A REVOLUTIONARY NEW TOOL FOR BIOMEDICAL RESEARCH: AGINGPORTFOLIO.ORG

While we still like the NIH RePORT tool, there is another great resource for analyzing grants, publications and other research materials in biomedical science - The International Aging Research Portfolio .

We performed a search using "cancer biomarker" in the advanced search and got great results. These are only top 25 results, but it is possible to see almost all of them at once and the Spore Grants have excellent descriptions.

We went ahead and Liked them at their FaceBook Page!

It is also possible to see the results as graphs and play around with the statistics.

Search results

Search Keywords In:  Title, Description, Tags

Keywords:  "cancer biomarker"

View as Graphs

Total Funding: $ 137,209,529

Total amount of an all project funded matched specified criteria.

In other words, sum of the "Funding" column by the all found records.

Number Of Funding: 304

Total count of an all project funded matched specified criteria.

In other words, count of the found rows in grid below.

Number Of Projects: 302

Total count of an unique projects matched specified criteria.

In other words, count of an unique projects, by which found funded were made.

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Project Funding

Project number	Project title	Investigators	Recipient organization	Funding organization	Year	Funding	Aging Limit ID

1U24CA126476-01	Measuring cancer biomarker candidates by targeted ms and ab enrichment	CARR STEVENA	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	NATIONAL CANCER INSTITUTE	2006	$2,904,304	4
5U24CA126476-05	Measuring cancer biomarker candidates by targeted ms and ab enrichment	CARR STEVENA	BROAD INSTITUTE, INC.	NATIONAL CANCER INSTITUTE	2009	$2,833,858	4
5U24CA126476-02	Measuring cancer biomarker candidates by targeted ms and ab enrichment	CARR STEVENA	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	NATIONAL CANCER INSTITUTE	2007	$2,764,919	4
5U54CA116847-02	Mechanisms of energy balance and cancer prevention	MCTIERNAN ANNEM	FRED HUTCHINSON CANCER RESEARCH CENTER	NATIONAL CANCER INSTITUTE	2006	$2,506,320	0
2P50CA058184-09	Spore in lung cancer	BAYLIN STEPHENB	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2003	$2,500,000	4
5P50CA058184-10	Spore in lung cancer	BAYLIN STEPHENB	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2004	$2,491,531	4
5P50CA058184-11	Spore in lung cancer	BAYLIN STEPHENB	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2005	$2,490,165	4
5U54CA116847-04	Mechanisms of energy balance and cancer prevention	MCTIERNAN ANNEM	FRED HUTCHINSON CANCER RESEARCH CENTER	NATIONAL CANCER INSTITUTE	2008	$2,478,429	0
