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Snippets: Apr 8, 2009


Komen to Fund Cancer PGx Research through New Grants

Susan G. Komen for the Cure, a non-profit organization dedicated to funding breast cancer research and education, has awarded $60 million in grants to US and international researchers, including nearly $19 million to fund research into pharmacogenomics.

The funding for the pharmacogenomic research is provided through the organization's Promise Grants.

Komen, along with the Triple Negative Breast Cancer Foundation, has awarded $6.4 million to the University of Alabama at Birmingham to study adding a new drug to chemotherapy in treating triple negative breast cancer. That research project includes looking for ways to predict which therapies will be most effective for triple negative breast cancer patients.

Indiana University will receive a $5.8 million Promise Grant to identify biomarkers to predict which breast cancer patients will benefit from the drug bevacizumab (Avastin), and which patients will suffer significant side effects from use of the drug.

Researchers at Thomas Jefferson University in Philadelphia will use a $6.7 million Promise Grant to find biomarkers to predict treatment response and match patients with the best treatment option.

Prostate Cancer Foundation Funds 'Omics Research

The Prostate Cancer Foundation has awarded $1 million in grants to ten researchers in order to support "innovative ideas that have the potential to achieve breakthroughs for the detection and treatment of prostate cancer," including $400,000 for biomarker studies and DNA mapping, gene expression, and microRNA studies, PCF said this week.

The Creativity Awards grant $100,000 for one year to researchers who have not previously received PCF funding, while 70 percent of the grant winners historically have gone on to receive multi-year funding from the PCF and other sources, the foundation said.

"These awards feed our pipeline of compelling ideas to cultivate new solutions for the prostate cancer problem," Howard Soule, executive VP and chief scientific officer of PCF, said in a statement. "Promising results will translate into better therapies for patients with advanced prostate cancer."

Cory Abate-Shen of Columbia University Medical Center will receive the Gordon Becker Creativity Award to study all the dysfunctional regulatory and signaling molecules that man and mouse have in common. The goal is to find targets for prostate cancer drugs by using mouse model testing.

Barbara Graves of the University of Utah will receive the Michael Vinecki Creativity Award to study over-expression of Ets genes, which could be the cause of over 40 to 60 percent of prostate cancer cases, according to PCF. She plans to map the DNA regions that bind the Ets proteins, which could be used to discover molecules that may help interrupt carcinogenesis.

David Nanus of Weill Cornell Medical College will use the Dan Fogelberg Creativity Award to study new capture technology for a biomarker that could help identify patients who may respond well to the drug Taxotere, as well as those who may have unwanted side effects.

Muneesh Tewari of the Fred Hutchinson Cancer Research Center will use the Arnie's Army Creativity Award to isolate exosomes and to purify microRNAs from prostate cancer models in order to develop personalized treatments.

NCI Outlines Priorities for Stimulus Spending

The National Cancer Institute has identified a number of priority areas for grant-seeking investigators who aim to receive funding from the American Recovery and Reinvestment Act of 2009.

The nine areas that NCI has labeled on its website as priorities would advance public health genomics, but original investigator-initiated ideas are also welcomed.

The ARRA stimulus funding for NCI, as with the other institutes and centers, includes challenge grants, competitive revision applications, and supplemental funding programs.

NCI wants to receive applications from researchers who are developing a prototype knowledge base for cancer genetic associations and gene-environment interaction. A concerted approach to reviewing genetic association, gene-gene, and gene-environment interactions has been put forward by the Human Genome Epidemiology Network, said NCI.

Another priority area for NCI is development of evidence for candidate genomic applications for cancer prevention, management, and prognosis. Such an evidence-based process for evaluating genetic tests is being developed by the Evaluation of Genomic Applications in Practice and Prevention initiative, which was created by the Centers for Disease Control and Prevention in collaboration with NCI and other federal partners.

The institute also will welcome applications to conduct population health genomics modeling. These research programs could aim to fulfill the need for incorporating family history and genomic information into population models to study the impact of family history and genetic testing, an area NCI calls "a crucial need."

Comparative effectiveness research in genomics also is a key area for NCI support. "To date, there has been no systematic research conducted to compare the effectiveness and cost-effectiveness of cancer care and prevention based on genomic tools and markers compared to existing standards of care and prevention that do not use genetic stratification tools," said NCI. "Without such research, the promise of personalized medicine may not be fulfilled."

The institute said that it intends to support research comparing the clinical validity and utility of risk-stratification tools and algorithms for cancer prediction based on genetic markers to existing algorithms. Such studies also could include comparing the clinical validity and utility of pharmacogenomic testing in cancer treatment and prophylaxis to existing treatments that do not use pharmacogenomic tests. Another use for comparative effectiveness studies would be to conduct cost-effectiveness analyses and other decision models to assess the value of genetic stratification in cancer care.

