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NHLBI, University of Houston, Illumina, Harvard Medical School, HapMap Consortium, Sorenson, NYU, GlobalOptions, Bode Technology, Invitrogen, Blue Heron Biotechnology, NSF, ABI, Bellevue Community College

NHLBI Plans to Fund Large-Scale Re-Sequencing, DNA Capture Tools in ‘08
The National Heart Lung and Blood Institute plans to fund as many as six grants next year to develop and validate large-scale genome-wide targeted re-sequencing and DNA-capture technologies, NHLBI said last week.
The technologies would “draw upon available massively parallel single-molecule DNA sequencing and region-specific DNA capture technologies” and would be aimed at lowering the cost of re-sequencing so that large numbers of genes and individual genomes could be re-sequenced more easily and effectively, the agency said.
“Recognition of the power of conventional re-sequencing of candidate genes to detect highly informative, low-frequency disease alleles provides the motivation for finding more cost-effective approaches that would allow expansion of re-sequencing to large numbers of genes and individuals,” the agency said in its “Notice of Intent to Publish a Request for Applications,” which can be read here.
“Recent advances in the development of single-molecule DNA sequencing technologies and efficient methods for capturing specific genomic segments are bringing the goal of large-scale targeted human genome re-sequencing in thousands of humans within reach,” the notice added.
NHLBI said its ultimate goal is to apply these technologies to large numbers of DNA samples collected in its bank of well-phenotyped populations.
The institute said it plans to issue a request for applications for these grants sometime in the late fall of 2007, and expects applications to be due in late winter of 2008. The awards will be disseminated in fiscal 2008, NHLBI said.

U. of Houston Plans to Buy an Illumina Sequencer for New Science and Engineering Center
The University of Houston's Institute for Molecular Design plans to use part of a $750,000 grant to purchase a next-generation sequencer to outfit a new lab in a planned complex, the university said last week.
The sequencer will be an Illumina Genome Analyzer, the university told GenomeWeb Daily News.
The school will use $500,000 of the grant, bestowed by the Cullen Foundation, to buy the instrument. The system, set to arrive in December, will be housed at the new Science & Engineering Research and Classroom Complex.
The school said it plans to use the sequencer, which it believes is the second Illumina GA in Houston, for stem cell research, among other areas.
The remaining $250,000 from the Cullen Foundation gift will be used to finish outfitting research labs.

Harvard Medical School Biopolymers Facility to Offer Services on Illumina GA
The Biopolymers Facility in Harvard Medical School’s Department of Genetics said earlier this month that it will be offering next-generation DNA sequencing services on an Illumina Genome Analyzer later this fall.
According to the facility’s website, funding for the instrument comes from Harvard Medical School institutional support through the Taplin Funds for Discovery Program as well as funds from a five-department consortium.
The new service will be made available to all users, but preference will be given to the laboratories that participated in the initial Taplin proposal.
Bob Steen, director of the Biopolymers Facility, told In Sequence last week that the instrument is scheduled to arrive in November.

HapMap Consortium Publishes 'Phase II' Genetic Variation Map with 3M SNPs
The International HapMap Consortium published a new version of its map of human genetic variation last week, which includes more than 3.1 million SNPs — three times more than the initial version of the map that was published in 2005.
The higher-resolution phase II haplotype map “offers greater power to detect genetic variants involved in common diseases, explore the structure of human genetic variation, and learn how environmental factors, such as infectious agents, have shaped the human genome,” said the National Human Genome Research Institute, which led the US component of the project.
An overview paper outlining the phase II findings and another related study using HapMap data were published in last week’s issue of Nature.
The overview paper shows "the surprising extent of recent common ancestry found in all of the population groups" involved in the study, NHGRI said.
Both phases of the HapMap project used blood collected from 270 volunteers from Nigeria, Japan, Beijing, and Utah. The consortium estimates that the phase II HapMap includes between 25 percent and 35 percent of common genetic variation in these populations.
Analysis of these samples showed that between 10 percent and 30 percent of the DNA segments from each representative population shared regions that signaled descent from a common ancestor within 10 to 100 generations.
NHGRI said the counterpart study describes how the new map can be used to "pinpoint pivotal changes in the human genome that arose in recent history." These changes became common through natural selection, which means "they were somehow beneficial to human health," but for the time being "their biological significance remains largely unknown."
The HapMap program will be expanded in the future to include samples from other populations, including Luhya and Maasai in Kenya, Tuscans in Italy, Gujarati Indian in Houston, Chinese in metropolitan Denver, and people of Mexican ancestry in Los Angeles.
The project to date has been a collaborative effort from scientists and funding agencies in Japan, the US, the UK, Canada, China, and Nigeria.
NHGRI said the development of the new HapMap "relied heavily on the high-throughput genotyping capacity of Perlegen Sciences," which "tested virtually the entire known catalog of human SNP variation" and "contributed some of its own resources to make the map possible."

