Posts Tagged ‘BioMed Central’

Nation’s BiobanksAcademic institutions, Research institutes and Hospitals – vary by Collections Size, Types of Specimens and Applications: Regulations are Needed

Reporter: Aviva Lev-Ari, PhD, RN

On this Open Access Online Scientific Journal a series of posts address the Gemonic Research Establishment

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3


Cancer Diagnostics by Genomic Sequencing: ‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

How to Tailor Cancer Therapy to the particular Genetics of a patient’s Cancer


‘No’ to Sequencing Patient’s DNA, ‘No’ to Sequencing Patient’s Tumor, ‘Yes’ to focus on Gene Mutation Aberration & Analysis of Gene Abnormalities

PRESENTED in the following FOUR PARTS. Recommended to be read in its entirety for completeness and arrival to the End Point of Present and Future Frontier of Research in Genomics

Part 1:

Research Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine


Part 2:

LEADERS in the Competitive Space of Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer Personalized Treatment


Part 3:

Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research


Part 4:

The Consumer Market for Personal DNA Sequencing


We present the State of Affairs of Nation’s BioBank Industry
Characterizing Biobank Organizations in the U.S.: Results from a National Survey

Gail E Henderson, R Jean Cadigan, Teresa P Edwards, Ian Conlon, Anders G Nelson, James P Evans, Arlene M Davis, Catherine Zimmer and Bryan J Weiner

Abstract (provisional)


Effective translational biomedical research hinges on the operation of “biobanks,” repositories which assemble, store, and manage collections of human specimens and related data. Some are established intentionally to address particular research needs; many, however, have arisen opportunistically, in a variety of settings and with a variety of expectations regarding their functions and longevity. Despite their rising prominence, little is known about how biobanks are organized and function beyond simple classification systems (“government, academia, industry”). Methods: In 2012, we conducted the first national survey of biobanks in the U.S., collecting information on their origins, specimen collections, organizational structures, and market contexts and sustainability. From a list of 636 biobanks assembled through a multi-faceted search strategy, representatives from 456 U.S. biobanks were successfully recruited for a 30 minute online survey (72% response rate). Both closed and open-ended responses were analyzed using descriptive statistics. Results: While nearly two-thirds of biobanks were established within the last decade, 17% have been in existence for over 20 years. Fifty-three percent listed research on a particular disease as the most important reason for establishment; 29% listed research generally. Other reasons included response to a grant or gift, and intent to centralize, integrate, or harmonize existing research structures. Biobank collections are extraordinarily diverse in number and types of specimens and in sources (often multiple) from which they are obtained, including from individuals, clinics/hospitals, public health programs, and research studies. Forty-four percent of biobanks store pediatric specimens, and 36% include post-mortem specimens. Most biobanks are affiliated in one or multiple ways with other entities: 88% are part of at least one or more larger organizations (67% of these are academic, 23% hospitals, 13% research institutes). The majority of biobanks seem to fill a particular “niche” within a larger organization or research area; a minority are concerned about competition for services, although many are worried about underutilization of specimens and long term funding. Conclusions: Effective utilization of biobank collections and effective policies to govern their use will require understanding the immense diversity found in organizational features, including the very different history and primary goals that many biobanks have.

The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.


US Sees Boom in Diverse Range of Biobanks, But Regulations are Lacking

January 25, 2013

NEW YORK (GenomeWeb News) – The past decade has seen a dramatic rise in the number and diversity of biobanks in the US, from academic institutions to research institutes and hospitals, and any efforts at creating regulations or governing rules for them will require more than a ‘one-size-fits-all’ approach, according to a new survey.

Funded by the National Human Genome Research Institute and published today in BioMed Central‘s Genome Medicinethe survey found that nearly two-thirds of the nation’s biobanks were launched over the past decade, and they are an “extraordinarily diverse” group, from the size of their collections to the types of specimens they harbor to their fields of study and applications.

The study’s lead author, Gail Henderson, professor and chair of the Department of Social Medicine at the University of North Carolina at Chapel Hill, told GenomeWeb Daily News this week that the “rise of genomics and large-scale gene-environment studies” have led biobanks to “play an increasingly important role in biomedical research.”

“Many articles discuss the ways they are changing the research enterprise – but they have never been systematically studied,” and there is little empirical data or details “on how they are run or on the policies and practices they have to manage their work,” Henderson said.

Although it is difficult to determine the exact number of biobanks operating in the US, by hunting through a range of sources the UNC-based research team was able to create a list of nearly 800 banks. Their online survey generated responses from 456 biobanks, and the team found that 59 percent of these were established after 2001.

