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Long-lost correspondence trove illuminates DNA discovery
Posted on September 30th, 2010 No commentsSep 30, 2010 – usatoday.com
A long-lost stash of correspondence between key players in the discovery of the structure of DNA is revealed in the journal Nature this week.
The letters, postcards and ephemera are from the papers of Francis Crick, one of the co-discoverers of the structure of DNA, for which he won a shared Nobel prize in 1962. They had long been believed to be lost, “thrown away without my knowledge by an over-efficient secretary,” in Crick’s words
But actually they’d been mixed in with the papers of Sydney Brenner, another researcher at Cambridge University in the United Kingdom, during one of several moves of the researchers’ shared offices. They were discovered earlier this year when Alexander Gann and Jan Witkowski were going through them at the Cold Spring Harbor Laboratory Library, to which Brenner had donated his ‘papers.
Dating from 1950 to 1976, the trove includes over 30 letters. The correspondence gives an intimate portrait of the rivalries between researchers and laboratories, the forward lurch of scientific progress, the race to be first to publish and some fairly negative statements directed at Rosalind Franklin, an X-ray crystallographer whose contribution to the discovery of DNA’s structure has long been controversial.
As the labs are circling around the problem, Crick and James Watson, writing to Maurice Wilkins in 1951, says “…so cheer up and take it from us that even if we kicked you in the pants it was between friends.” The three ended up winning the prize jointly for the discovery.
When Franklin is getting ready to leave to work in a different research group in London in 1953, Wilkins wrote to Crick “I hope the smoke of witchcraft will soon be getting out of our eyes.”
In March of 1953, as three groups, Watson and Crick, Wilkins and Franklin, were readying manuscripts to publish in Nature about the discovery, Wilkins writes to Crick “I feel your remarks about Bruce’s model, in your note, not in very good style. Why be bitter about it?”
This trove of correspondence, while offering no earth-shattering revelations, helps flesh out the background of one of the most important discoveries in biology of the 20th century.
By Elizabeth Weise
DNAWellnessinfo.com Resource: http://content.usatoday.com/communities/sciencefair/post/2010/09/long-lost-correspondence-trove-illuminates-dna-discovery/1
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Cancer treatment found among junk DNA
Posted on September 27th, 2010 No commentsSeptember 27, 2010
AAP
Australian scientists have found a new and potent way to fight cancer among what was once thought of as junk DNA.
The experimental technique, proven to shrink tumours in mice, involves “microRNA”.
Dr Alex Swarbrick said this new class of genes was until recently considered to be junk DNA, the term used to describe the bulk of information contained in the genome that has no apparent purpose.
But far from being junk, he said one specific type of microRNA (microRNA 380) has been found to play a pivotal role in allowing certain types of cancer to grow.
Dr Swarbrick and his research colleagues also found that blocking the action of this microRNA in mice with neuroblastoma cancers caused their tumours to shrink.
“The revolutionary thing about this finding is that it’s the first time anyone has blocked the growth of a primary tumour by the simple delivery of a microRNA inhibitor…,” Dr Swarbrick, from Sydney’s Garvan Institute of Medical Research, said.
“That, of course, makes this microRNA a potential therapeutic target for all cancers that depend on it.”
The discovery points to a new way to combat cancer that could be as simple as a twice-weekly injection of a microRNA inhibitor.
MicroRNA 380 has its cancer-promoting effect on the body by disabling another gene (P53), which is known as the “guardian of the genome” because of its role in suppressing tumour growth.
Dr Swarbrick said the studies in mice showed how their P53 gene was disabled by “overproducing” microRNA 380.
He said this microRNA served a necessary purpose in embryos when cells needed to divide quickly and it should play no role in a “normal adult’s cells”.
It was not yet known why it could become active and with cancer-causing effects later in life.
“By blocking it, you’re effectively returning cells to normal,” Dr Swarbrick said.
“We still don’t know why it gets switched on again in certain cancers.
“(However) understanding that certain cancers appear to be regulated like this gives us a new avenue to explore in their treatment.”
Dr Swarbrick said the technique could also be applied to treat brain tumours as well as melanoma, which are known to be caused by a disabled P53 gene.
The research was conducted along with Brisbane-based Dr Susan Woods from the Queensland Institute of Medical Research, and a colleague in the US.
The results are reported in the journal Nature Medicine on Monday.
© 2010 AAP
DNAWellnessinfo.com Resource: http://news.smh.com.au/breaking-news-national/cancer-treatment-found-among-junk-dna-20100927-15sv8.html
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Zombie DNA Can Cause Muscular Dystrophy
Posted on August 19th, 2010 No commentsAugust 19, 2010, 4:24 PM vanityfair.comHere is something new and terrifying to worry about: zombie DNA. According to The New York Times, dead “junk” genes, basically thought to be dormant and harmless, are capable of becoming reanimated somehow and causing muscular dystrophy.We have lots of dead genes left over from the process of evolution; the Times likens them to “broken and useless junk” in an attic. But some of the genes can apparently come back from the dead and cause facioscapulohumeral muscular dystrophy, or FSHD, which causes muscles in the shoulders and face to become progressively weaker. In some people, having fewer than 10 repeated copies of one particular dead gene causes FSHD—no one with more than 10 copies of the gene gets the disease.
By way of explanation, geneticist and NIH director Dr. Francis Collins said, “The first law of the genome is that anything that can go wrong, will.” Well, that’s reassuring.
