New 'genetic bar code' technique establishes ability to derive DNA information from RNA
Discovery may create dialogue about DNA and RNA data bank privacy issues
2012-04-10
(Press-News.org) Researchers from Mount Sinai School of Medicine have developed a method to derive enough DNA information from non-DNA sources—such as RNA—to clearly identify individuals whose biological data are stored in massive research repositories. The approach may raise questions regarding the ability to protect individual identity when high-dimensional data are collected for research purposes. A paper introducing the technique appears in the April 8 online edition of Nature Genetics.
DNA contains the genetic instructions used in the development and functioning of every living cell. RNA acts as a messenger that relays genetic information in the cell so that the great majority of processes needed for tissue to function properly can be carried out.
To date, access to data bases with DNA information has been restricted and protected as it has long been considered the sole genetic fingerprint for every individual. However, vast amounts of RNA data have been made publicly available via a number of databases in the United States and Europe. These databases contain thousands of genomic studies from around the world.
In this study, lead authors Eric E. Schadt, PhD, and Ke Hao, PhD, developed a technique whereby a person's DNA could be inferred from RNA data using gene-expression levels monitored in any of a number of tissues. In contrast, most studies involving DNA and RNA begin with DNA sequences and then seek to associate expression patterns with changes in DNA between individuals in a population. This is the first time going from RNA levels to DNA sequence has been described.
"By observing RNA levels in a given tissue, we can infer a genotypic barcode that uniquely tags an individual in ways that enables matching the individual to an independently derived DNA sample," said Dr. Schadt, Director of the Institute for Genomics and Multiscale Biology, the Jean C. and James W. Crystal Professor of Genomics, and Chair of the Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine. "The potential uses for this information are significant. Not only can genotypic barcodes be deduced from RNA, but RNA levels in some tissue can inform not only individual characteristics like age and sex, but on diseases such as Alzheimer's and cancer, as well as the risks of developing those diseases."
Schadt adds, "The significance of our findings goes beyond medicine. For example, barcodes derived from individuals who participated in a research study, where RNA levels were monitored and deposited into publicly available databases, could be tested against DNA samples left at a crime scene as a way of identifying persons of interest."
Deducing a person's DNA sequence from gene expression patterns could have repercussions in health care and privacy. While specific laws and government regulations have been written to protect DNA-based information from misuse, it is unclear whether such laws apply to RNA—even though this study shows that RNA is informative at a deeper level compared to DNA regarding the current state of health of an individual.
"Rather than developing ways to further protect an individual's privacy given the ability to collect mountains of information on him or her, we would be better served by a society that accepts the fact that new types of high-dimensional data reflect deeply on who we are," Dr. Schadt said. "We need to accept the reality that it is difficult—if not impossible—to shield personal information from others. It is akin to trying to protect privacy regarding appearances, for example, in a public place."
Dr. Schadt said he hopes the research will catalyze a discussion that might ultimately help resolve privacy debates, and encourage patients to provide data that will help their doctors better diagnose and treat their conditions. Increased access to, and greater quantities of, DNA and other biological information would also contribute to the greater good of medical science.
In the Nature Genetics study, Drs. Schadt and Hao, Associate Professor of Genetics at Mount Sinai School of Medicine, together with Sangsoon Woo, PhD, from the Department of Biostatistics at the University of Washington, analyzed RNA and DNA from 378 livers donated by European-Americans for transplant, as well as liver and adipose tissues from 580 people from the same population group undergoing gastric bypass surgery. The authors found that levels of RNA across many genes correlate with age, sex, body weight, and other risk factors for diseases like diabetes and heart disease, but then they also correlate in many cases with changes in DNA that are unique to a given individual.
The investigators used an algorithm that matches patterns of gene expression to variations at 1,000 single-DNA-base sites in the genome. It is an application of integrative biology that examines multiple dimensions of data (DNA and RNA) to better inform a given dimension (RNA).
"The relationship of DNA to RNA is like that of an orchestra and the symphony it plays," said Schadt describing the new technique. "The DNA (orchestra) remains the same, while the RNA pattern (quality of the music) changes in response to outside factors. The new technique is like hearing a symphony and deducing which instruments are in the orchestra, essentially unwinding the developmental process to trace tissue samples back to RNA and the gene that instructed it."
###
About The Mount Sinai Medical Center
The Mount Sinai Medical Center encompasses both The Mount Sinai Hospital and Mount Sinai School of Medicine. Established in 1968, Mount Sinai School of Medicine is one of the leading medical schools in the United States. The Medical School is noted for innovation in education, biomedical research, clinical care delivery, and local and global community service. It has more than 3,400 faculty in 32 departments and 14 research institutes, and ranks among the top 20 medical schools both in National Institutes of Health (NIH) funding and by U.S. News & World Report.
The Mount Sinai Hospital, founded in 1852, is a 1,171-bed tertiary- and quaternary-care teaching facility and one of the nation's oldest, largest and most-respected voluntary hospitals. In 2011, U.S. News & World Report ranked The Mount Sinai Hospital 16th on its elite Honor Roll of the nation's top hospitals based on reputation, safety, and other patient-care factors. Of the top 20 hospitals in the United States, Mount Sinai is one of 12 integrated academic medical centers whose medical school ranks among the top 20 in NIH funding and U.S. News & World Report and whose hospital is on the U.S. News & World Report Honor Roll. Nearly 60,000 people were treated at Mount Sinai as inpatients last year, and approximately 560,000 outpatient visits took place.
