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Wellcome Trust Sanger Institute, RainDance Technologies, Integrated DNA Technologies, Genome Reference Consortium, Clinical and Laboratory Standards Institute, 23andMe, Albert Einstein College of Medicine

RainDance Relocating to Massachusetts
RainDance Technologies this month will relocate its operations from Guilford, Conn., to Lexington, Mass., the company said this week.
The firm, which is working on droplet-based microfluidic systems for life science applications, said it will open the new 28,000-square-foot facility and begin commercial and manufacturing operations on May 27.
“With the launch of our first life sciences applications scheduled for the fourth quarter of this year, it’s important for RainDance to be located in the nation’s preeminent biotechnology center,” RainDance President and CEO Chris McNary said in a statement.
RainDance currently has around 35 employees and expects to hire another 30 by the end of the year. It also plans to purchase more than $500,000 in scientific and office equipment.
Among other applications, the company is working on PCR-amplification of DNA targets for sequencing (see In Sequence 10/23/2007).

New International Consortium Aims to Improve Reference Genome Issues
A newly formed international consortium recently unveiled a resource for improving the human reference genome.
The Genome Reference Consortium represents a small group of centers and institutions that are actively working to not only take stock of the gaps and small errors in the human reference genome, but also to incorporate new information about the magnitude of normal variation in the genome.
The group launched a new web site two weeks ago to coincide with the Biology of Genomes meeting at Cold Spring Harbor Laboratory. The site lets users access information on individual chromosomes and report problems with specific regions of the reference sequence.
“Pretty much everyone, uniformly, thought it was a good idea,” NCBI staff scientist Deanna Church, who presented a poster introducing the GRC at the Biology of Genomes meeting, told In Sequence’s sister publication GenomeWeb Daily News.
The GRC consists of members from the Wellcome Trust Sanger Institute, the Genome Center at Washington University, the European Bioinformatics Institute, and the National Center for Biotechnology Information. The project is being funded by the National Human Genome Research Institute and the Wellcome Trust.
The wet bench work will be done at the Sanger Institute and Washington University’s Genome Center, Church said, while the EBI and NCBI are offering “bioinformatics support to make curation for experimentalists simpler.”
“It is now apparent that some regions of the genome are sufficiently variable that they are best represented by multiple sequences in order to capture all of the sequence potentially available at these loci,” the GRC website states. “The goal of this group is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible, and to produce alternative assemblies of structurally variant loci when necessary.”
The first seeds of the GRC were planted several years ago. Even as researchers were publishing papers on chromosomes sequenced during the human genome project, they realized that they weren’t capturing all the information necessary for a complete reference. “It was appreciated at the time that there were still gaps and things like this,” Tim Hubbard, head of informatics at the Sanger Institute, explained. “There was the question of what to do about that.”
Newer technology, sequencing of additional human genomes, and an increasing appreciation of normal human genetic variation underscore the need to re-assess the reference genome.
“Overall, [the human reference] is really quite a good assembly.” Church said. But, she added, that doesn’t mean the specific locus a researcher might be interested in is 100 percent correct.
“We have issues, I think, for pretty much every chromosome right now,” she said, noting that the consortium has heard of reports of problems in all but one or two chromosomes. “We are very aware that there are certain regions in the genome associated with copy number variations and disease phenotypes.”
The GRC website currently includes literature related to each of the human chromosomes along with potential problems or concerns that have been noted for each so far. For instance, the site includes a table summarizing the regions currently under review in the reference genome. That, and other features on the site, will be updated shortly, Church noted. It also houses similar information for the mouse reference genome.
In order to improve the human and mouse reference genomes, the GRC is asking researchers to report any issues they have discovered in particular regions of the reference genome. New data is also being collected by members of the collaboration and through projects such as the 1,000 Genomes Project to inform future reference assemblies.
For instance, the GRC website currently contains information on builds 35 and 36 of the human reference genome. The collaboration hopes to release the next build in the spring of 2009 and update it annually after that, Hubbard said. Though he noted that it may inconvenience those who have to remap their data each time a build is released, Hubbard emphasized the need for an accurate and complete reference genome.
“Overall, it’s necessary. It’s really important to do this to make sure people aren’t being misled,” Hubbard said, adding, “We’re open for business in terms of collecting information.”
By Andrea Anderson; originally published by GenomeWeb Daily News