DNAWellnessinfo.com Resource: http://www.vanityfair.com/online/daily/2010/08/zombie-dna-can-cause-muscular-dystrophy.html
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Human cells can copy not only DNA, but also RNA, says team from Pitt, Helicos BioSciences
Posted on August 10th, 2010 No commentsscienceblog.com
by bjs on August 10, 2010
PITTSBURGH, Aug. 10 — Single-molecule sequencing technology has detected and quantified novel small RNAs in human cells that represent entirely new classes of the gene-translating molecules, confirming a long-held but unproven hypothesis that mammalian cells are capable of synthesizing RNA by copying RNA molecules directly. The findings were reported in Nature by researchers from the University of Pittsburgh School of Medicine, Helicos Biosciences Corp., Integromics Inc., and the University of Geneva Medical School.
“For the first time, we have evidence to support the hypothesis that human cells have the widespread ability to copy RNA as well as DNA,” said co-author Bino John, Ph.D., assistant professor, Department of Computational and Systems Biology, Pitt School of Medicine. “These findings emphasize the complexity of human RNA populations and suggest the important role for single-molecule sequencing for accurate and comprehensive genetic profiling.”
Scientists had thought that all RNA in human cells was copied from the DNA template, Dr. John explained. The presence of mechanisms that copy RNA into RNA, typically associated with an enzyme called RNA-dependent RNA polymerase, has only been documented in plants and simple organisms, such as yeast, and implicated in regulation of crucial cellular processes. Since thousands of such RNAs have been detected in human cells and because these RNAs have never before been studied, further research could open up new fronts in therapeutics, particularly diagnostics, Dr. John said.
In the study, the researchers profiled small RNAs from human cells and tissues, uncovering several new classes of RNAs, including antisense termini-associated short RNAs, which are likely derived from messenger RNAs of protein-coding genes by yet uncharacterized, pervasive RNA-copying mechanisms in human cancer cell lines.
“This class of non-coding RNA molecules has been historically overlooked because available sequencing platforms often are unable to provide accurate detection and quantification,” said Patrice Milos, Ph.D., chief scientific officer at Helicos Biosciences. “Our technology provides the platform capability to identify and quantify these RNAs and reinforces the potential clinical advantages of our single molecule-sequencing platform.”
Co-authors include A. Paula Monaghan, Ph.D., and Sang Woo Kim, Ph.D., University of Pittsburgh School of Medicine; Sylvain Foissac, Ph.D., Integromics Inc.; Stylianos Antonarakis, M.D., Ph.D., and Christelle Borel, Ph.D., University of Geneva Medical School; and Philipp Kapranov, Ph.D., and others from Helicos BioSciences.
The research was funded by the American Cancer Society, the National Institutes of Health, the Swiss National Science Foundation, Integromics Inc., and Helicos BioSciences Corporation.
DNAWellnessinfo.com Resource: http://scienceblog.com/37388/human-cells-can-copy-not-only-dna-but-also-rna-says-team-from-pitt-helicos-biosciences/
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DNA Mutation in c-Myb Gene linked to Leukaemia
Posted on August 10th, 2010 No commentsthglobalherald.com
Australian researchers have uncovered a novel DNA mutation in the c-Myb gene that may be linked to the development of leukaemia, breast and colon cancer.
A team led by Dr Peter Papathanasiou from the John Curtin School of Medical Research at The Australian National University and Associate Professor Andrew Perkins from the Institute for Molecular Bioscience at The University of Queensland completed a three-year screening project to find the genes that control the development and turnover of stem cells.
“We’ve shown that blood stem cells with this genetic mutation behave the same way as those present in human bone marrow diseases, including diseases that can evolve into leukaemia,” said Dr Papathanasiou, who is also affiliated with the Australian Phenomics Facility at ANU.
“By understanding more about the genetic blueprint of these kinds of disorders, we can start to develop new ways of targeting diseases,” Dr Perkins said.
“Currently, there is no treatment for this group of blood diseases, but the discovery of this mutation provides new avenues for investigation.”
As a result of the screening project, the researchers have also identified five other abnormal blood stem cell profiles, adding to understanding of the genetic diversity of blood cells. The project has also led to a better understanding of how blood cells develop and how this process becomes corrupted.
“Given that the same genes that operate in stem cells also function in cancer cells – albeit with genetic mutation – this research also has potential implications for regenerative medicine, by understanding how to stimulate the growth of new blood cells,” Dr Papathanasiou said.
The project was the first in the world to mutate the mammalian genome in a specific search for novel genetic regulators of stem cells.
The following is taken from the research paper’s abstract:
Here we demonstrate that chemical mutagenesis of mice combined with advances in hematopoietic stem cell reagents and genome resources can efficiently recover recessive mutations and identify genes essential for generation and proliferation of definitive hematopoietic stem cells and/or their progeny.
We employed high-throughput FACS to analyze nine subsets of blood stem cells, progenitor cells, circulating red cells and platelets in >1,300 mouse embryos at embryonic day (E) 14.5. From 45 pedigrees we recovered six strains with defects in definitive hematopoiesis.
We demonstrate rapid identification of a novel mutation in the c-Myb transcription factor that results in thrombocythemia and myelofibrosis as proof-of-principal of the utility of our FACS-based screen.
The work was made possible by grants from the National Health & Medical Research Council, the Leukaemia Foundation, and by the Australian Government’s National Collaborative Research Infrastructure Strategy to establish the Australian Phenomics Network.
