AMDeC

AMDeC BioSNPs - April 2011

BioSNPs
April 2011
Stories include Supporting Human Gene Discovery at Rutgers, AMDeC's Expanded Vendor Partnership Program, Updates on AMDeC's ROAD Project, and more...

Supporting Human Gene Discovery at Rutgers

What might be considered one of the world’s largest information reservoirs is the Rutgers University Cell & DNA Repository (RUCDR).  The information in question is genetic code – the DNA, RNA, and genetic sequences that define who we are at the most elemental level and what diseases are most likely to affect us. Established in 1998 in conjunction with a newly formed Department of Genetics at Rutgers, the State University of New Jersey, the RUCDR plays a critical role, not only in maintaining hundreds of thousands of samples of genetic material, but also in adding to our understanding of the genetic causes of complex human disease.   

“The RUCDR is more than just a housing project for these precious materials,” explains Jay A. Tischfield, Ph.D., Scientific Director of the RUCDR, Duncan & Nancy Macmillan Professor of Genetics, and Director, The Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey.  The repository, a 33,000 ft2 state-of-the-art facility, provides a complete range of services, from sample acquisition to data analysis, for researchers and organizations involved in the search for genes contributing to complex human disease.

In addition to processing blood components to create continuous cell lines for DNA/RNA extraction and cryopreservation, the RUCDR provides consultation and assistance with the design of new projects, performs whole genome and regional SNP genotyping, and conducts small and large scale gene expression analyses via a number of high-throughput technologies, to name just a few of its vast array of analytical services.  All of this is supported by sophisticated and numerous back-up systems to ensure the long-term viability of samples and data.   

The RUCDR meets or exceeds various federal and special interest requirements in the biobanking community including ISBER’s (International Society of Biological and Environmental Repositories) Best Practices for Repositories, which may be why the number of public and private collections it maintains has grown over the years.  Both the private and public collections housed here offer researchers a unique window into the genetic profiles of individuals and families with a specific disease, individuals who display a specific trait (such as longevity), and individuals from the general population who are being followed over time.   

A broad range of collections available

For some of the collections housed at the RUCDR, such as those from the Collaborative on the Genetics of Alcoholism (COGA), the National Institute on Drug Abuse (NIDA) Center for Genetic Studies, and the Center for Collaborative Studies of Mental Disorders of the National Institute of Mental Health (NIMH), identifying affected individuals and obtaining samples is relatively easy.  Samples from individuals enrolled in studies on addiction or mental illness, for example, are frequently obtained as part of a drug treatment protocol.  What is more challenging, according to Dr. Tischfield, is reassuring participants they will not be subject to criminal proceedings (in the case of those who have used illegal substances) and insurance or other discrimination, nor will information about their identity and health status be revealed.  

For rare diseases, one of the advantages of compiling a very large number of well-characterized samples in one repository is the greater likelihood of being able to identify the specific genetic mutations responsible.  For the extremely rare disease progeria (accelerated aging disease), The Progeria Research Foundation Cell & Tissue Bankhoused at the RUCDR includes samples from as far afield as Kazakhstan and Nigeria.  Analyzing all the samples collected enabled Francis Collins (now Director of the National Institutes of Health) to identify gene mutations specific to progeria.  

The nature of the mutation suggested that some previously tested cancer treatments might have a therapeutic effect.  And now, within five years of identifying the genetic mutation, a clinical trial is under way – all because of the ability to collect and aggregate genetic material from a very small number of patients.  Dr. Tischfield points to this as an excellent demonstration of the incredible power of a biorepository such as the RUCDR.   

Most of the collections housed at the RUCDR are disease focused.   One exception is AMDeC’s New York Cancer Project Collection, which contains one of the world’s largest, non-disease related cohorts of an ethnically and racially diverse population living in a single metropolitan area.  Dr. Tischfield points to the uniqueness of AMDeC’s NYCP Collection, noting that “it is rare to find such a large, ethnically diverse population as this with so much depth of information and follow up.” The collection includes DNA samples obtained between 2000 and 2002 from more than 18,000 New Yorkers.  

The value of these samples is enhanced by two important factors:  One is the availability of detailed medical history and lifestyle information on each participant.  This includes personal and family history on a range of conditions, including: angina, heart attack, stroke, high blood pressure, high cholesterol, colon and rectal polyps, ulcerative colitis, arthritis, diabetes, Parkinson’s disease, HIV, and many common cancers. 

The second distinction is that all participants have consented to broad use of these samples, meaning they can be used to study the genetics of any disease state.  In addition, the advanced robotic technology for biomaterial storage and dispensing that exists at the RUCDR allows for customized distribution of the NYCP collection, in just about whatever format is required by an investigator.    

Value of collections increases over time

Dr. Tischfield believes strongly that the value of these collections increases over time, so it is critically important to retain the samples and the data over the long term. “When studying the human genome, the first obvious thing to concede is that we are all different.  The more samples we can gather from a broad range of individuals, the more likely we’ll be able to pinpoint the basis for those differences.  For some common diseases, we may need to collect samples from tens of thousands of individuals before we can properly identify the genetic variation responsible,” he noted.    

He added that samples accumulated over the long term may provide answers for questions yet to be defined or for which we don’t yet have the proper evaluation tools. Can we identify the exact effect of specific environments on diseases? How valid are the predictions made about genetic risk 30 or 50 years previously?  What is the predictive value of the research from these samples on the health of one’s children, grandchildren and generations to come?  And, as we discover new biological paradigms, it will be important to evaluate and validate this information against older samples. 