CLSI Publishes Guidelines for Sequence-Based ID of Bacteria and Fungi
The non-profit Clinical and Laboratory Standards Institute has issued a set of guidelines aimed at helping researchers involved in identifying and classifying bacteria and fungi use DNA sequencing.
By establishing interpretive criteria for identifying microorganisms, the CLSI hopes to help “catalyze the entry of molecular microbiology into clinical usage,” CLSI said in a statement.
Because broad-range DNA sequencing for routine clinical use has not been well delineated, CLSI states in the report, there is a need to develop “a systematic and uniform approach” to identifying these microorganisms.
The guideline, “Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline,” reviews issues concerning DNA target sequences; sequence length and quality; intergenus, intragenus, interspecies, and intraspecies variability; and database selection.
The guideline emphasizes microorganisms that are clinically relevant or commonly encountered in a clinical lab.
It specifies recommendations for clinical labs that use amplification and Sanger-based sequencing for identifying bacteria, mycobacteria, and fungi from cultured clinical isolates. CLSI offers guidelines for selection of DNA targets and target size and establishes quality control parameters for amplification and sequencing.
The report also offers guidelines for measurement of the quality of sequence, assessing reference sequences and databases, and comparison of sequences for identification. It also establishes interpretive criteria for identity scores from gene sequencing and reports strategies that are clinically relevant for specific groups and microorganisms.
While molecular technology has “made some inroads into clinical microbiology,” CLSI stated in the report, developments are in early phases and the guidelines are aimed at expanding the rapid, accurate, and economical identification of clinically relevant microorganisms.
The CLSI report is being sold through the institute for $120. More information is available at the CLSI website.

23andMe Inks Collaboration with Parkinson's Institute
Consumer genomics firm 23andMe said last week that it will collaborate with the Parkinson’s Institute and Clinical Center in an effort aimed at advancing methods for clinical and epidemiological research into Parkinson’s disease.
Under the collaboration, which is receiving financial support from the Michael J. Fox Foundation, patients of the Parkinson’s Institute will enroll in 23andMe’s Personal Genome Service. 23andMe anticipates that the DNA submitted for genotyping will generate more than 580,000 data points per patient.
In addition, patients will provide specific information about individual environmental exposures, family history, disease progression, and treatment response.
23andMe and the institute will develop web-based clinical assessment tools that can be administered to online communities, they said in a joint statement. Patients’ risk factors and clinical data will be merged with their genetic data to conduct research into Parkinson’s disease.
The partners also said that they will develop and use new surveys for an increasing number of participants, which will generate new risk-factor and clinical data for comparison with the existing genetic data.
"By building a social network for the Parkinson's disease community, and combining it with the world-class expertise of Parkinson's Institute researchers, we hope to establish an entirely new paradigm for how genetic research is conducted that actively involves the patient,” Linda Avey, co-founder of 23andMe, said in a statement.

Albert Einstein College of Medicine to Use $25M Donation for Epigenomics, Translational, Stem Cell Research
The Albert Einstein College of Medicine of Yeshiva University will use part of a $25 million private gift to establish an epigenomics research facility and to fund genetics and translational medical research.
The college said last week that it plans to use $7 million of the donation from Ruth and David Gottesman to start the Center for Epigenomics, which will be headed by Einstein researcher John Greally, who has developed a method for detecting the methylation patterns that characterize certain cancers.
Last year, Greally and his collaborators at the Broad Institute won a three-year, $1.5 million NIH grant as part of the ENCODE project to develop high-throughput sequencing methods for mapping histone modifications and cytosine methylation (see In Sequence 11/27/2007).
Some of the money will support the Michael F. Price Center for Genetic and Translational Medicine, and $15 million will be used to start the David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research. The college also said that it will use $3 million to start a Clinical Skills Facility.
Ruth Gottesman, a former faculty member at the college, was elected chair of Einstein's board of overseers in 2007. "In discussions with the college, we determined that stem cells, epigenomics, and clinical training were areas where we could help make an important contribution, both to Einstein and to the future of biomedical research," she said in a statement.
The Price Center for Genetic and Translational Medicine is scheduled to open in June.