Get the full paper by visiting: http://bloodjournal.hematologylibrary.org/cgi/content/abstract/blood-2010-04-269951v1
DNAWellnessinfo.com Resource: http://theglobalherald.com/science-dna-mutation-in-c-myb-gene-linked-to-leukaemia/5384/
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DNA Test May Speed Colon Cancer Diagnosis
Posted on August 9th, 2010 No commentsNICHOLAS WADE
Published: August 9, 2010
nytimes.comA new generation of DNA tests for colon cancer seems likely to improve the detection both of cancers and of the precancerous polyps that precede them. The tests, if validated, could reduce the burden of disease substantially by detecting tumors at an early stage, including those not picked up by a colonoscopy.
Colorectal cancers tend to grow slowly and are easily removed if caught early. But many people over 50 do not comply with the recommendation to have a colonoscopy — a time-consuming procedure in which a tube is threaded up the intestine — and even colonoscopies do not catch everything. Colorectal cancer has become the second most common cancer in the United States; each year it causes more than 50,000 deaths and costs about $14 billion to treat.
Colon tumors provide considerable evidence of their presence by shedding blood and cells that are detectable in the stool. Tests for blood have reduced deaths from colorectal cancer only modestly, because they are not very sensitive to precancerous polyps, the stage at which cancer is best prevented.
Researchers turned to measuring mutations in DNA after Dr. Bert Vogelstein of Johns Hopkins University discovered the series of mutations by which a colon polyp advances to full cancer. But no single mutation predicts a patient’s risk, and the mutation tests, though more accurate than the blood tests, have not been a decisive improvement.
By 2004 it was clear that looking for the Vogelstein mutations was “neat biology but not a home run,” said Dr. David Ransohoff, an expert on colon cancer screening at the University of North Carolina.
A new generation of tests being developed depends on a different process in cancer cells. All cells switch off the genes they do not need by attaching small chemicals called methyl groups to certain sites along their DNA. In cancer cells, there is generally less methylation than usual, except for certain regions of DNA where the methylation process is taken to excess, perhaps because the cells need to shut down tumor suppressor genes. These and other genes are highly methylated in colon tumors and other kinds of cancer.
Exact Sciences, a company based in Madison, Wis., is developing a colon cancer test based on highly methylated DNA. Its researchers reported last month that by testing for methylated DNA at four markers, pieces of DNA drawn from specific genes, they could detect colon tumors and polyps, distinguishing them from normal tissue with 100 percent sensitivity and with no false positives.
The tests of methylated DNA were performed directly on tumors and are expected to be less accurate in the real world, in which they would have to work in stool samples. Almost all of the DNA in stool is from bacteria, and the methylated DNA is a fraction of the 0.01 percent that is human DNA.
Still, Kevin T. Conroy, chief executive of Exact Sciences, said he expected that the four-marker test, when applied to stool samples, would detect at least half of all precancerous polyps and 85 percent of actual cancers. Results of a trial now under way in 1,600 patients will be reported in October, he said.
The test would cost less than $300, and samples could be collected at home. Patients would be advised to take the test every three years. People with a positive result would then have a colonoscopy to verify and remove any polyps, with the result that colonoscopies could be focused on high-risk patients instead of the population at large.
Exact Sciences’ test is based on work by Dr. Vogelstein, Dr. Sanford Markowitz at Case Western Reserve University and Dr. David A. Ahlquist of the Mayo Clinic. Dr. Ahlquist, who is a scientific adviser to the company, identified some of the highly methylated genes the company is testing as markers for colon cancer.
Dr. Ahlquist said that if the test worked as well as hoped on stool samples, “this will be the first noninvasive test that will reliably detect malignant lesions.” Cervical cancer has been virtually eliminated by the Pap test, he said, and “we feel that colon cancer could be eliminated to the same extent.”
The four-marker test can pick up a kind of precancerous tissue called a serrated polyp which is often missed by colonoscopies, Dr. Ahlquist said. It also ignores most innocuous small polyps.
Using different sets of four markers, other kinds of cancer can be detected. “We can detect all of the cancers above the colon — pancreas, esophagus, stomach, bile duct,” Dr. Ahlquist said. Thus in principle, all the cancers of the gastrointestinal tract, which account for nearly a quarter of all cancer deaths in the United States, should be detectable from stool samples.
Dr. Vogelstein said tests for DNA mutations would be better in theory than tests for DNA methylation because “mutations are entirely specific and they are what is driving the tumor”; the methylation is less causative and increases naturally with age.
But the DNA methylation tests are promising in principle, he said, and it seems feasible for Exact Sciences to get a sensitivity of better than 90 percent and a false positive rate of only 5 to 10 percent. “We can tolerate 5 to 10 percent false positives because those people will just get colonoscopies,” he said.
For cancers above the colon, there are many enzymes that digest DNA, so whether such cancers can be detected efficiently can be answered only with experiments, Dr. Vogelstein said. And false positives would be more of a problem, since for these cancers there is no easy verification method like colonoscopy. “That’s when these false positives really start to be the devil,” he said.
Dr. Ransohoff said the Exact Sciences test was still at a preliminary point. “This is neat and it’s promising,” he said. “But we’ve been down this road before and we need to be hopeful without being carried away.”
