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NHGRI, JCVI, ABI, Emory University, University of Southern California, Framingham Heart Study, Keck School of Medicine, Sorenson Genomics, Massachusetts Institute of Technology, Invitrogen, Natural Selection

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NHGRI Unveils Second Phase of ENCODE Project With $80M in Grants
 
The National Human Genome Research Institute has fired up the second phase of its Encyclopedia of DNA Elements project by doling out $80 million in new grants over four years this week in hopes of building a “parts list of biologically functional elements” in the entire human genome.
 
The new ENCODE initiative comes four months after the program’s pilot project released its data.
 
The pilot project, which looked at 1 percent of the human genome, “produced findings that are reshaping many long-held views about our genome,” NHGRI Director Frances Collins said in a statement this week. The research will now move forward “with a full-scale initiative to build a parts list of biologically functional elements in the human genome.”
 
The scaled-up ENCODE project plans to “build a comprehensive catalog of the components of the human genome that are crucial to biological function,” Elise Feingold, program director for ENCODE in the NHGRI Division of Extramural Research, said in a statement.
 
The data generated from the ENCODE project will be dropped into public databases as soon as they are verified, according to Peter Good, the NHGRI’s extramural research director for genome informatics.
 
The following groups are receiving funding for the scale-up phase:
 
Bradley Bernstein of the Broad Institute of the Massachusetts Institute of Technology and Harvard University, who will use $4.8 million to investigate chromatin immunoprecipitation followed by high-throughput DNA sequencing to map modifications of histones in various human cells; 
 
Gregory Crawford of Duke University’s Institute for Genome Sciences and Policy, who will use $6.5 million to identify and characterize regions of open chromatin through DNase I hypersensitivity assays, formaldehyde-assisted isolation of regulatory elements, and chromatin immunoprecipitation;
 
Thomas Gingeras of Affymetrix, who will use $10.2 million to identify protein-coding and non-protein-coding RNA transcripts using microarrays, high-throughput sequencing, sequenced paired-end ditags, and sequenced cap analysis of gene-expression tags;
 
Tim Hubbard of the Wellcome Trust Sanger Institute, who will use $8.5 million to use “computational methods, manual annotation, and targeted experiments … to annotate gene features in the human genome;”
 
Richard Myers of Stanford University, who received $14.6 million to study global annotation of regulatory elements in the human genome, and will use high-throughput sequencing to determine the methylation status of CpG-rich regions in the human genome;
 
Michael Snyder of Yale University, who will use $11.5 million to start a production center for global mapping of regulatory elements;
 
John Stamatoyannopoulos of the University of Washington, Seattle, who will use $9.7 million to map and classify DNase I hypersensitive sites across major human cell lineages;
 
Scott Tenenbaum of the State University of New York at Albany, who received $2.2 million for research aimed at comprehensively identifying ENCODE RNA-based cis-regulatory elements;
 
Zhiping Weng of Boston University, who will use $1.5 million to identify transcriptional factor-binding sites in human promoters; and
 
W. James Kent of the University of California, Santa Cruz, who will use $5 million to establish the UCSC ENCODE Data Coordination Center, which will collect, organize, store, manage, and provide access to data from ENCODE projects.
 
Additional information can be found here.
 

 
JCVI to Re-Sequence Venter With ABI SOLiD; Large-Scale Human Sequencing Planned
 
The J. Craig Venter Institute plans to resequence Craig Venter’s genome using Applied Biosystems’ new SOLiD platform. It will also embark on large-scale human resequencing, starting with 10 to 30 individuals next year, but has not yet decided which technology to use. 
 
According to a report in the Wall Street Journal last week, the institute wants to evaluate the SOLiD system by resequencing Venter’s genome and comparing the results to his recently published genome sequence (see In Sequence 9/4/2007).
 
A JCVI spokeswoman told In Sequence by e-mail that the institute has been using and evaluating several new sequencing technologies. “ABI’s just happens to be one that is now ready for use for resequencing Craig’s genome,” she said.
 
The WSJ article also reported that the institute plans to sequence between 10 and 30 individuals next year, and eventually sequence 10,000 genomes over the next decade.
 
According to the spokeswoman, “those are estimates and goals that Craig and the team have set.” She added that the institute has not yet decided which technology to use to sequence more individual genomes.
 
She did not say which sequencing platforms institute scientists are evaluating but indicated that they are looking broadly. “The JCVI and its sequencing facility have had a new technologies lab since it opened in 2003, so [it is] safe to say that as new technologies came out or were in beta testing, JCVI was/is evaluating them.”
 