At the same time, the accumulation of ever increasing amounts of information can be challenging.  When considering that a DNA from just one parent equals 3.3 billion base pairs, imagine the challenge of obtaining and analyzing genetic information from even a small collection of samples.  Dr. Tischfield observes that, despite the speed of today’s computers, our ability to truly understand the information contained within the genome is still limited because there aren’t enough people who can navigate the interface between life science and computer science.   

Toward the “Promised Land”

The ultimate promise of working with this vast array of genetic information is the availability of truly personalized medicine – crafted to address the unique genetic blueprint for a given individual’s illness. To be sure, progress has already been made in this direction, especially in cancer medicine, in which tumors have been shown to have a unique genetic “fingerprint.”

But biorepositories have already yielded a wealth of information about the genetic blueprint of many diseases – Huntington’s disease, Fragile X, and Cystic Fibrosis, among them – and with each discovery we move closer to the possibility of finding a treatment.  Perhaps as important, suggests Dr. Tischfield, they provide answers to the most fundamental questions we ask about ourselves – how we develop, grow and mature, how we live, and how we die.     

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For Information about the RUCDR
Contact: Jay A. Tischfield, Ph.D., jay@biology.rutgers.edu  Phone:  732-445-1027

For information about the New YorkCancer Project Collection:
Contact: Taylor Palumbo, palumbo@amdec.org  Phone:  212-218-4605.

BioSNPs News Briefs

Vendor Partnership Program Yielding Large Savings

Over the past two years, AMDeC Members have saved more than $1.7 million from preferred pricing agreements with just two of the companies that are part of AMDeC’s Vendor Partnership Program.  With funding for NIH now $260 million less than it was in FY10, savings from programs such as this become even more important.Information about savings with newer Vendor Partners will be available after sufficient utilization information is available.  In addition to providing preferred pricing, AMDeC’s Vendor Partners also provide valuable educational seminars and hands-on product training: NuGEN Technologies will be hosting a two-day lab training event in June, open to AMDeC Members researchers in nextgen sequencing.  If you are interested in attending this event, please contact William Palumbo at williamp@amdec.org, Phone: 212-218-5632

Speaker Silver’s Efforts Lead to $1.5 Million Grant for AMDeC Foundation, Inc.

AMDeC was awarded a grant of $1.5 million for the purchase of capital equipment to facilitate and promote academic medical research and collaboration. This funding, spearheaded by New York State Assembly Speaker Sheldon Silver, was awarded by the New York State Assembly.  The funding will be administered through the New York State Dormitory Authority. The capital equipment to be purchased with this grant will be accessible to AMDeC Member institutions in order to facilitate collaborative research. The equipment will be listed on AMDeC F.I.R.S.T.™, an online, real-time registry of academic medical research core facilities, research services and instrumentation.

Continued Expansion of Vendor Partnership Program

The latest additions to AMDeC’s Vendor Partnership Programare Sigma Life Science, a leading life science and high technology company, and BioStorage Technologies, a global leader in scientific asset management, biomaterial storage, and cold chain logistics. Sigma products covered by the agreement include the comprehensive custom oligo and peptide product portfolio (DNA, RNA, siRNA and peptide libraries), as well as core reagents that cater to the genomic and proteomic workflows. BioStorage Technologies is providing AMDeC Members with tiered pricing based on cumulative volume stored by all Members, which could amount to savings of 30-55%. For more information on all AMDeC Vendor Partners, click here to sign into AMDeC F.I.R.S.T. and then click on the Vendor Partners tab.

Poster Presentations Demonstrate Value of AMDeC F.I.R.S.T.™

Poster presentations at three meetings in the region have showcased the utility of AMDeC F.I.R.S.T.  The most recent presentation was made at the 20th Annual New York Biotech Association (NYBA) Meeting, held in New York City in early April.  Previously, presentations on AMDeC F.I.R.S.T. also were given at The Northeast Regional Life Sciences Core Directors Meeting and the NCRR-sponsored Moving Forward in the Efficient Management and Use of Core Facilities conference.

First Manuscript from ROAD Project Now in Press

The first paper out of AMDeC’s ROAD (Reduce Obesity and Diabetes) Project is now in press.  The manuscript, titled “Pubertal Advancement Improves Endothelial Function as Measured by Peripheral Arterial Tonometry (PAT)” is now in press in the journal Hormone and Metabolic Research.

Updated Core Listings on AMDeC F.I.R.S.T. Keep Researchers Informed on Available Services

The Rockefeller University has recently updated information about their Core facilities on AMDeC F.I.R.S.T., adding BD FACSAriaII and Illumina sequencing instruments and services to several cores. AMDeC F.I.R.S.T. supports research throughout the consortium, enabling researchers to quickly and easily identify a broad range of research resources at Member institutions.  For this reason, it is important that the information listed on the registry be kept current.  AMDeC encourages all Member Core Directors to log on to review their pages and make any necessary additions or updates.

Log into AMDeC F.I.R.S.T. by clicking here.

Get Listed on the AMDeC F.I.R.S.T. Events Calendar

Members can now go to a single location – the Events Calendar on AMDeC F.I.R.S.T. – to learn about activities throughout the AMDeC consortium that may be of interest to Member researchers.  Members can view the calendar by logging onto AMDeC F.I.R.S.T. and clicking on Calendar and Events on the left-hand navigation bar.  New events can be added by contacting William Palumbo at williamp@amdec.org; Phone:  212-218-5632.

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