DNAWellnessinfo.com Resource: http://www.nytimes.com/2010/08/10/health/10cancer.html?_r=1
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How DNA Evidence Works
Posted on August 8th, 2010 No commentshowstuffworks.com
he CBS drama “CSI: Crime Scene Investigation” routinely draws more than 20 million viewers per episode, making it one of television’s greatest successes. The show’s popularity owes a great deal to the writers and actors who bring the stories to life. But another intriguing element is the cutting-edge technology used by the Las Vegas crime lab trying to solve crimes. Collecting and analyzing DNA evidence tops the list of the lab’s forensic toolkit, and its ubiquity in shows like “CSI” and “Cold Case” has increased public awareness to the point that many jurors in real-world courtrooms expect to see DNA evidence presented — whether a case calls for it or not.It’s hard to believe that DNA evidence has come so far so fast. The techniques that make it possible to identify a suspect using his or her unique genetic blueprint have only been around since 1985. That’s when Alec Jeffreys and his colleagues in England first demonstrated the use of DNA in a criminal investigation. Since then, DNA evidence has played a bigger and bigger role in many nations’ criminal justice systems. It has been used to prove that suspects were involved in crimes and to free people who were wrongly convicted. And, in the United States, it has been integral to several high-profile criminal cases.At the heart of DNA evidence is the biological molecule itself, which serves as an instruction manual and blueprint for everything in your body (see How Cells Work for details). A DNA molecule is a long, twisting chain known as a double helix. DNA looks pretty complex, but it’s really made of only four nucleotides:
- Adenine
- Cytosine
- Guanine
- Thymine
These nucleotides exist as base pairs that link together like the rungs in a ladder. Adenine and thymine always bond together as a pair, and cytosine and guanine bond together as a pair. While the majority of DNA doesn’t differ from human to human, some 3 million base pairs of DNA (about 0.10 percent of your entire genome) vary from person to person.
In human cells, DNA is tightly wrapped into 23 pairs of chromosomes. One member of each chromosomal pair comes from your mother, and the other comes from your father. In other words, your DNA is a combination of your mother’s and your father’s DNA. Unless you have an identical twin, your DNA is unique to you.
This is what makes DNA evidence so valuable in investigations — it’s almost impossible for someone else to have DNA that is identical to yours. But catching a criminal using DNA evidence is not quite as easy as “CSI” makes it seem, as this article will demonstrate. Our first step in exploring DNA evidence is the crime scene — and the biological evidence gathered there by detectives.
DNA Analysis: Specialized Techniques
Although most labs use either RFLP or STR techniques for their DNA analysis, there are situations that require a different approach. One such situation is when there are multiple male contributors of genetic material, which sometimes happens in sexual assault cases. The best way to resolve the complex mixture and sort out exactly which men were involved is Y-marker analysis. As its name suggests, this technique examines several genetic markers found on the Y chromosome. Because the Y chromosome is transmitted from a father to all his sons, DNA on the Y chromosome can be used to identify DNA from different males. Y-marker analysis can also be used to trace family relationships among males.
Another situation involves identifying old remains or biological evidence lacking nucleated cells, such as hair shafts, bones and teeth. RFLP and STR testing can’t be used on these materials because they require DNA found in the nucleus of a cell. In these cases, investigators often use mitochondrial DNA (mtDNA) analysis, which uses DNA from a cell’s mitochondria. Investigators have found mtDNA testing to be very useful in solving cold cases, which are murders, missing-person cases or suspicious deaths that are not being actively investigated. Cold cases often have biological evidence in the form of blood, semen and hair that has been stored for a long time or improperly stored. Submitting those degraded samples for mtDNA testing can sometimes break the case open and help detectives find the perpetrator.
A relatively new technique — SNP analysis — is also useful in certain cases where forensic labs are presented with highly degraded DNA samples. This technique requires that scientists analyze variations in DNA where one nucleotide replaces another. Such a genetic change is called a single nucleotide polymorphism, or SNP (pronounced “snip”). SNPs make excellent markers and are most often used to determine a person’s susceptibility to a certain disease. But forensics labs turn to SNP analysis on occasion. For example, forensic scientists used SNP technology successfully to identify several Sept. 11 World Trade Center victims for whom other methods had failed.
In reality, analyzing a DNA sample is just a first step. Up next, we’ll take a look at what happens after the analysis is complete.
Matching DNA
The main objective of DNA analysis is to get a visual representation of DNA left at the scene of a crime. A DNA “picture” features columns of dark-colored parallel bands and is equivalent to a fingerprint lifted from a smooth surface. To identify the owner of a DNA sample, the DNA “fingerprint,” or profile, must be matched, either to DNA from a suspect or to a DNA profile stored in a database.
Let’s consider the former situation — when a suspect is present. In this case, investigators take a DNA sample from the suspect, send it to a lab and receive a DNA profile. Then they compare that profile to a profile of DNA taken from the crime scene. There are three possible results:
- Inclusions — If the suspect’s DNA profile matches the profile of DNA taken from the crime scene, then the results are considered an inclusion or nonexclusion. In other words, the suspect is included (cannot be excluded) as a possible source of the DNA found in the sample.
- Exclusions — If the suspect’s DNA profile doesn’t match the profile of DNA taken from the crime scene, then the results are considered an exclusion or noninclusion. Exclusions almost always eliminate the suspect as a source of the DNA found in the sample.
- Inconclusive results — Results may be inconclusive for several reasons. For example, contaminated samples often yield inconclusive results. So do very small or degraded samples, which may not have enough DNA to produce a full profile.