1U54CA116847-01	Mechanisms of energy balance and cancer prevention	MCTIERNAN ANNEM	FRED HUTCHINSON CANCER RESEARCH CENTER	NATIONAL CANCER INSTITUTE	2005	$2,472,758	0
5U54CA116847-03	Mechanisms of energy balance and cancer prevention	MCTIERNAN ANNEM	FRED HUTCHINSON CANCER RESEARCH CENTER	NATIONAL CANCER INSTITUTE	2007	$2,463,212	0
5U54CA116847-05	Mechanisms of energy balance and cancer prevention	MCTIERNAN ANNEM	FRED HUTCHINSON CANCER RESEARCH CENTER	NATIONAL CANCER INSTITUTE	2009	$2,461,328	0
5P50CA058184-12	Spore in lung cancer	BAYLIN STEPHENB	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2006	$2,430,329	4
5P50CA058184-13	Spore in lung cancer	BAYLIN STEPHENB	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2007	$2,359,850	4
2P50CA058184-14A1	Spore in lung cancer	BAYLIN STEPHENB	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2009	$2,300,000	0
R44CA139803-02	Field of injury based biomarkers for lung cancer	HALLAM E	ALLEGRO DIAGNOSTICS, INC.	NATIONAL CANCER INSTITUTE	2010	$1,823,081	4
5U24CA126476-03	Measuring cancer biomarker candidates by targeted ms and ab enrichment	CARR STEVENA	MASSACHUSETTS INSTITUTE OF TECHNOLOGY	NATIONAL CANCER INSTITUTE	2008	$1,758,222	4
7U24CA126477-02	Targeted and global proteomic strategies for early breast cancer detection	FISHER SUSANJ	UNIVERSITY OF CALIFORNIA SAN FRANCISCO	NATIONAL CANCER INSTITUTE	2006	$1,711,403	0
P50CA058184-15	Spore in lung cancer	BAYLIN B	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2010	$1,710,038	0
5U24CA126477-04	Targeted and global proteomic strategies for early breast cancer detection	FISHER SUSANJ	UNIVERSITY OF CALIFORNIA SAN FRANCISCO	NATIONAL CANCER INSTITUTE	2008	$1,642,172	0
5U24CA126477-03	Targeted and global proteomic strategies for early breast cancer detection	FISHER SUSANJ	UNIVERSITY OF CALIFORNIA SAN FRANCISCO	NATIONAL CANCER INSTITUTE	2007	$1,539,272	0
1R01CA105274-01A1	Prospective study of breast cancer survivorship	KUSHI LAWRENCEH	KAISER FOUNDATION RESEARCH INSTITUTE	NATIONAL CANCER INSTITUTE	2004	$1,487,114	4
1U24CA126480-01	Apt: the analytical proteomics team	REGNIER FREDE	PURDUE UNIVERSITY WEST LAFAYETTE	NATIONAL CANCER INSTITUTE	2006	$1,264,608	4
5U24CA126480-02	Apt: the analytical proteomics team	REGNIER FREDE	PURDUE UNIVERSITY WEST LAFAYETTE	NATIONAL CANCER INSTITUTE	2007	$1,193,024	4
3P50CA058184-13S1	Spore in lung cancer	BAYLIN STEPHENB	JOHNS HOPKINS UNIVERSITY	NATIONAL CANCER INSTITUTE	2008	$1,179,925	4
5U24CA126480-03	Apt: the analytical proteomics team	REGNIER FREDE	PURDUE UNIVERSITY WEST LAFAYETTE	NATIONAL CANCER INSTITUTE	2008	$1,164,358	4