For more information, visit http://www.mountsinai.org/.
Find Mount Sinai on:
Facebook: http://www.facebook.com/mountsinainyc
Twitter @mountsinainyc
YouTube: http://www.youtube.com/mountsinainy
END
ELSE PRESS RELEASES FROM THIS DATE:
2012-04-10
Scientists at Trinity College Dublin have discovered that a part of the immune system called the inflammasome is involved in regulating the development of one of the most common forms of blindness, called Age-Related Macular Degeneration (AMD). They have discovered that controlling an inflammatory component IL-18, in cases of Age-Related Macular Degeneration (AMD) could prevent the development of the disease.
The disease AMD involves loss of central vision, people with advanced disease being unable to read, watch TV, enjoy the cinema, drive, or use a computer − ...
2012-04-10
VIDEO:
In their extraordinary quest to decode human metabolism, researchers at the Salk Institute for Biological Studies have discovered a pair of molecules that regulates the liver's production of glucose --...
Click here for more information.
In their extraordinary quest to decode human metabolism, researchers at the Salk Institute for Biological Studies have discovered a pair of molecules that regulates the liver's production of glucose---- the simple sugar that is the ...
2012-04-10
A major study of the relationships between maternal metabolic conditions and the risk that a child will be born with a neurodevelopmental disorder has found strong links between maternal diabetes and obesity and the likelihood of having a child with autism or another developmental disability.
Conducted by researchers affiliated with the UC Davis MIND Institute, the study found that mothers who were obese were 1-2/3 times more likely to have a child with autism as normal-weight mothers without diabetes or hypertension, and were more than twice as likely to have a child ...
2012-04-10
KANSAS CITY, MO—Cells on the move reach forward with lamellipodia and filopodia, cytoplasmic sheets and rods supported by branched networks or tight bundles of actin filaments. Cells without functional lamellipodia are still highly motile but lose their ability to stay on track, report researchers at the Stowers Institute for Medical Research in the April 9, 2012, online issue of the Journal of Cell Biology.
Their study provides new insight into cell motility, a complex and integrated process, which, when gone awry, can lead to various disease conditions such as cancer ...
2012-04-10
STANFORD, Calif. — Using computational methods, Stanford University School of Medicine investigators have strongly implicated a novel gene in the triggering of type-2 diabetes. Their experiments in lab mice and in human blood and tissue samples further showed that this gene not only is associated with the disease, as predicted computationally, but is also likely to play a major causal role.
In a study to be published online April 9 in Proceedings of the National Academy of Sciences, the researchers combed through freely accessible public databases storing huge troves ...
2012-04-10
Insulin is required for the regulation of blood sugar levels. In type I diabetes, the cells that produce insulin are destroyed by the immune system. Chantal Mathieu and colleagues at the University of Leuven have attempted to circumvent this response by taking advantage of the fact that the immune system accepts foreign gut bacteria. The Mathieu group engineered gut bacteria so that they produce a form of insulin, and asked if these bacteria could retrain the immune system in mice with type I diabetes to accept insulin-producing cells. They found that these special bacteria ...
2012-04-10
EDITOR'S PICK
Moving toward a better treatment for autoimmune diabetes
Insulin is required for the regulation of blood sugar levels. In type I diabetes, the cells that produce insulin are destroyed by the immune system. Chantal Mathieu and colleagues at the University of Leuven have attempted to circumvent this response by taking advantage of the fact that the immune system accepts foreign gut bacteria. The Mathieu group engineered gut bacteria so that they produce a form of insulin, and asked if these bacteria could retrain the immune system in mice with type I diabetes ...
2012-04-10
People with a history of high cholesterol who come from higher income countries or countries with lower out-of-pocket healthcare expenses, as well as those from countries with high performing healthcare systems, defined using World Health Organization (WHO) indices, tend to have lower subsequent cholesterol rates, according to new research in the American Heart Association journal Circulation.
"We found that patients living in countries in the highest third of gross national income or WHO health system achievement and performance/efficiency indices had a significantly ...
2012-04-10
CHICAGO – Patients for whom colonoscopy was recommended were less likely to complete colorectal cancer screening than those patients for whom fecal occult blood testing (FOBT) was recommended or those patients who were given a choice between FOBT or colonoscopy, according to a study published in the April 9 issue of Archives of Internal Medicine, a JAMA Network publication.
Colorectal cancer (CRC) is a prevalent condition that can be diagnosed through screening and treated during an asymptomatic phase to prevent the morbidity and mortality associated with the unscreened ...
2012-04-10
CHICAGO – Persistent ocular tremors that prevent eye stability during fixation appear to be common among patients with Parkinson disease (PD) suggesting that precise oculomotor testing could provide an early physiological biomarker for diagnosing PD, according to a report published Online First by Archives of Neurology, a JAMA Network publication.
"Although a number of studies describe various oculomotor abnormalities in subjects with PD, conflicts about the specific deficits remain," writes George T. Gitchel, M.S., of the Southeast Parkinson's Disease Research, Education, ...
LAST 30 PRESS RELEASES:
[Press-News.org] New 'genetic bar code' technique establishes ability to derive DNA information from RNA
Discovery may create dialogue about DNA and RNA data bank privacy issues
