care providers if desired.

Stanford-Led Team Develops Sequencing-Based Maternal Blood Test for Fetal Chromosomal Abnormalities
Using short-read sequencing, researchers from Stanford University and the Howard Hughes Medical Institute have developed a method to test for fetal chromosomal abnormalities, including Down syndrome, based on a mother’s blood sample.
In a paper appearing online last week in the Proceedings of the National Academy of Sciences, Stanford University bioengineer Stephen Quake and his team demonstrated that their approach was effective in a small study of 18 women. If those results hold in larger studies, researchers say, the test could eventually enter the clinic — replacing more invasive testing procedures such as amniocentesis and chorionic villus sampling.
“We’re using the fruits of the human genome project,” Quake told In Sequence’s sister publication GenomeWeb Daily News. By shotgun sequencing the mixture of fetal and maternal DNA in maternal blood and mapping the reads back to the genome, the team could see which chromosomes, if any, are over- or under-represented.
Quake and his team looked at whether they could use digital PCR to amplify fetal DNA from maternal blood samples.
“We and others argued that it should be possible, in principle, to use digital PCR to create a universal, polymorphism-independent test for fetal aneuploidy by using maternal plasma DNA,” Quake and his colleagues wrote, “but because of technical challenges relating to the low fraction of fetal DNA, such a test has not yet been practically realized.”
Instead of trying to isolate fetal DNA and then sequence it, the team used shotgun sequencing to sequence all of the cell-free DNA in the mother’s blood plasma. For this paper, they mainly used an Illumina Genome Analyzer to randomly sequence a mixture of maternal and fetal DNA fragments that were between 25 and 30 base pairs long.
They then determined how many sequences came from each chromosome to determine how many copies of each chromosome were present. For instance, a woman carrying a fetus with Down syndrome, or trisomy 21, will have more chromosome 21 sequences in her blood.
“By counting the number of sequence tags mapped to each chromosome, the over- and under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected,” the authors wrote.
For the 18 pregnancies tested, the researchers detected all nine cases of Down syndrome as well as two cases of trisomy 18 (also known as Edward syndrome), and a lone case of trisomy 13, called Patau syndrome. These chromosomal abnormalities were evident in a mother’s blood as early as 12 or 14 weeks into her pregnancy.
In theory, Quake said, the approach should be useful for picking up all potential chromosomal aberrations. But because the sequencing method used in the paper has a slight G/C bias, he said, it may not be possible to get at all potential chromosomal aberrations just yet.
Quake said the team also plans to test the method using other sequencing technologies, including the Helicos BioSciences platform, which relies on a single-molecule sequencing approach that Quake helped to pioneer.
Quake, who is also a founder of and consultant for Fluidigm, has applied for a patent related to the methodology outlined in the paper, along with lead author Christina Fan, a bioengineering graduate student at Stanford University. Quake could not disclose who potential licensees of the technology might be.
The current cost of the assay is about $700. Quake predicts the cost will drop to roughly $300 as sequencing costs decrease. If larger trials — currently in the design stage — prove successful, Quake estimated that the blood test could reach the clinic in two or three years.
“My goal is to make invasive technologies obsolete,” he said.
San Diego-based firm Sequenom is currently running clinical trials on its own non-invasive test for Down syndrome. It recently announced that the SEQureDx test successfully tested for Trisomy 21 in 219 patients with no false positives or negatives.
— By Andrea Anderson; originally published on GenomeWeb Daily News

JHU Researchers, Collaborators Integrate Copy Number and Sequence Analysis for Breast, Colorectal Cancers
New research is providing an integrated look at the copy number and sequence changes in breast and colorectal cancers, suggesting the cancers are more complex than once imagined.
A team of researchers from Johns Hopkins University and elsewhere used SNP analysis and digital karyotyping to characterize copy number variations and sequence alterations in breast and colorectal cancer cell lines, pinpointing, on average, more than a dozen alterations per tumor. The work, appearing online this week in the Proceedings of the National Academy of Sciences, also provides clues about the genes and pathways affected by these changes.
The team previously sequenced genes in 11 breast and 11 colorectal cancers (see In Sequence’s sister publication, GenomeWeb Daily News, 9/12/2006. Also, in a set of papers published earlier this year, several research groups assessed the sequence alterations, copy number variations, and gene expression changes associated with pancreatic cancer and glioblastoma multiforme (see In Sequence 9/9/2008).
For the latest study, the team integrated SNP and digital karyotyping data on copy number alterations with sequence data from 18,191 genes from the RefSeq database to begin rounding out their view of these cancers.
“[T]he alterations detected by sequencing represent only one category of genetic change that occurs in human cancer,” the authors wrote. “A comprehensive picture of genetic alterations in human cancer should therefore include the integration of sequence-based alterations together with copy number gains and losses.”
Using statistical approaches, the researchers integrated the new copy number information with sequence data. They also used Illumina arrays to look at copy number changes in the 11 breast and 11 colorectal tumors samples described in previous sequence studies.
From there, the team focused in on the genes and pathways that were most often affected in these cancers. That led them to some genes that were already known to have a role in cancer — including MYC and EGFR — as well as new candidates.
In particular, genes involved in intracellular signaling, cell cycle transitions, cell-cell interactions, and DNA topological control pathways tended to be affected by copy number and/or sequence changes. Interestingly, the researchers detected both amplifications and deletions in the same pathways in some cases, suggesting that there can be consequences to tinkering with signal regulation, regardless of the direction.
Combining copy number and sequence data also holds promise for determining whether particular point mutations have a functional effect, the researchers noted. For example, if a gene turns up with a deletion in one sample and a point mutation in another, it could indicate that that point mutation is inactivating.
In the future, the researchers noted, incorporating information on other genome-wide changes such as translocations and epigenetic changes could provide even greater insight into cancer, as will trying to determine the timing with which genetic alterations occur in cells.