 
Emory Lands $3M Grant for Autism Research; Will Use NimbleGen Arrays, Solexa Sequencing
 
The Simons Foundation has awarded Emory University's School of Medicine a $3 million grant for genetic research into why males have higher autism rates than females, Emory said last week.
 
Emory professor and principal investigator Michael Zwick told In Sequence’s sister publication GenomeWeb Daily News last week that the award will support a three-pronged approach in which the researchers will use Nimblegen’s microarrays for copy number variation studies; Illumina’s Genome Analyzer for sequencing; and a new technique for targeting specific DNA regions developed at Emory’s department of genetics that is featured in an upcoming issue of Nature Methods.
 
Men are four to nine times more likely to have autism than women, which has led to theories that the cause of the disorder is buried somewhere in the X chromosome.
 
“However, the ability to comprehensively examine the entire X chromosome for abnormalities has not been technically feasible until now,” the university said in a statement.
 
Emory's geneticists plan to study 330 autism patients with the goal of identifying X-linked variation for autism susceptibility.
 
One team will scan the X chromosome’s 155 million bases with Nimblegen's hi-resolution microarrays in a hunt for "subtle deletions or duplications."
 
A second group will sequence all 1,098 genes on the X chromosome with the Illumina sequencer.
 
The third team will scan the X chromosome to find evidence of epigenetic links.
 

 
USC to Lead $8.4M Effort to Study Autism Genotypes and Phenotypes
 
A group of institutions led by the University of Southern California has been awarded a five-year, $8.4 million grant from the National Institutes of Health to study genotype and phenotype variations of autistic children, USC said last week.
 
USC said it will use the funding to create a Center for Genomic and Phenomic Studies in Autism, and it will “increase the reach and ethnic diversity” of the Autism Genetic Resource Exchange, a repository of genetic information on families who have two or more children with autism.
 
The center will not be based at USC, but will be “a virtual center of sorts, which is part of the innovation,” explained Clara Lajonchere, a USC professor who specializes in autism and oversees the AGRE.
 
Much of the clinical and evaluative work will be performed in patient's homes across the country, and some research requiring on-site work such as MRIs will be performed at the MIND Institute at the University of California, Davis, Lajonchere added.
 
Working with USC on these autism studies are the MIND Institute; Children’s Hospital Los Angeles; the University of Michigan at Ann Arbor; and the University of Massachusetts Medical School.
 
Thomas Lehner, who heads the NIH Genomics Research Branch, said one goal of the center is to “better distinguish among the many forms of autism and to explore the difference in their genetic profiles.”
 
“We are trying to establish a correspondence between gene and phenotype, with the phenotype being autism and its many manifestations,” Lehner said.
 

 
NIH Releases Genetic and Clinical Data from 60-Year Framingham Heart Study
 
The National Institutes of Health said last week that it is releasing genetic and clinical data from the Framingham Heart Study free to qualified investigators.
 
Calling the program “one of the most extensive collections of clinical and genetic data ever made freely available to researchers worldwide,” the NIH said the data will allow researchers to study the genetic, clinical, and lab results from as many as 9,300 participants spanning three generations of more than 900 families and more than 550,000 SNPs.
 
The data set, called the SNP Health Association Resource, or SHARe, can be accessed through the National Center for Biotechnology Information’s Database of Genotypes and Phenotypes, which NCBI launched in December 2006.
 
The prospective Framingham Heart Study began in 1948 and originally included more than 5,200 participants. Around 5,000 spouses and children were added to the study in 1971 and another 4,000 were enrolled in 2002, the NIH said. As the study is ongoing, more data will continue to be added to the database.
 
Genotyping for the study was conducted by Affymetrix under a contract with the National Heart, Lung, and Blood Institute. Along with NHLBI, the Framingham study is being conducted with collaborators from Boston University’s School of Medicine and School of Public Health.
 
"As one of the most comprehensive studies ever undertaken, the Framingham Heart Study will play a vital role in laying the foundation for this vast dataset to help researchers link genes and disease," said NHLBI director Elizabeth Nabels in a statement, adding that data from the ongoing study will be added over time, and that NHLBI will also incorporate data from other large studies.
 

 
USC's Keck School Lands $10M Gift for EpigenomicsCenter
 
The University of Southern California said last week that its Keck School of Medicine has received a $10 million donation to build its planned Epigenome Center, which it expects to open in January.
 
USC said it will use the gift from the Kenneth T. & Eileen Norris Foundation to buy equipment, hire new staff, and position the center to land more funding from the National Institutes of Health, which identified epigenomics as one of several new priority areas under its Roadmap initiative earlier this year.
 