Sometimes, investigators have DNA evidence but no suspects. In that case, law enforcement officials can compare crime scene DNA to profiles stored in a database. Databases can be maintained at the local level (the crime lab of a sheriff’s office, for example) or at the state level. A state-level database is known as a State DNA index system (SDIS). It contains forensic profiles from local laboratories in that state, plus forensic profiles analyzed by the state laboratory itself. The state database also contains DNA profiles of convicted offenders. Finally, DNA profiles from the states feed into the National DNA Index System (NDIS).
To find matches quickly and easily in the various databases, the FBI developed a technology platform known as the Combined DNA Index System, or CODIS. The CODIS software permits laboratories throughout the country to share and compare DNA data. It also automatically searches for matches. The system conducts a weekly search of the NDIS database, and, if it finds a match, notifies the laboratory that originally submitted the DNA profile. These random matches of DNA from a crime scene and the national database are known as “cold hits,” and they are becoming increasingly important. Some states have logged thousands of cold hits in the last 20 years, making it possible to link otherwise unknown suspects to crimes.
Using DNA Evidence Beyond the Courtroom
DNA evidence plays a pivotal role in the modern criminal justice system, but the same techniques that prove guilt or exonerate an innocent person are just as useful outside the courtroom. Here are a few examples:
- Paternity testing and other cases where authorities need to prove whether individuals are related or not — One of the more infamous paternity cases of late occurred after Anna Nicole Smith’s death in 2007. Five different men claimed to be the father of Smith’s baby daughter, Dannielynn. After a DNA test, Larry Birkhead was proven to be the child’s father.
- Identification of John or Jane Does — Police investigators often face the unpleasant task of trying to identify a body or skeletal remains. DNA is a fairly resilient molecule, and samples can be easily extracted from hair or bone tissue. Once a DNA profile has been created, it can be compared to samples from families of missing persons to see if a match can be made. The military even uses DNA profiles in place of the old-school dog tag. Each new recruit must provide blood and saliva samples, and the stored samples can subsequently be used as a positive ID for soldiers killed in the line of duty. Even without a DNA match to identify a body conclusively, a profile is useful because it can provide important clues about the victim, such as his or her sex and race.
- Studying the evolution of human populations — Scientists are trying to use samples extracted from skeletons and from living people around the world to show how early human populations might have migrated across the globe and diversified into so many different races. In the 1980s, scientists at the University of California, Berkeley, used mitochondrial DNA analysis to speculate that all living humans are related to a single woman — “Eve” — who lived roughly 150,000 years ago in Africa. Other scientists, using increasingly more sensitive DNA analysis, have since confirmed this to be true.
- Studying inherited disorders — Scientist also study the DNA fingerprints of families with members who have inherited diseases like Alzheimer’s disease to try to ferret out chromosomal differences between those without the disease and those who have it, in the hope that these changes might be linked to getting the disease.DNA testing can also reveal a person’s susceptibility to certain diseases. Several companies, such as 23andMe, deCODEme and Navigenics, offer at-home genetics tests that can evaluate your risk for hundreds of diseases and traits, including breast cancer, rheumatoid arthritis and Type 2 Diabetes.
- Catching poachers — Wildlife biologists are now turning to DNA tests to catch people who hunt illegally. For example, the hunting season for doe on public lands lasts only two days in many states. If a wildlife official suspects a hunter has shot a female deer after the official close of the season, he can analyze DNA from the meat and determine the species and gender of the animal.
- Clarifying history — Historians are turning to DNA evidence to learn more about the past. For example, Y-chromosome testing was used in 1998 to determine whether Thomas Jefferson, the third president of the United States, fathered children with one of his slaves or not. And in May 2009, a group of historians asked a Philadelphia museum if they could have access to a strip of a pillowcase stained with the blood of Abraham Lincoln. Their goal was to analyze Lincoln’s DNA to see if he suffered from a rare genetic cancer syndrome called multiple endocrine neoplasia type 2B, but the museum’s board would not allow the test at the time.
Limitations of DNA Evidence
DNA evidence is powerful, but it does have limitations. One limitation is related to misconceptions about what a DNA match really means. Matching DNA from a crime scene to DNA taken from a suspect is not an absolute guarantee of the suspect’s guilt. Instead, forensic experts prefer to talk about probability. For example, they might make a statement like this: The chance is 1/7,000 that an unrelated person would by chance have the same DNA profile as that obtained from the evidence. Combine that statistical analysis with other evidence, and you can see how prosecutors can make strong cases against a suspect.
A contributing factor to public misconception is how DNA analysis is portrayed in movies and television. Some lawyers and judges complain that a so-called “CSI effect” is influencing criminal justice. The CSI effect manifests itself when jurors demand DNA tests in cases where they are unnecessary or rely too heavily on DNA evidence to the exclusion of other physical evidence taken at a crime scene.
Even more troubling are cases of DNA fraud — instances where criminals plant fake DNA samples at a crime scene. In 1992, Canadian physician John Schneeberger planted fake DNA evidence in his own body to avoid suspicion in a rape case. Planting fake DNA obtained from someone else is only part of the problem. Scientists at Nucleix, an Israeli company, recently reported that they could, with access to profiles stored in one of the DNA databases, manufacture a sample of DNA without obtaining any tissue from that person.
Nucleix has developed a test to distinguish real DNA samples from fake ones, with the goal of selling the test to forensic laboratories. But taking these extra precautions to ensure the validity of its results will only slow down busy labs even more. In fact, forensic casework backlogs are becoming a serious problem. A study conducted by the Bureau of Justice Statistics found that more than half a million cases were backlogged in forensic labs, which means felons and other violent offenders could be walking the streets while their DNA evidence sits in a queue, waiting to be tested [source: Houck].