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New epigenetic biomarker test for melanoma?

In a paper that recently appeared online in the journal Pigment Cell & Melanoma Research, a team of UNC researchers tested whether DNA methylation profiling could be accomplished on melanoma and mole tissues that had been preserved in fixatives for typical pathology examination after biopsy. They found that results on tissues prepared in this way were reliable and DNA methylation distinguished malignant melanomas from non-malignant moles.

http://www.sciencedaily.com/releases/2011/01/110124102925.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29&utm_content=Google+Feedfetcher

Advances in Ovarian Cancer Diagnostics

Two interesting articles on OC dx:

Levels of circulating cell-free nuclear and mitochondrial DNA in benign and malignant ovarian tumors.

Rebecca R Zachariah, Seraina Schmid, Nicole Buerki, Ramin Radpour, Wolfgang Holzgreve, Xiaoyan Zhong


Abstract OBJECTIVE: To analyze the levels of circulating cell-free nuclear DNA and circulating cell-free mitochondrial DNA in patients with benign and malignant ovarian tumors using a gold-standard assay and to investigate whether quantitative alterations of the circulating cell-free species have values in the management of the patients. METHODS: One hundred four patients were recruited for this study. We developed a quantitative, multiplex polymerase chain reaction to measure the levels of circulating cell-free nuclear DNA and circulating cell-free mitochondrial DNA in serum and plasma of patients with epithelial ovarian cancer, benign epithelial ovarian tumors, or endometriosis. The levels of the circulating cell-free DNA were compared with those of a healthy, age-matched control group. RESULTS: The patients with epithelial ovarian cancer had significantly higher amounts of circulating cell-free nuclear DNA and circulating cell-free mitochondrial DNA in plasma compared with the healthy control group (mean of nuclear DNA 10,723/2,591 and mean of mitochondrial DNA 4,918,978/2,294,264, P=.009 and 0.022, respectively) and with the other group with benign ovarian diseases (mean of nuclear DNA 10,723/2,965 and mean of mitochondrial DNA 4,918,978/1,597,551, P=.027 and 0.002, respectively). However, no relationship between levels of the circulating cell-free DNA and the pathological parameters as well as CA 125 measurement in patients with epithelial ovarian cancer was found. A significant difference between the epithelial ovarian cancer and endometriosis group was found in circulating cell-free mitochondrial DNA but not in circulating cell-free nuclear DNA (mean of mitochondrial DNA 4,918,978/2,273,988 and mean of nuclear DNA 10,723/3,291, P=.013 and 0.105, respectively). CONCLUSION: Elevated levels of circulating cell-free nuclear DNA and circulating cell-free mitochondrial DNA in epithelial ovarian cancer may have diagnostic value. Our finding suggests that the circulating molecules might be potential biomarkers in the disease.
Authors Rebecca R Zachariah, Seraina Schmid, Nicole Buerki, Ramin Radpour, Wolfgang Holzgreve, Xiaoyan Zhong (Affiliation: Laboratory for Prenatal Medicine and Gynaecologic Oncology, Women's Hospital/Department of Biomedicine, University of Basel, Basel, Switzerland.)

http://www.curehunter.com/public/pubmed1...

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OncoMap Gene Sequencing Finds 50 Mutations in Ovarian Tumors

By: JENNIE SMITH, Internal Medicine News Digital Network

11/17/10

Mutational analysis using a Sequenom-based technique of ovarian cancer samples has unveiled more mutations than were previously known, and could become part of a personalized standard of care for these difficult-to-treat cancers, according to investigators.

Dr. Ursula Matulonis of Dana-Farber Cancer Institute and Harvard Medical School, both in Boston, plans to elaborate on the findings Nov. 17 at the 22nd EORTC-NCI-AACR Symposium on Molecular Targets and Cancer Therapeutics in Berlin.......

http://www.internalmedicinenews.com/news...

Memorial Sloan-Kettering gets an approval to use Sequenom system for cancer diagnostics (lung, colorectal, thyroid & melanoma)

Kudos go to the Memorial Sloan-Kettering...

As the number of targeted cancer therapies grows, it is becoming increasingly important that hospital laboratories be able to perform timely and accurate genetic diagnostic tests on patients' tumor samples. These tests allow pathologists to determine the gene mutations within each patient's tumor cells so that oncologists can prescribe treatments that are most likely to be effective.

Now Memorial Sloan-Kettering has made an important step forward in efficiently diagnosing gene mutations in patients' cancers on an individual basis. The Center recently received approval from the New York State Department of Health to use a new, more sensitive and more efficient technology to look for mutations in the genes EGFR, KRAS, and BRAF in biopsy samples from patients with lung, colorectal, and thyroid cancers, as well as melanoma.

The test uses technology from a company called Sequenom. "To our knowledge, we are the only hospital to have New York State approval to use the Sequenom technology for this purpose," explained Marc Ladanyi, Chief of the Molecular Diagnostics Service and Director of the Diagnostic Molecular Pathology Laboratory. Dr. Ladanyi led the Memorial Sloan-Kettering team, including Laetitia Borsu, Chris Lau, and Khedoudja Nafa, that developed the protocols for and validated the performance characteristics of this new clinical application of Sequenom technology. Angela Marchetti will be the lead technologist for clinical testing.