Nearly 50 percent of these banks said that the main biomolecule that they store is DNA, 11 percent said RNA, 7 percent said protein, 20 percent said they do not store biomolecules, and 9 percent said ‘other’.

In total, these banks may house from tens of millions to over 50 million samples, the researchers found, and 53 percent of these specimens were stored to support research on particular diseases or disease types. By far, the largest portion of these is being used for cancer research, which is followed by biospecimens stored for neurological diseases like Alzheimer’s and HIV/AIDS.

As for the types of biological specimens these repositories store, 77 percent said they hold serum/plasma, 69 percent store solid tissues, 55 percent store whole blood, and 49 percent house peripheral blood cells or bone marrow. Around 7 percent of the biobanks store pathological body fluids, and around two or three percent have hair and toenail samples.

The rise of genome-focused research after the completion of the sequencing of the human genome a decade ago appears as if it may be a key driver in the biobank explosion. Since then, biobanks have been created to facilitate research generally, rather than to support studies of single diseases or to focus on one area of human biology.

“While there are likely multiple explanations for these results, it is possible that the changing landscape of genomic technology has facilitated a broadening of scope in research pursuits, so that biobanks are not as likely to limit their work to one disease,” the authors stated in the paper.

The expansion and use of new biobanks likely is “all about genomic information,” Henderson told GWDN.

“When we talk about specimens, and look at the numbers and kinds of specimens that people are saving, and the fact that the majority of our banks are cancer banks, and cancer research is fundamentally about DNA,” it is hard not to come to the conclusion that much of this growth is about genomics, she said.

Henderson also said the survey uncovered a “huge diversity” in the types of biobanks in the US.

“They get established for a variety of reasons, some accidental, some intentional, and they vary in size, in when they were established, how formal they are as organizations, what kind of specimens they hold, and where those specimens come from,” she said.

Biobanks also are diverse in their structural affiliations, although nearly 90 percent are embedded within other institutions, and nearly 80 percent of those embedded banks are located within academic institutions. Hospitals house around a quarter of these biobanks, and around 15 percent are part of a research institute.

While they house the samples that are helping to fuel genomics and molecular research, biobanks also can bring up ethical and policy questions that have caught the eye of policy-watchers at NHGRI.

Several issues that have been flagged by the institute’s Ethical, Legal, and Social Implications Research program are stirred up by the expansion of biobanks, such as questions about policies governing data sharing and security, privacy and the identifiability of genomic information, how and when to return research results and incidental findings, how governance structures function at genomic repositories, and informed consent issues caused by the multiple uses for samples by genome researchers.

“Given the diversity in biobank organizational characteristics, it is likely that management and governance policies will have to be tailored to fit the particular context. One size will not fit all,” Henderson said.

For example, she said, the biobanks in the survey showed a range of policies regarding who may access the data, with some enabling only the researchers who run the repository to access it, and others providing nearly universal access with no applicants denied.

There currently are few or no specific guidelines and laws that specifically govern biobanks and biorepositories, she explained.

A list of voluntary best practices for biospecimen resources published by the National Cancer Institute is probably the best available guidelines for biobanks to follow, Henderson explained, but there is not enough specificity in those or other rules or guidelines to apply them to the range of biobanks that are out there now.

“It’s not as is if there are no federal regulations that affect biobanks,” she said. “Certainly, human subject regulations do, and material transfer agreements and commercialization [rules] fall under certain federal regulatory guidance, but none are specific to biobanks.”

In some ways, she said, the biobanking and biorepository boom has created a “Wild West” landscape that will require further study, Henderson said. She and her fellow investigators now plan to begin to tack their research aims toward the ethical and regulatory issues that the proliferation of and multiple new uses for biobanks have brought about.

Matt Jones is a staff reporter for GenomeWeb Daily News. He covers public policy, legislation, and funding issues that affect researchers in the genomics field, as well as the operations of research institutes. E-mail him here or follow GWDN’s headlines at@DailyNewsGW.

ACMG Issues Guidelines on Sequencing for Dx, Screening Purposes

March 29, 2012

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – The American College of Medical Genetics last night released a policy statement and guidelines for the use of genomic sequencing for diagnostic genetic screening applications.

The guidelines cover how clinical whole-genome and whole-exome sequencing should be applied, distinguishing between cases where the technology is applied to diagnose a specific condition and when it is used as a screening purpose on asymptomatic individuals. It also asserted that the guidelines are applicable to sequencing for clinical purposes, not research.

In a statement, ACMG said that it recognizes that “genomic sequencing approaches can be of great value in the clinical evaluation of individuals with suspected germ-line genetic disorders,” and there are already “instances in which genomic sequencing approaches can and should contribute to clinical care.”

The organization also distinguished between returning results directly associated with the patient’s phenotype or clinical condition and secondary findings or results generated from screening asymptomatic individuals.