Pharmacogenomics studies also could identify and characterize validity and utility of using genetic markers for cancer care and prevention. NCI is focusing on building research opportunities in pharmacogenomic epidemiology and beginning to study how to translate discoveries to the population. An ongoing challenge will be to study whether and when matching drug therapies to patients' genetic profiles can influence their adherence to drug regimens.

NCI said that NIH is seeking a trans-disciplinary "teams-of-the-future" approach that would involve researchers from genetics, social sciences, epidemiologists, and clinicians working together to understand multiple influences on specific health disparities.

NCI also would like to fund translational research programs for genomic applications in cancer care and prevention. Such projects could include studies that evaluate the validity, utility, and impact of genomic applications in the real world, and translation programs, clinical, and community genomics activities that will help to integrate validated genomic knowledge into the practice of medicine and public health.

NCI also seeks to fund training in public health genomics, including analysis and interpretation of the evidentiary standards for genomic applications in cancer control and prevention, as well as designing and evaluating communication strategies for conveying genetic information.

NIAMS Offers SBIR Funds for Multiplex Dx

The National Institute of Arthritis and Musculoskeletal and Skin Diseases plans to fund $100,000 for phase I and $750,000 for phase II Small Business Innovation Research grants to companies seeking to develop multiplex diagnostic tests that could apply to a variety of diseases.

NIAMS wants to fund projects that will develop multiplex assay methodologies for candidate biomarkers for musculoskeletal, rheumatic, and skin diseases.

The phase I grants, which will fund initial development and feasibility testing, will cover up to a six-month period. The phase II grants will cover research that will focus on completing development of the technology over a two-year period.

The assay technologies NIAMS wants to support would "enable accurate measurement of multiple candidate biomarkers in small volumes of blood or other body fluid or small biopsies".

These technologies are sought because many of the diseases that NIAMS investigates "are chronic and very complex in nature," the institute said in a request for applications. Because some of these diseases develop and progress slowly, there are a spectra of biological markers circulating in the blood, but resources to evaluate these markers are in limited supply, it said.

Digestive Disease Commission Urges 'Omics Research

A number of research areas, including genomics and other molecular biology studies, will be needed if researchers are to better understand and aggressively deal with the digestive diseases that strike worldwide, according to the recommendations of a National Institutes of Health Panel released last week.

The National Commission on Digestive Diseases, which was chartered in 2005 by NIH Director Elias Zerhouni, outlined a number of areas of need, including broad research areas and a number of disease-specific programs. The plan is supposed to outline the program areas that NIH will pursue and support, which include a variety of genomic, metagenomic, and biomarker studies, bioimaging advancement, and a number of other specific needs.

The commission was designed to tackle the future approach to diseases such as inflammatory bowel disease, pancreatic diseases, digestive system cancers, stomach and small intestine diseases, and others.

"To build on these advances and break new ground, we'll be looking for investigator-initiated projects and developing new initiatives that respond to the commission's recommendations," Griffin Rodgers, who is director of the National Institute of Diabetes and Digestive and Kidney Diseases, said in a statement.

"The commission's recommendations provide a guidepost for digestive diseases research to be addressed over the next decade," added NIDDK Division of Digestive Diseases and Nutrition Director Stephen James. "We hope that this broad-based research plan leads to new findings that help reduce the pain and suffering experienced by the millions who suffer from digestive diseases."

The committee advises conducting more metagenomic analysis of the microbes in the human colon, and gaining a better understanding of the bacterial products, enzymes, and compounds that can help elucidate the role of bacteria in intestinal diseases. There also should be studies of how microbes and hosts interact, and analysis of genome sequences from colonic bacteria in order to identify gene transfer events by using advanced computational methods, it said.

The committee advises starting metagenomic analysis of the microflora of healthy people and determining the extent of person-to-person or diet-related variation.

It also suggests that researchers develop a comprehensive understanding of the intestinal microbiome and the effect of the host genome on microbial colonization, as well as the consequences of interactions between gastrointestinal pathogens and normal gut microflora.

Another goal should be to develop high-throughput genomic and proteomic facilities to complement the Cancer Genome Anatomy Project in order to profile digestive tract cancers and their subtypes, said the commission. It also said that researchers should aim to discover biomarkers and surrogate markers for digestive diseases in order to improve the efficiency of clinical trials, which potentially could lead to improvements in clinical care.

More information about the NIH commission's report is available here.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.