As advances in DNA testing are made, some of these challenges may become less severe. But other, unforeseen challenged will likely emerge. Up next, we’ll examine some of these advances and their implications.
Collecting DNA Evidence
For many years, fingerprints were the gold standard for linking suspects to a crime scene. Today, the gold standard is DNA evidence because DNA can be collected from virtually anywhere. Even a criminal wearing gloves may unwittingly leave behind trace amounts of biological material. It could be a hair, saliva, blood, semen, skin, sweat, mucus or earwax. All it takes is a few cells to obtain enough DNA information to identify a suspect with near certainty.
For this reason, law enforcement officials take unusual care at crime scenes. Police officers and detectives often work closely with laboratory personnel or evidence collection technicians to make sure evidence isn’t contaminated. This involves wearing gloves and using disposable instruments, which can be discarded after collecting each sample. While collecting evidence, officers are careful to avoid touching areas where DNA evidence could exist. They also avoid talking, sneezing and coughing over evidence or touching their face, nose or mouth.
The following list shows some common sources of DNA evidence:
- A weapon, such as a baseball bat, fireplace poker or knife, which could contain sweat, skin, blood or other tissue
- A hat or mask, which could contain sweat, hair or dandruff
- A facial tissue or cotton swab, which could contain mucus, sweat, blood or earwax
- A toothpick, cigarette butt, bottle or postage stamp, all of which could contain saliva
- A used condom, which could contain semen or vaginal or rectal cells
- Bed linens, which could contain sweat, hair, blood or semen
- A fingernail or partial fingernail, which could contain scraped-off skin cells
When investigators find a piece of evidence, they place it in a paper bag or envelope, not in a plastic bag. This is important because plastic bags retain moisture, which can damage DNA. Direct sunlight and warmer conditions may also damage DNA, so officers try to keep biological materials at room temperature. They label the bags with information about what the material is, where it was found and where it will be transported. These are chain-of-custody procedures, which ensure the legal integrity of the samples as they move from collection to analysis.
Analysis occurs in a forensic laboratory, the topic of our next section.
DNA Analysis: Traditional Techniques
From the crime scene, a piece of DNA evidence travels to a forensic laboratory. These labs vary quite a bit, both in terms of how they are structured and what kind of analyses they offer. Public laboratories are often associated with a law enforcement entity or the district attorney’s office, while others are independent government entities. Private forensic laboratories, some dedicated just to DNA analysis, also exist.
Many labs have the ability to conduct testing on nuclear DNA, which is the copy of DNA that exists in the nucleus of every cell. But only a few labs offer more specialized techniques, such as Y-chromosome or mitochondrial DNA analysis. Let’s look at some of these techniques in greater detail.
Restriction fragment length polymorphism (RFLP) analysis was one of the first forensic methods used to analyze DNA. It analyzes the length of strands of DNA that include repeating base pairs. These repetitions are known as variable number tandem repeats (VNTRs) because they can repeat themselves anywhere from one to 30 times.
RFLP analysis requires investigators to dissolve DNA in an enzyme that breaks the strand at specific points. The number of repeats affects the length of each resulting strand of DNA. Investigators compare samples by comparing the lengths of the strands. RFLP analysis requires a fairly large sample of DNA that hasn’t been contaminated with dirt.
Many laboratories are replacing RFLP analysis with short tandem repeat (STR) analysis. This method offers several advantages, but one of the biggest is that it can start with a much smaller sample of DNA. Scientists amplify this small sample through a process known as polymerase chain reaction, or PCR. PCR makes copies of the DNA much like DNA copies itself in a cell, producing almost any desired amount of the genetic material.
Once the DNA in question has been amplified, STR analysis examines how often base pairs repeat in specific loci, or locations, on a DNA strand. These can be dinucleotide, trinucleotide, tetranucleotide or pentanucleotide repeats — that is, repetitions of two, three, four or five base pairs. Investigators often look for tetranucleotide or pentanucleotide repeats in samples that have been through PCR amplification because these are the most likely to be accurate.
The Federal Bureau of Investigation (FBI) has chosen 13 specific STR loci to serve as the standard for DNA analysis. The likelihood that any two individuals (except identical twins) will have the same 13-loci DNA profile can be as high as 1 in 1 billion or greater.
Advances in DNA Evidence
In 1985, DNA entered the courtroom for the first time as evidence in a trial, but it wasn’t until 1988 that DNA evidence actually sent someone to jail. This is a complex area of forensic science that relies heavily on statistical predictions. In early cases where jurors were hit with reams of evidence heavily laden with mathematical formulas, it was easy for defense attorneys to create doubt in jurors’ minds. Since then, a number of advances have allowed criminal investigators to perfect the techniques involved and face down legal challenges to DNA fingerprinting. Improvements include:
- New testing procedures — RFLP analysis required large amounts of relatively high-quality DNA. Newer procedures require far less DNA and can be completed faster.
- Source of DNA — Science has devised ingenious ways of extracting DNA from sources that used to be too difficult or too contaminated to use. And in some cases, detectives are using DNA analysis in ingenious ways to get a conviction. For example, detectives in Phoenix, Ariz., were able to link a suspect to a murder victim by testing the DNA of a palo verde tree found at the crime scene. Palo verde trees feature pods containing seeds. Some of these pods were found in the suspect’s truck. To prove that the pods came from the tree found at the crime scene and not some other palo verde tree, detectives turned to DNA analysis. The pods found in the truck matched each other — and matched the pods taken from the tree at the crime scene. It was the first time the DNA fingerprint of a plant was used in a criminal trial.