For secondary findings, or returning results to asymptomatic individuals, “it is critical that the standards for what is reportable be high to avoid burdening the health care system and consumers with what could be very large numbers of false positive results,” it wrote. By contrast, “a lower threshold for reporting is appropriate” for returning “diagnostic results that are clearly related to a patient’s phenotype or clinical condition.”

ACMG said whole-genome or whole-exome sequencing should be considered as a diagnostic test for individuals when the phenotype or family history data strongly implicate a genetic etiology, but the disorder is unknown and a specific genetic test is not available; when a patient presents with a defined genetic disorder with a high degree of genetic heterogeneity, making multiple single-gene tests less practical; when a patient has a likely genetic disorder, but available tests have failed at diagnosing the disorder; and when a fetus has a likely genetic disorder, but available tests have failed to diagnose it.

Prior to testing, ACMG recommends patients and families receive genetic counseling and be informed about the expected outcomes, likelihood of finding incidental results, and what types of results will be returned. Labs performing the tests should have clear policies related to disclosing secondary findings, and patients should also have the option of not receiving certain results.

Additionally, patients should be informed if a laboratory’s institutional review board has approved a protocol that allows variants of unknown significance to be used for further research, and patients should consent to this use of their data.

The test itself, and every component of it, including the bioinformatics and interpretation, should be performed in a lab directed by a board-certified individual with broad medical genetics and genomics training, ACMG said.

Regarding what results it recommends returning, ACMG said that test results could include variants known to be associated with the patient’s condition; novel variants whose “genetic, biological, and pathological features” indicate that they are likely involved with the patient’s phenotype; and secondary findings not associated with the patient’s condition, but that are known to be associated with a phenotype.

ACMG has different recommendations for whole-genome or whole-exome sequencing done not for diagnostic purposes, but as a screen of asymptomatic individuals. In these instances, it stresses that the threshold for determining which results should be returned should be “significantly higher” than when the technology is used for a specific diagnostic purpose.

Additionally, it said that individuals should be informed of the “virtual certainty of finding variants of unknown significance.”

While many in the field assume that everyone will eventually have their genomes sequenced at birth, the ACMG’s current position is that sequencing should not be used as a first-tier approach for newborn screening. Whole-genome or whole-exome sequencing should also not be used as a method for prenatal screening, it wrote.

However, whole-genome or whole-exome sequencing could be considered for preconception carrier screening to “focus on genetic variants known to be associated with significant phenotypes in homozygous or hemizygous progeny,” ACMG said.

ACMG acknowledged that the field is rapidly evolving and said that its recommendations would likely be revised over time.

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Reporter: Prabodh Kandala, PhD

You know that vegetables are good for you. And cruciferous vegetables – broccoli, cabbage, cauliflower, brusselsprouts – are especially healthful. New studies are demonstrating the anti-cancer effects of an ingredient in these green goddesses.

Diindolylmethane (DIM) is the wonder ingredient found in cruciferousvegetables. DIM is also sold over-the-counter as a supplement.

Researchers have found that DIM kills ovarian cancer cells in the laboratory and also improves the effectiveness of a commonly used chemotherapy agent.

Prabodh K. Kandala and Sanjay K. Srivastava, researchers in the Department of Biomedical Sciences and Cancer Biology Center at Texas Tech University Health Sciences Center, made the discoveries.

Researchers already knew that DIM slows the growth of ovarian cancer cells. In a detailed look at how the chemical behaves, they learned that DIM works by blocking the gene STAT3, which is seen in 90 percent of ovarian cancers.

In addition to causing cell death, DIM also prevented the cancer cells from invading or developing blood vessel structures which are key processes in cancer growth.

A platinum-based chemotherapy drug – cisplatin – is used to treat women with ovarian cancer. The drug doesn’t always work, though, and some patients become resistant to it.

For this study, researchers found that when DIM was combined withcisplatin, tumor growth in mice was slowed 50 percent more than when the chemo was used alone.

“DIM increases the effect of cisplatin, without being toxic to normal ovarian cells, by targeting STAT3 signaling and increasing apoptosis,” the authors explained.

“Cisplatin is very toxic and has severe side effects. If co-treatment with DIM means that a low dose of cisplatin can be given to patients without the loss of therapeutic effect, but with reduced side effects, it would represent a significant breakthrough in clinical practice,” Kandala andSrivastava concluded.

For the experiments, the supplement BioResponse DMI was used.

A number of clinical trials are currently under way to study the impact of DIM on a variety of malignancies including cancers of the breast, prostate, pancreas, kidney and others.

This new research was published in BioMed Central‘s open access journalBMC Medicine.




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