Sanger Researchers Use RNA-Seq to Illuminate Fission Yeast Transcriptome Dynamics
Researchers at the Wellcome Trust Sanger Institute have used RNA-Seq and tiling microarrays to map the dynamics of the Schizosaccharomyces pombe transcriptome.
The team, which published a report in the advance online edition of Nature this week, reported that more than 90 percent of the genome is transcribed, and identified hundreds of new transcripts detected at low levels. They were also able to analyze untranslated regions in the genome and pinpoint splicing events that varied with time, location, and transcript levels. Their report comes three weeks after researchers at Yale University published an analysis of the budding yeast transcriptome in Science (see In Sequence 5/6/2008).
In an effort to understand the S. pombe transcriptome as completely as possible, senior author Jürg Bähler, at the time a functional genomics researcher at the Sanger Institute, and his team synthesized complementary DNA from poly-A-enriched RNA isolated from S. pombe grown under different conditions. They then used an Illumina Genome Analyzer to sequence this cDNA and mapped the reads back to the reference genome.
They also verified their results in rapidly growing cells, meiotic cells, cells grown under oxidative stress or heat shock, and RNA processing mutants by using high-density Affymetrix tiling arrays.
Based on more than 23 million reads from exponentially growing cells and more than 99 million reads from cells at five different stages of meiosis, they reported that almost the entire genome — more than 90 percent — was detectably transcribed.
“[W]e obtained sequence data from ~94 percent and >99 percent of the nuclear and mitochondrial genomes, respectively,” Bähler and his colleagues wrote, “suggesting that almost the entire genome is transcribed to some degree, consistent with the considerable overlap and complexity among different transcripts reported for other eukaryotes.”
And, like the budding yeast Saccharomyces cerevisiae, the fission yeast transcriptome is proving to be more complex than expected. The S. pombe transcriptome held surprises, both within coding and non-coding regions of the genome. Based on sequencing and tiling chip data, the team made 75 revisions to protein-coding regions in the fission yeast gene annotation and pinpointed some 20 new introns in previously identified genes.
They also identified at least 453 new transcripts within the fission yeast transcriptome. Just 26 of these were predicted to code for proteins, while three dozen or so were non-coding RNAs that overlapped with the antisense strand of known genes. When the researchers used RT-PCR to look more closely at 14 non-coding transcripts, they also found evidence for bi-directional transcription across the genome.
Still, the authors noted that, “[g]iven the ubiquitous transcription throughout the genome, the novel transcripts described here probably only hint at the true level of transcriptional complexity” in the S. pombe genome.
In general, the researchers found fewer reads for the newly transcribed regions, and subsequent experiments suggest most of them are transcribed at low levels. Just 13 could be picked up in actively growing cells by tiling arrays, and another 80 or so were only detected under specific conditions, particularly during meiosis or quiescence.
The researchers also reported new information about the nature of untranslated regions, splicing, and polyadenylation in fission yeast. For example, they found dozens of transcripts that had alternative start sites during meiosis or when S. pombe cells were grown under stressful conditions. About 187 transcripts had variable polyadenylation sites.
The team also found a surprisingly large pool of unprocessed messenger RNA, containing introns and exons. And more than 250 genes actually seemed to be spliced more efficiently during meiosis. Splicing efficiency also seemed to increase with higher gene expression, the researchers noted, suggesting that transcription and splicing are “mechanistically linked.”
“[O]ur results reveal a surprising genome-wide regulation of splicing, largely reflecting transcript levels during proliferation or differentiation,” the authors concluded. “These data point to a global and condition-specific coupling between splicing efficiency and transcription, which may help to optimize and streamline gene expression programs.”
Alterations from the study have been incorporated into the S. pombe database.

Integrated DNA Technologies Creates New Unit
Integrated DNA Technologies said last week that it has created a new business unit called Clinical and Commercial Manufacturing, which will manufacture oligonucleotides for use in diagnostic products.
The firm also said that it has received ISO 13485:2003 certification at its facility in Coralville, Iowa, which houses the new unit.
"This new business unit has evolved through years of partnership and interaction with our family of customers researching and performing in vitro diagnostics,” Trey Martin, COO of IDT, said in a statement. “This arrangement allows IDT to further improve our service to these customers by offering dedicated processing, purification, analysis, formulation, functional testing and final fill services in purpose-built clean room suites with assigned senior production staff.”

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.