- Expanded DNA databases — The databases managed by the CODIS software continue to expand. Prior to 2006, only convicted felons were required to have their DNA profiles entered into the database. But a January 2006 law, which was signed by President Bush and funded in 2008, has expanded collection of DNA samples beyond convicts to include federal arrestees, as well as suspected illegal immigrants or captives in the war on terrorism. Justice officials estimate the new collecting requirements will add DNA from an additional 1.2 million people to the database each year [source: UPI].
- Training — Crime labs have developed formal protocols for handling and processing evidence, reducing the likelihood of contamination of samples. On the courtroom side, prosecutors have become savvier at presenting genetic evidence, and many states have come up with specific rules governing its admissibility in court cases. See How CSI Works for more details.
The advances that have made DNA evidence an invaluable tool in the criminal justice system have also galvanized public interest. Classroom study of DNA and its properties has become more in-depth and widespread in many schools. And television crime dramas that feature DNA evidence so prominently continue to flourish. All of that awareness brings good news and bad news, but the real bad news is reserved for criminals, who will find it increasingly difficult to leave a crime scene without leaving a piece of incriminating biological evidence behind.
DNAWellnessinfo.com Resource: http://science.howstuffworks.com/environmental/life/genetic/dna-evidence.htm
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Listen to Consumer DNA Test Company Sales Reps Behaving Badly!
Posted on July 23rd, 2010 No commentsWSJ’s blog on health and the business of health – July 23, 2010, 11:30 AM ET
By Katherine Hobson
Direct-to-consumer genetic-testing companies were in the hot seat this week, with scrutiny from both the FDA and Congress. Fodder for some of the discussion was a new GAO report that focused on the scientific accuracy and marketing efforts of tests by companies including 23andMe, Pathway Genomics, deCODE genetics and Navigenics.
You can read about the GAO report in this story from today’s WSJ. And here’s the GAO report itself.
Investigators from the independent agency, which works on behalf of Congress, sent DNA samples for assessment of the risk of different diseases and conditions. The report found analyses of the same samples varied, in many cases wildly; the companies say they use different genetic markers, which means results won’t be uniform — though some agreed that there is a need for some common standards.
But for some Friday fun, listen to or read the transcripts of undercover calls to unnamed genetic-testing companies made by GAO investigators. (Undercover contact was made with 15 companies, including the four listed above.)
One fake customer asked a company rep, “So if I’m high risk, does that mean I’ll definitely get breast cancer?”
Rep: “You … you’d be in the high risk of, you know, pretty much getting it so …”
(The GAO notes these tests are not diagnostic and that this company didn’t even test for the BRCA gene variations that are linked to a higher chance — but by no means a certainty — of getting breast cancer. Experts consulted by the GAO called the rep’s response “horrifying.”)
Another marketing rep told a fake customer that “we can repair DNA damage.”
Fake customer: “You can, really?”
Rep: “Oh yeah, it’s called epigenetics and …”
Fake customer: “That’s repairing DNA?”
Rep: “Yeah … The genes are considered now not to be the source of our biology, they’re a symptom.”
(Experts told the GAO there was “no scientific basis for these claims.”)
The transcript also features company reps agreeing to process a DNA sample obtained surreptitiously, for a “surprise” analysis ordered by a woman for her fiancé (in most states, that’s an illegal breach of privacy); falsely claiming Lance Armstrong as a celebrity endorser, and claiming supplements can cure disease.
DNAWellnessinfo.com Resource: http://blogs.wsj.com/health/2010/07/23/listen-to-consumer-dna-test-company-sales-reps-behaving-badly/
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Urine in Public Pools Could Cause Cell Damage
Posted on July 22nd, 2010 No commentsfoxnews.com
Thursday, July 22, 2010Public swimming pools are more dangerous than you might think, a new study suggests. When sweat and urine, among other organics, mix with the disinfectants in pool water, the result can be hazardous to health.
The findings, announced this week, link the application of disinfectants in recreational pools to genetic cell damage that has been shown to be linked with adverse health outcomes such as asthma and bladder cancer.
Pool water represents extreme cases of disinfection that differ from the disinfection of drinking water as pools are continuously exposed to disinfectants. But with so many people cooling off and exercising in pools and water parks (339 million visits across the United States each year), the disinfectants are a must to prevent outbreaks of infectious disease.
Chlorine and Pee Don’t Mix
The problem occurs when the sanitizers mix with organic matter.
“All sources of water possess organic matter that comes from decaying leaves, microbes and other dead life forms,” said study researcher Michael Plewa, University of Illinois professor of genetics. “In addition to organic matter and disinfectants, pool waters contain sweat, hair, skin, urine and consumer products such as cosmetics and sunscreens from swimmers.”
These consumer products are often nitrogen-rich, and when mixed with disinfectants, these products may become chemically modified and converted into more toxic agents.Long-term exposure to these disinfection byproducts can mutate genes, induce birth defects, accelerate the aging process, cause respiratory ailments, and even induce cancer, according to the researchers. While the new study did not examine actual effects on humans, it suggests such research might be warranted.
Pool Samples
In this study, researchers evaluated water samples from public pools and a control sample of tap water. They tested whether the byproduct chemicals in the samples could induce gene mutations using a so-called systematic mammalian cell genotoxicity analysis.