The center will focus on epigenomics sequencing and the role of epigenetics in disease treatment and prevention. Cancer research will be a point of emphasis.
 
"We shall now be able to use high-throughput techniques to sequence entire epigenomes for the first time. Such approaches would have been unthinkable even a short while ago," said Peter Jones, director of the USC/Norris Comprehensive Cancer Center, in the statement.
 
USC said the Epigenome Center will be located in the Norris Cancer Research Tower, which is a recently opened 172,440-square-foot building at USC's Health Sciences Campus.
 
Peter Laird, a lead researcher and associate professor of surgery, biochemistry, and molecular biology, has been named director of the Epigenome Center.
 

 
Sorenson Genomics to Merge Identigene, GeneTree Arms Into Single Unit
 
Sorenson Genomics has merged into a single segment its Identigene arm, which specializes in forensic-DNA research for law enforcement, and its GeneTree arm, which focuses on DNA-based paternity testing, the company said this week.
 
Sorenson said the new unit will operate under the Identigene brand name and will continue to operate from Identigene’s bases in Houston and Salt Lake City.
 
Sorenson bought Identigene in June for an undisclosed sum. Identigene and GeneTree, both founded in the mid-1990s, perform forensics casework for law enforcement and DNA paternity testing, and the newly formed division will continue to offer both services, Sorenson said.
 
The reorganization comes one month after Sorenson said it is expanding its lab facilities and is boosting its staff in the Salt Lake City region. Sorenson also said it is buying new sequencers and sample-prep tools in an effort to expand its capacities five-fold.
 

 
MIT Wins $100M Gift to Create Cancer Research Institute That Melds Genomics, Cell Bio, Engineering
 
The Massachusetts Institute of Technology said this week that an alumnus has awarded it a $100 million gift to create a new research center that will pool the school’s molecular genetics, cell biology, and engineering disciplines to study cancer.
 
The gift from Koch Industries executive David Koch will help build the David H. Koch Institute for Integrative Cancer Research, which will house genomics, cellular imaging, nanotech, and other technologies and employ around 25 scientists and engineers “to develop new ways to detect, diagnose, treat, and manage” cancer, MIT said today in a statement.
 
The school said that the center will be using genomics technologies, along with imaging and micro-scale monitoring technologies, to push cancer diagnosis and prevention to “earlier and earlier” stages of the disease.
 
It also said it will attempt to discover “specific vulnerabilities” of cancer cells through diagramming “key pathways,” engineering new nanotechnology, studying how tumors evade recognition by the immune system, and studying the “molecular and cellular basis for metastasis.”
 
MIT said the center is scheduled to open in 2010. Tyler Jacks, the David H. Koch Professor of Biology at MIT, will serve as the director of the Koch Institute.
 

 
Invitrogen, Natural Selection Partner on microRNA Sequences
 
Invitrogen said last week that it has licensed a set of predicted human and mouse microRNA sequences from Natural Selection, a developer of pattern recognition tools.
 
Invitrogen said the microRNA sequences have been verified experimentally using deep sequencing, array profiling, and qRT-PCR methods. The firms will submit the sequences to the Wellcome Trust Sanger Institute’s miRNA database, and Invitrogen will integrate the sequences into its miRNA arrays.
 
Under the agreement, Invitrogen will release a larger set of computationally predicted microRNA sequences over the next few years.
 
Financial terms of the agreement were not released.
 

 
NIH to Fund Technology and Methods Development for Genomics, Population Genomics, ELSI
 
The National Human Genome Research Institute, along with the National Institute on Deafness and Other Communication Disorders, the National Institute of Dental and Craniofacial Research, and the National Institute of Mental Health, has issued a Funding Opportunity Announcement, inviting grant applications for research related to genomics. Research areas include the analysis of genome structure and function; genetic variation; population genomics; and ethical, legal, and social implications. 
 
NHGRI said it is looking for research projects that address technology and methods development in several areas, such as new approaches to bioinformatics that facilitate data management and data dissemination, new computational biology approaches to data analysis, new strategies to apply genomics to clinical problems, new approaches that combine genomics and population studies, and studies of the ethical, legal and social implications of genomics research, including the exploration of new policy approaches to address social issues raised by new capabilities in genomics.
 
NIH did not say how much funding it has allocated to the program. “Because the nature and scope of the proposed research will vary from application to application, the size and duration of each award will also vary. The total amount awarded and the number of awards will depend upon the mechanism numbers, quality, duration, and costs of the applications received,” the FOA states.
 
More information can be found here.

The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.