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Beijing Genomics Institute, Roche Applied Science, National Science Foundation, NHGRI, UNC, UPenn, DNAPrint, BioServe, Genetic Technologies, Biosearch Technologies

Chinese Scientists Plan to Sequence 99 Human Genomes
Researchers at the Beijing Genomics Institute, Shenzhen; the National Engineering Research Center of Bioinformatics Systems; and the Beijing Institute of Genomics of the Chinese Academy of Sciences plan to sequence 99 human genomes as a first stage of a larger human sequencing study, a spokeswoman told In Sequence this week.
The project, reported by last week, follows the sequencing of the first Asian human genome by the same group on Illumina’s Genome Analyzer (see In Sequence 9/25/2007).
“We hope to do more individual genomes in the future,” the spokeswoman said in an e-mail message. “At the first stage, we are planning the next 99 genomes now.”
Institute scientists presented a map of the first Chinese diploid genome at the 9th China High-Tech Fair in Shenzhen last week.

Roche Applied Science Revenue Surge 10 Percent Over Past Nine Months
Roche reported this week that revenues for its diagnostics business, which includes Roche Applied Science, rose 5 percent year over year.
Diagnostics sales overall rose to CHF 6.8 billion ($5.7 billion). Roche Applied Science, a business are of Roche Diagnostics, posted a 10-percent increase in nine-month sales. The segment's main growth drivers were the LightCycler 480 and Genome Sequencer 20 systems, and research reagents, according to the company.
454 Life Sciences and NimbleGen Systems are part of Roche Applied Science.

NSF Unveils $85.8M Worth of Awards for Its Plant Genome Research Program
The National Science Foundation last week disclosed 26 new awards totaling $85.8 million for its Plant Genome Research Program that will go to researchers in 45 US and international institutions.
The awards, which run for two to five years and range between $400,000 and $7.9 million, support research and tool development aimed at helping researchers better understand plant genome structure and function.
The awards are also aimed at helping researchers better understand gene function and interactions between genomes and the environment in “economically vital” crops such as corn, rice, and cotton.
First-time award recipients include Auburn University, Dana-Farber Cancer Institute, SUNY Stony Brook, the University of Alaska Fairbanks, the University of Toledo, and the University of Virginia.
The following projects are among those funded:
A study by researchers at the University of Alaska, Fairbanks, that uses poplar to develop population genetics tools to identify genes involved in phenotypic variation in bud set, “a critical adaptive trait for cold tolerance and growth rate.” This project is supported in part by the NSF Office of Polar Programs and includes collaborations with scientists in Canada and Sweden;
A project led by Michigan State University that uses a combination of computational and functional genomics resources to “learn more about low-temperature regulatory networks and factors involved with” freezing tolerance in tomato and potato;
A study at Washington State University that uses biochemical genomics to “reveal components of biosynthesis pathways” necessary to produce novel fatty acids in oilseeds. Plants are natural producers of non-saturated fatty acids; and
A project led by Alabama A&M University that aims to identify regulatory gene networks responsible for changes in gene expression in response to nematode infection in cotton plants. 
The Plant Genome Research Program is also helping to develop tools that can enable researchers to better understand the structure and function of economically important plants.
Example of these projects include:
A multidisciplinary team of investigators at the University of Wisconsin-Madison developing technology using cameras, robotics, and computational tools to enable high-throughput analysis of traits in mutant or naturally varying plant populations; and
A project led by the Dana-Farber Cancer Institute that uses Arabidopsis and rice genomic resources to produce a plant protein interactome. Such a map will provide scientists with testable predictions of how genes and the proteins they encode interact to carry out complex functions within a plant cell. 