In patients with certain types of cancer, the presence or absence of specific genetic mutations determines which therapies they are likely to respond to and, therefore, should receive. Knowing as much as possible about the genetic makeup of tumors helps ensure that patients get the treatments most likely to help them, while avoiding drugs that will not benefit them and the side effects that can accompany those drugs.

For example, lung cancer patients with mutations in the gene EGFR can be treated with the drug erlotinib (Tarceva®), which targets the product of the mutated gene. However, if patients instead have a mutation in the gene KRAS, they will not respond to the drug. In colorectal cancer, patients with mutations in KRAS and BRAF do not respond to the drugs cetuximab (Erbitux®) and panitumumab (Vectibix®), both of which also target the EGFR protein. In melanoma, patients whose tumors contain mutations in BRAF have recently been shown to respond well to a new BRAF inhibitor currently in clinical trials.

Memorial Sloan-Kettering has been at the forefront of testing for these mutations, starting with EGFR mutation testing in 2004, using then-standard DNA testing approaches.

"There's really been an evolution in molecular diagnostics," Dr. Ladanyi said. "We are moving from tests that are very labor intensive to tests that can be done in an automated, high-throughput manner. In addition, this new testing technology can provide results more quickly, as well as look for multiple mutations at the same time, something the old tests could not do."

Dr. Ladanyi added that the new technology also is more sensitive, allowing pathologists to perform molecular testing on biopsy samples that contain fewer tumor cells than what was required with the previous approaches. "This is important especially for patients who have already received therapy," he explained. "Treatments can cause a lot of inflammation in the tumor, and then immune cells and other normal cells can outnumber the actual tumor cells. It's also important in cancers where tumor cells are infiltrating connective tissue. This sensitivity and the ability to work with smaller tumor samples should make molecular diagnostic testing possible in cases where it was not before."

"The Sequenom technology brings personalized medicine right into the mainstream of our colorectal cancer program," said Leonard Saltz, co-leader of the colorectal disease management team. "We have known for a long time that colorectal cancer is a conglomerate of many diseases that all look roughly the same but have different genetic mutations. Now we will be able to break it down into patients with specific mutations in their tumors and target their therapies specifically at those mutations."

In addition to testing for mutations in the EGFR, KRAS, and BRAF genes, the new technology will enable investigators to look for mutations in other, less-well-known genes and to enroll patients in clinical trials for new, experimental therapies targeted at those genes.

"Not only will we be able to rapidly get the full mutational profile that helps us with decisions on the use of standard chemotherapies, but we can now have a much broader mutational profile on each patient's tumor, so that we can offer experimental treatment options to those patients who have a particular profile for which an experimental drug is likely to be effective," Dr. Saltz added. "Some of these profiles are relatively rare; but by screening everyone, we expect to be able to identify which patients are most likely to benefit from one particular research option versus another."


SOurce: http://www.mskcc.org/mskcc/html/98446.cfm

A merger between Sequenom Inc (NASDAQ: SQNM) and Helicos Biosciences (NASDAQ: HLCS) will solve many problems

Looking at relative strengths of both companies, I think that it can be a very strategic move for HLCS to propose a merger with Sequenom. I am a long shareholder of both companies and there is most definitely a lot of synergy.
The combined entity can most definitely be successful in both diagnostics and equipment businesses.

Sequenom has excellent distribution channels for equipment and close ties with most genomics & epigenetics centers worldwide. It also has one operating and one planned CLIA labs and most innovative diagnostics assays in development.
Helicos has a great sequencing platform, which can be used for high-throughput diagnostics. The companies are a great fit and a merger could solve many problems for both companies and create a major superpower in Oncology, Prinatal Diagnostics and Ophthalmology.

Just my two cents...