Sorenson Launches Genetic-Genealogy Social Networking Web Site
The Sorenson Molecular Genealogy Foundation, Sorenson Genomics, and Sorenson Media have jointly launched GeneTree, a family history networking website that integrates DNA information, the companies said this week.
GeneTree will link to the SMGF database that currently contains information on more than 6 million ancestors through linked genetic and pedigree data from approximately 90 percent of the world's countries, according to the company. Sorenson Genomics, a web-based consumer genetic testing company, will provide DNA analysis services.
Participants in GeneTree collaborate on assembling detailed family histories with software for building family trees. Users can choose to have their DNA tested and map the results with the website’s genetic genealogy collection. Several types of mitochondrial DNA tests are available, ranging in price from $99 to $149.
Relatedness testing services provided by a division of Sorenson Genomics formerly named GeneTree will now be offered through Identigene, which was recently acquired by Sorenson Genomics.
The Sorenson companies were founded by biotech billionaire James LeVoy Sorenson and his son, James Lee Sorenson, who is also CEO of GeneTree.

NYU, Collaborators to Study Rice Genome for Possible Improvements
New York University will use a recent $4.4 million grant from the National Science Foundation to study the genomics of rice in an effort to learn more about links between the grain's genes and its characteristics as a domesticated food crop.
NYU's Center for Genomics and Systems Biology will use the funding under the NSF's Plant Genome Research Program to conduct genome-wide association studies aimed at linking genes to interesting characteristics.
"Using new, genome-wide techniques in evolutionary genomics we can identify regions of the rice genome that contain genes important for grain size, plant height, and other traits that are involved in plant yield," NYU researcher Michael Purugganan said in a statement.
NYU said it is the lead institution in the rice study, but collaborating institutions include Washington University at St. Louis, Purdue University, and Cornell University.

Bode Technology Wins Two Gov’t Contracts Worth $2.5 M for DNA Identification Work
GlobalOptions said last week that its Bode Technology operating unit has won two federal government contracts worth $2.5 million in total to “leverage” Bode’s experience with DNA identification technologies.
"We are pleased to have been selected as the primary company to perform DNA research for these high profile projects," said Howard Safir, CEO of Bode Technology and head of GlobalOptions' Security Consulting and Investigations unit, in a statement.
Bode has provided DNA-based identifications from degraded samples such as those collected at the World Trade Center. The company continues to develop methods to extract DNA from a variety of soil types, water, dust, and textile samples. The firm, which has received clearances to perform government classified research, has worked under government contracts since 1995.
GlobalOptions, based in New York, provides domestic and international risk mitigation and management services.

Invitrogen No Longer Exclusive Distributor of Blue Heron's Synthetic Genes
Invitrogen said last week it will now co-exclusively distribute Blue Heron Biotechnology’s custom synthesis genes worldwide, after it had been the exclusive distributor since last year.
Terms of the updated deal call for Invitrogen to continue to supply Blue Heron’s GeneMaker technology to its pharmaceutical and life sciences customers worldwide.
In the original agreement, disclosed in December 2006, Invitrogen said it made an undisclosed equity investment in Blue Heron in return for becoming its exclusive worldwide distributor. Invitrogen said at that time it was shifting away from its history as a provider of clones to becoming a synthetic gene provider.
Financial terms of the revamped agreement were not disclosed.

NSF Grant and ABI Gift Enables Seattle-Area Undergrads to Sequence, Analyze Bacteria
Undergraduates at Seattle-area Bellevue Community College will use a new Applied Biosystems sequencer and around $500,000 in grants to study a bacterium that may help combat root disease in wheat and barley, according to the school.
The three-year project, announced earlier this month, will use $478,000 from the National Science Foundation and $10,000 from chemical supplier Univar, and will partner with the US Department of Agriculture’s Agricultural Research Service at Washington State University to sequence and analyze the genome of Pseudomona fluorescens.
The students will submit the results of their work to the National Center for Biotechnology’s global genomic library, BCC said.
BCC will use the funds to buy an ABI 3130 sequencer, and the company will contribute in-kind support toward the purchase, BCC said.
If the project is successful, the school will apply for an additional $2 million grant aimed at disseminating the program to other community colleges around the country, BCC professor and project director Gita Bangera told GenomeWeb Daily News last week.

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.