Scientists Sequence Genome of Green Algae C. reinhardtii; Study May Boost Alternative Energy Research
An international team of researchers has sequenced the genome of a green algae and has found hundreds of genes that are “uniquely associated” with capturing carbon dioxide and generating biomass, the scientists said last week.
Among the more than 15,000 genes sequenced from the genome of single-celled Chlamydomonas reinhardtii were those that encode the structure and function of the chloroplast, which is responsible for converting light to chemical energy.
The sequence also provides a “glimpse back through time” to the last common ancestor of plants and animals, the researchers said.
The project, which appears in the Oct. 12 issue of Science, was led by the US Department of Energy Joint Genome Institute; the University of California, Los Angeles; the Carnegie Institution; and included contributions from more than 100 international collaborators.
”The genome is like a green time capsule that affords a view into the complex core machinery that gave rise to today's energy-capturing and oxygen-producing chloroplasts,” Daniel Rokhsar, DOE JGI Computational Biology Program head, said in a statement.
Rokhsar co-led the study with DOE JGI Computational Scientist Simon Prochnik, Arthur Grossman of the Carnegie Institution and Stanford University, and Sabeeha Merchant of UCLA. He said that their particular interest in the organism is its “keen ability to efficiently capture and convert sunlight into energy, and its role in managing the global pool of carbon.”
He added that the sequence will further enable other researchers to study biology-based solar energy capture, carbon assimilation, and detoxification of soils by employing algae to remove heavy metal contaminants.
The analysis will also shed light on how other algae can produce biodiesel and biocrude as alternatives to fossil fuels, and could help researchers figure out the construction of chloroplasts, which house the machinery inside plant and algal cells that can absorb sunlight and couple carbon dioxide and water to produce the starting materials that fuel all other metabolic processes, the scientists said in the statement.
The published analysis of the genome shows approximately 120 million nucleotides, and found that the algae shares nearly 7,000 genes with other organisms. More than a third of these are shared by both humans and flowering plants, which helps support the argument for their common ancestry, the scientists said.

NHGRI Gives $11M to UNC and UPenn to Build Centers of Excellence for ELSI in Genomics and Genetics
The National Human Genome Research Institute will spend $11 million to help two US universities establish Centers of Excellence to address the ethical, legal, and social issues surrounding genomics and genetics in research, medicine, economics, and politics, the NHGRI said last week.
Over the next five years, the University of North Carolina at Chapel Hill and the University of Pennsylvania will use these grants to establish the Centers of Excellence in Ethical, Legal and Social Implications Research.
"Examining the emerging ethical, legal and social implications of genomic research is central to our goal of safely and effectively moving discoveries into the clinic," NHGRI Director Francis Collins said in a statement.
Collins said the centers will focus on "the most pressing issues being confronted by individuals, families, and communities as a result of genetic and genomic research,” including genetics and race and genetic privacy.
Both centers will pull together a team of experts representing a broad range of disciplines, including bioethics, law, behavioral and social sciences, clinical research, theology, public policy, and genetic and genomic research.
The University of North Carolina will use $5.6 million to fund The Center for Genomics and Society, which will use an interdisciplinary team to study the ethical, legal, and social questions surrounding large-scale genomics research, such as studies aimed at specific racial, ethnic, or other socially defined groups.
The UNC center also will study the effect of large-scale genomics research on informed consent, use and regulation of DNA samples, and the control and spread of data sets from large studies, according to the NHGRI.
The University of Pennsylvania, meantime, will receive $5.4 million to create the Penn Center for ELSI Research, which will study the ethical, legal, and social factors associated with the development and expansion of genetic testing technologies, the NHGRI said.
The Penn Center's researchers will explore such themes as the consequences of prenatal testing, patient provider perceptions of the barriers and utility of a preventive test for disease susceptibility, long-term effects of medical effects of genetic testing, and counseling for breast cancer on African American women and their families.

DNAPrint, BioServe Team to Offer DNA Samples Tagged With Ancestral Data
DNAPrint Genomics said last week it has allied with BioServe to supply integrated clinical DNA samples tagged with genetic ancestral information to biomedical researchers.
Under the agreement, DNAPrint will use its genetic ancestry test to analyze and categorize BioServe’s Global Repository of nearly 600,000 human biological samples.
“With the added dimension of ancestry information to clinical samples, medical researchers will be able to determine whether certain biological markers are artifacts of genetic ancestry or are true markers for a disease or drug response in a disease,” the companies said in a joint statement.
DNAPrint CEO Richard Gabriel said that "by removing the question of ancestry from a clinical sample, researchers can more readily evaluate which medicines will produce side effects within certain ethnic groups, and which medicines will work for the widest spectrum of a population.”
The agreement also allows the company to offer supportive services such as sample extraction and preparation, genotyping, and gene expression.
Financial terms of the deal were not released.

Biosearch Technologies Licenses Genetic Technologies' Non-Coding DNA IP
Genetic Technologies has licensed certain of its non-coding DNA patents to Biosearch Technologies for research purposes, GTG said last week.
BTI will use the worldwide license, which includes IP for SNP genotyping and allelic discrimination, to manufacture and distribute oligos, probes, and primers for research use only.
All of BTI’s customers will be covered under the GTG patents, GTG said.
Financial terms of the agreement were not released.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.