The NIH underfunding the fundamental cancer biomarker research

After querying the NIH grant databases with "oncology and biomarkers" search terms (abstracts where both terms are present) for 2008, 2009 and 2010 and then filtering out grants into clinical research, infrastructure investments and behavioral & social sciences, we got surprising results:

	FY Total Cost		Project Title		Principal Investigator	Organization	Year	NIH Institute
	$1,968,645		PROSTATE CANCER IMAGING		CHOYKE, PETER L	NATIONAL CANCER INSTITUTE	2009	NCI
	$1,686,909		MOLECULAR PROFILING OF CLINICAL SPECIMENS		EDELMAN, DANIEL	NATIONAL CANCER INSTITUTE	2009	NCI
	$1,476,952		HUMAN RECQ HELICASES IN BIOLOGY AND ONCOLOGY		MONNAT, RAYMOND J	UNIVERSITY OF WASHINGTON	2009	NCI
	$1,309,745		NANOTECHNOLOGY LINKING BIOMARKERS WITH CANCER BEHAVIOR		NIE, SHUMING	EMORY UNIVERSITY	2008	NCI
	$787,458		ANGIOGENESIS IMAGING		CHOYKE, PETER L	NATIONAL CANCER INSTITUTE	2009	NCI
	$657,451		A PROTEOMICS PLATFORM FOR QUANTITATIVE, ULTRA-HIGH THROUGHPUT, AND ULTRA-SENSITIV		SMITH, RICHARD D	BATTELLE PACIFIC NORTHWEST LABORATORIES	2010	NCI
	$581,526		EPITOMIC BIOMARKERS OF PROSTATE CANCER		CHINNAIYAN, ARUL M	UNIVERSITY OF MICHIGAN AT ANN ARBOR	2008	NCI
	$524,925		"MOLECULAR SIGNATURES OF LETHAL AND INDOLENT PROSTATE CANCER"		RUBIN, MARK A.	WEILL MEDICAL COLLEGE OF CORNELL UNIV	2010	NCI
	$476,035		DEVELOPMENT OF IMAGING BIOMARKERS FOR TREATMENT RESPONSE		ROSS, BRIAN D.	UNIVERSITY OF MICHIGAN AT ANN ARBOR	2009	NCI
	$449,756		EPITOMIC BIOMARKERS OF PROSTATE CANCER		CHINNAIYAN, ARUL M	UNIVERSITY OF MICHIGAN AT ANN ARBOR	2009	NCI
	$397,168		A PROTEOMICS PLATFORM FOR QUANTITATIVE, ULTRA-HIGH THROUGHPUT, AND ULTRA-SENSITIV		SMITH, RICHARD D	BATTELLE PACIFIC NORTHWEST LABORATORIES	2009	NCI
	$377,561		NOVEL BIOMARKERS IN OVARIAN CANCER		BIRRER, MICHAEL	MASSACHUSETTS GENERAL HOSPITAL	2010	NCI
	$320,588		PROTEOMIC BIOMARKERS OF ALK+ LYMPHOMA		LIM, MEGAN S	UNIVERSITY OF MICHIGAN AT ANN ARBOR	2010	NCI
	$319,550		PROGNOSTIC MARKERS FOR OVARIAN CANCER		MOK, SAMUEL C	UNIVERSITY OF TEXAS MD ANDERSON CAN CTR	2010	NCI
	$311,250		HDGF: A NOVEL BIOMARKER AND THERAPETIC TARGET OF LUNG CANCER		MAO, LI	UNIVERSITY OF MARYLAND BALTIMORE	2009	NCI
	$305,000		A TOOL FOR ANALYSIS OF GENE-SPECIFIC DNA METHYLATION IN CLINICAL SAMPLES		LEVENSON, VICTOR V	NORTHWESTERN UNIVERSITY	2009	NCRR
	$283,708		CAP METASTASIS BIOMARKERS: VALIDATION/GENOMICS/BIOLOGY		PARIS, PAMELA L	UNIVERSITY OF CALIFORNIA SAN FRANCISCO	2009	NCI
	$259,674		GLYCAN MARKERS FOR THE EARLY DETECTION OF BREAST CANCER		HANCOCK, WILLIAM S	NORTHEASTERN UNIVERSITY	2009	NCI
	$258,053		DISCOVERY OF BIOMARKERS FOR LUNG CANCER METASTASIS		PATZ, EDWARD F	DUKE UNIVERSITY	2008	NCI
	$248,413		NOVEL HYPERPOLARIZED C-13 AND N-15 BIOMARKERS FOR METABOLIC MR IMAGING OF CANCER		CHEKMENEV, EDUARD	VANDERBILT UNIVERSITY	2009	NCI
	$223,194		INTEDRATED IMAGAING AND TISSUE BIOMARKERS IN GLIOBLASTOMA MULTIFORME POST THERAPY		CHANG, SUSAN M	UNIVERSITY OF CALIFORNIA SAN FRANCISCO	2009	NCI
	$178,380		BIOMARKER MODELS OF PROSTATE CANCER OUTCOME AFTER RADIOTHERAPY		POLLACK, ALAN	UNIVERSITY OF MIAMI SCHOOL OF MEDICINE	2009	NCI
	$174,701		PPARGAMMA: BIOMARKER FOR BREAST CANCER IN OLDER WOMEN		SEO, PEARL H	UNIVERSITY OF MIAMI SCHOOL OF MEDICINE	2009	NIA
	$128,711		ACUPUNCTURE FOR DYSPHAGIA AFTER CHEMORADIATION FOR HEAD AND NECK CANCER		LU, WEIDONG	HARVARD UNIVERSITY (MEDICAL SCHOOL)	2009	NCCAM
	$127,656		MOLECULAR PROFILES OF COLORECTAL ADENOMAS BY ARRAY CGH		HOSTETTER, GALEN H	TRANSLATIONAL GENOMICS RESEARCH INST	2009	NCI