Sequencing Projects Provide New Clues About Malaria Parasites
In a pair of papers appearing online in Nature last week, two international research teams described their efforts to sequence and begin deciphering the genomes of Plasmodium knowlesi, a malaria parasite infecting kra monkeys that’s increasingly found in human malaria cases in parts of Asia, and P. vivax, the parasite causing the bulk of human malaria infections outside of Africa.
Together, the new papers are providing new insights into malaria biology, giving researchers the opportunity to begin comparing the genomes of several malaria culprits.
“The most important thing is [the genomes’] availability,” Elizabeth Winzeler, a cell biologist affiliated with the Scripps Research Institute and the Genomics Institute of the Novartis Research Foundation, who was not involved in either study, told In Sequence’s sister publication GenomeWeb Daily News. “It sets such an important foundation for future work.”
Winzeler, who penned a review accompanying the Nature articles, said that by comparing the genomes of different Plasmodium species, it should be possible to root out core set of genes essential to parasite life. Ultimately, researchers hope to uncover targets that could help them combat the disease with new drugs or vaccines.
Six years ago, a team of researchers reported that they had sequenced the genome of P. falciparum, the parasite causing the deadliest form of malaria.
But P. falciparum is not alone in causing human disease. While that species is most common in Africa, another, called P. vivax, causes roughly a quarter of all malaria cases and is the prevalent human pathogen in Asia and the Americas. P. ovale and P. malariae have also been linked to human disease. And more recently, it’s been shown that P. knowlesi, a species known to infect monkeys, can also infect humans, leading many to argue that P. knowlesi is an under-appreciated cause of human malaria.
Arnab Pain, a researcher at the Wellcome Trust Sanger Institute, and his colleagues sequenced the 23.5 million base P. knowlesi genome to eight times coverage using whole-genome shotgun Sanger sequencing and subsequently identified 5,188 protein-coding genes. Some 80 percent of these had known orthologues in P. falciparum and the newly sequenced P. vivax, underscoring the notion that P. knowlesi could serve as a useful model organism for the yet-unculturable P. vivax.
The genome sequence also yielded unexpected information, Pain said. For instance, the researchers discovered that P. knowlesi is capable of molecular mimicry. It apparently employs proteins that are identical to human host proteins to evade the human immune system. “This kind of identical host match is the first of its kind in any malaria parasite,” Pain said.
They also found that genes involved in antigen variation and host evasion tend to be dispersed throughout the P. knowlesi genome. That’s distinct from other Plasmodium species, which typically concentrate these genes at the ends of chromosomes in sub-telomeric regions.
Meanwhile, a research team led by investigators at the Institute for Genomic Research, the J. Craig Venter Institute, and New York University focused their efforts on P. vivax, the second most common cause of malaria in humans. P. vivax was the “obvious next choice to sequence,” lead author Jane Carlton, a parasitologist at New York University’s Langone Medical Center, told GenomeWeb Daily News, since it has not yet been cultured in the lab, and is relatively poorly understood. 
For this paper, the researchers sequenced the 26.8 million base pair P. vivax genome to ten times coverage using whole-genome shotgun Sanger sequencing. Analyzing the P. vivax genome was challenging, Carlton noted, because it has an isochore-like structure with G/C-rich regions as well as A/T-rich telomeric regions.
Within the P. vivax genome, the researchers found that gene families involved in immune response and the production of proteins found on the surface of red blood cells were larger than those in other Plasmodium species — gene amplification that may help the parasite evade host immune systems.
Next, the team compared the genomes of P. vivax, P. knowlesi, P. falciparum, and P. yoelii yoelii, a rodent parasite whose genome sequence was published in 2002. In general, they found that these Plasmodium genomes tend to be between 23 megabases and 27 megabases and contain roughly 5,500 genes. Unexpectedly, some 77 percent of these genes are orthologous between all four species. In addition, the researchers noted, the parasites share many genes with similar gene structure.
Notably, P. vivax seems to share a number of metabolic pathways with P. falciparum, the authors noted, suggesting it may be possible to target P. vivax with some of the same drugs and vaccine candidates currently being developed to combat P. falciparum.
At the moment, the researchers are working with collaborators at the Broad Institute to sequence six additional P. vivax strains from Brazil, Mauritania, India, Indonesia, Papua New Guinea, and North Korea, Carlton said. This sequencing effort will likely rely on a combination of Sanger sequencing and next-generation sequencing, such as Roche 454’s GS FLX platform.
Sequence data for this and other Plasmodium sequencing projects is available through the PlasmoDB database. There are also genome-scale reagents such as a long-oligo array and a complete clone set of the genome available at National Institute of Allergy and Infectious Disease-funded repositories MR4 and PFGRC.
By Andrea Anderson; originally published by GenomeWeb Daily News

Wisconsin Launches Collaborative Genomics Research Project
Four Wisconsin-based research institutions have banded together to form the Wisconsin Genomics Initiative, with a focus on personalized healthcare research.
The collaborators include the Marshfield Clinic, the Medical College of Wisconsin, the University of Wisconsin School of Medicine and Public Health, and the University of Wisconsin-Milwaukee. The institutions will combine resources to conduct research on predicting individual susceptibility to disease, targeting personalized treatments, determining how patients respond to specific treatments, and disease prevention.
“By aligning the intellectual capital of four major research institutions, we will meet an important scientific and public health need that could otherwise not be met, and which cannot be accomplished anywhere else but Wisconsin,” Wisconsin Governor Jim Doyle said in a statement.
One of the participants, Marshfield Clinic, is home to the Personalized Medicine Research Project, a population-based genetic research project that has collected DNA and medical records from around 20,000 people thus far.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

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.