This sensitive DNA technology can detect genomic damage in mammalian cells, allowing researchers to investigate damage at the level of each nucleus within each cell.
Results proved that all disinfected pool samples had more genomic DNA damage than the source tap water, Plewa said.
The findings are published in the journal Environmental Science & Technology. The work was supported by grants from the National Science Foundation.
Cleaner PoolsAll this doesn’t mean you need to ditch your pool plans. Plewa offers recommendations for pool operators and swimmers to reduce hazardous chemicals and make for safer pool water.
“Care should be taken in selecting disinfectants to treat recreational pool water,” Plewa advised.
“The data suggest that brominating agents should be avoided as disinfectants of recreational pool water. The best method
to treat pool waters is a combination of UV treatment with chlorine as compared to chlorination alone.”In addition, organic carbon should be removed prior to disinfection when the pool water is being recycled, Plewa said.
Swimmers can also help by showering before entering the water, which would mean fewer organics and so reduce the genotoxicity of the pool water. One recommendation that may seem obvious: Don’t pee in the pool. Plewa suggests pool owners remind patrons about the potential harm caused by urinating in a pool.
DNAWellnessinfo.com Resource: http://www.foxnews.com/story/0,2933,597467,00.html
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Human Genome Project will live up to its potential: NIH director
Posted on July 11th, 2010 No commentsEnglish.news.cn 2010-07-06 05:51:08
By Xinhua writer Ren Haijun
WASHINGTON, July 5 (Xinhua) — A decade after the historic completion of the “book of life” — the first blueprint of human DNA, the benefits of the Human Genome Project still lie ahead. However, Francis Collins, director of the U.S. National Institute of Health (NIH), is “confident” the project will live up to its potential.
“The First Law of Technology states that a truly transformational discovery will always have its immediate consequences overestimated — and its long-term consequences, underestimated. That certainly is turning out to be true from what we are learning about the human genome sequence!” Collins told Xinhua in an interview.
“The greatest significance of the Human Genome Project is the door that it has opened into the vast and complex landscape of human biology,” Collins said. “Exploring this landscape in a way that benefits human health will require creative thinking and hard work by researchers in the United States, China, and everywhere else around the globe.”
Collins, noted for his leadership of the project, thought having the complete sequence of the human genome is similar to having all the pages of an instruction manual needed to make the human body.
“Thanks to the sequencing of the human genome, we have much more powerful tools to study the role that genetic factors play in more complex diseases, such as cancer, diabetes, and heart disease, and even in susceptibility to infectious diseases, such as acquired immunodeficiency syndrome (AIDS),” he said. “Genomic sequencing has facilitated the diagnosis of genetic conditions, ranging from very rare to quite common. It is shedding new light on the process of aging and providing tantalizing clues to the secrets of longevity. If we fully understand this instruction manual, it could become the most powerful textbook of medicine imaginable!”
The famous U.S. physician-geneticist thought cancer is one category of disease in which he expects genomic research to have a major impact in the near future.
Cancer is caused by changes in a cell’s genome. However, the pattern of these genomic changes varies among different types of cancer — and even among subsets of patients with the same cancer. So, it is important to produce genomic classification systems for many types and subtypes of cancer.
In the United States, the NIH is supporting an effort to build comprehensive catalogs of the key genomic changes in 20 major types and subtypes of cancer. This project, called The Cancer Genome Atlas, is working collaboratively with researchers in China and elsewhere around the world through the International Cancer Genome Consortium. The information generated by such research is already proving useful in developing new cancer therapies, as well as in matching individual cancer patients with the therapies most likely to work for them.
However, Collins warned that amid all the excitement over the promise of genomics research, we need to remember that genes do not operate in a vacuum. There are other important factors that influence people’s risk of developing most common diseases. These factors include smoking, diet, exercise, and exposure to pollution.
“Unless we as humans dramatically change our lifestyles and our environment, I do not see a future in which all common diseases are completely prevented or eradicated,” he said.
Collins, a supporter of free access to human genome sequencing data, thought human genetic information should be kept in the public domain to allow researchers to analyze it and to give members of the public fair access to medical treatments.“From the outset, the Human Genome Project and the international endeavors that built upon its foundation, such as the International HapMap Project and 1,000 Genomes Project, have made all their data rapidly available to scientists around the globe,” he said. “In many ways, this is one of the most significant legacies of the Human Genome Project — and one that gives me hope that worldwide research community will come up with innovative ways to use this treasure trove of information to fight disease.”
Collins thought there are two major challenges associated with the application of sequencing technologies. The first is lowering the cost of DNA sequencing. “We’ve made dramatic progress in that area over the past 10 years. The cost of sequencing the first human genome was about 400 million dollars. Today, the cost of sequencing one genome is about 9,500 dollars, and we expect that cost to fall to 1,000 dollars or less within the next four or five years.”
The second, perhaps even bigger, challenge is figuring out how to analyze the tidal wave of data being generated by genomic sequencing and then translate those findings in ways that benefit patients in the clinic. However, “this is a challenge that can be met if we pull together the best minds in biology, medicine, statistics, and computer science.”
Collins also thought the completion of the human genome sequence was just the beginning of the effort to understand how all the parts of the genome work together to contribute to health and disease.
“Genomic research is not a sprint, it is a marathon that requires sustained commitment over a long period of time to yield maximum success,” he said.
DNAWellnessinfo.com Resource: http://news.xinhuanet.com/english2010/sci/2010-07/06/c_13384897.htm
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