There are only 25 meaningful projects in 2008, 2009 and 2010 with over $120,000! And that is considering hundreds of millions spent on minority research, billions spent on social and behavioral sciences... The NIH should definitely clean house sometime soon...

Multidrug resistance in oncology and beyond

At this moment, blockade
of specific growth factor receptors, intracellular targets, and
tyrosine kinase signaling has increased the efficacy of classic chemotherapy
in several cancer types. However, despite this success
a lot of patients do not benefit of the addition of these therapies.
To select patients up front and follow up treatment response,
new tracers and imaging modalities that represent changes in
intra- and extracellular tumor targets, antigens located in the
extracellular matrix or at the blood vessels of tumors during therapy
might support treatment follow-up. As indicated, growth
factor receptors present on the membrane of tumor cells, such as
HER2, EGFR, etc., are suitable candidates for this. Another
approach is to use a downstream product whose transcription is
increased in MDR and by other oncogenic processes. As indicated,
VEGF is such a target that could serve as a specific readout
modality for MDR and the response of new targeted therapies.
Besides intact mAb molecules such as trastuzumab and bevacizumab
(molecular weight, 150 kDa), mAb fragments and engineered
variants are also used, like F(ab)2, F(ab), Fab, single chain
Fv (scFv), and the covalent dimers scFv2, diabodies, and minibodies
(molecular weights ranging from 25 to 100 kDa), as well
as several types of protein therapeutics based on nontraditional
scaffolds, like, for example, domain antibodies, affibodies, nanobodies,
and anticalins could be used for this purpose (85). During
the development of these tracers, one of the main goals should
be to observe whether baseline values and/or changes during
therapy correspond with patient outcome and ultimately patient
survival. All this will lead to more patient-tailored therapy.

Methods Mol Biol. 2010;596:15-31.
Multidrug resistance in oncology and beyond: from imaging of drug efflux pumps to cellular drug targets.

Nagengast WB, Munnink TH, Dijkers EC, Hospers GA, Brouwers AH, Schröder CP, Hooge ML, de Vries EG.