Category Archives: DNA

PUBLIC RELEASE DATE:

3-Nov-2013

Contact: Rachel Steinhardt rsteinhardt@licr.org 212-450-1582 Ludwig Institute for Cancer Research

November 3, 2013, New York, NY and San Diego, Calif. A new technique successfully takes on a longstanding challenge in DNA sequencing determining whether a particular genetic sequence comes from an individual's mother or father. The method, described in a Ludwig Cancer Research study in Nature Biotechnology, promises to accelerate studies of how genes contribute to disease, improve the process of matching donors with organs and help scientists better understand human migration patterns.

"The technique will enable clinicians to better assess a person's individual risk for disease. It is potentially transformative for personalized medicine," says Bing Ren, Ludwig scientist at the University of California, San Diego School of Medicine, who led the research on the new technique, called "HaploSeq."

"Current sequencing technologies are fast and rapidly getting cheaper an individual's genome can now be sequenced in about a week for $5,000," says Ren. "In the not too distant future, everyone's genome will be sequenced. That will become the standard of care." But, he explains, "There has been a problem with this scenario." Except for the sex chromosomes, everyone has two copies of each chromosome. One copy comes from mom, and the other from dad. Current techniques cannot distinguish between the two copies of each gene and, therefore, are not very good at determining whether particular genetic differences, such as a single-letter change in the DNA, originate with an individual's mother or father muddying genetic analyses.

Ren's new technique, a mixture of molecular biology and computational biology approaches, bypasses this problem. The method enables researchers to quickly determine which genetic variants occur together on the same stretch of chromosome and, therefore, came from the same parent. "This advance has direct implications for the utility of genomics in clinical practice and will also have profound effects on genetic research and discovery," says Ludwig scientist Siddarth Selvaraj, who contributed to the study with Ren and fellow Ludwig researcher Jesse Dixon.

More immediately, the technique will enable clinicians to better assess a person's individual risk for disease, a cornerstone of personalized medicine. For instance, people at risk for a disease such as cancer often have more than one DNA mutation. HaploSeq could enable clinicians to determine if the two mutations are on the same chromosome or on different chromosomes, which can help in risk assessment for instance, risk may be reduced if two mutations are on the same chromosome, since the 'good' chromosome can often compensate.

Similarly, the method, with further honing, has the potential to refine the currently cumbersome process of determining whether there is a genetic match between an organ donor and recipient. A large number of genes contribute to compatibility between donor and recipient, but there is a lot of genetic variability in these genes. The new technique could help determine whether DNA differences between donor and recipient are likely to be a good match. "This will require more study," says Ren, "but by creating a DNA database, it may be possible to more accurately and expediently pair recipients and donors."

The new method will also help researchers analyze human migration and determine ancestry from their DNA sequences. "In principal," says Ren, "you could compare your genetic sequence to your neighbor's and ask if you have any recent ancestors in common. With our technique we can study each individual and how they relate to other individuals. As we accumulate data from many individuals we can more precisely determine their relationships." Such findings will also bolster an ongoing international project to assess worldwide human genetic variation, the HapMap project.

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Is DNA from mom or dad?

Nov. 3, 2013 A new technique successfully takes on a longstanding challenge in DNA sequencing -- determining whether a particular genetic sequence comes from an individual's mother or father. The method, described in a Ludwig Cancer Research study in Nature Biotechnology, promises to accelerate studies of how genes contribute to disease, improve the process of matching donors with organs and help scientists better understand human migration patterns.

"The technique will enable clinicians to better assess a person's individual risk for disease. It is potentially transformative for personalized medicine," says Bing Ren, Ludwig scientist at the University of California, San Diego School of Medicine, who led the research on the new technique, called "HaploSeq."

"Current sequencing technologies are fast and rapidly getting cheaper -- an individual's genome can now be sequenced in about a week for $5,000," says Ren. "In the not too distant future, everyone's genome will be sequenced. That will become the standard of care." But, he explains, "There has been a problem with this scenario." Except for the sex chromosomes, everyone has two copies of each chromosome. One copy comes from mom, and the other from dad. Current techniques cannot distinguish between the two copies of each gene and, therefore, are not very good at determining whether particular genetic differences, such as a single-letter change in the DNA, originate with an individual's mother or father -- muddying genetic analyses.

Ren's new technique, a mixture of molecular biology and computational biology approaches, bypasses this problem. The method enables researchers to quickly determine which genetic variants occur together on the same stretch of chromosome and, therefore, came from the same parent. "This advance has direct implications for the utility of genomics in clinical practice and will also have profound effects on genetic research and discovery," says Ludwig scientist Siddarth Selvaraj, who contributed to the study with Ren and fellow Ludwig researcher Jesse Dixon.

More immediately, the technique will enable clinicians to better assess a person's individual risk for disease, a cornerstone of personalized medicine. For instance, people at risk for a disease such as cancer often have more than one DNA mutation. HaploSeq could enable clinicians to determine if the two mutations are on the same chromosome or on different chromosomes, which can help in risk assessment -- for instance, risk may be reduced if two mutations are on the same chromosome, since the 'good' chromosome can often compensate.

Similarly, the method, with further honing, has the potential to refine the currently cumbersome process of determining whether there is a genetic match between an organ donor and recipient. A large number of genes contribute to compatibility between donor and recipient, but there is a lot of genetic variability in these genes. The new technique could help determine whether DNA differences between donor and recipient are likely to be a good match. "This will require more study," says Ren, "but by creating a DNA database, it may be possible to more accurately and expediently pair recipients and donors."

The new method will also help researchers analyze human migration and determine ancestry from their DNA sequences. "In principal," says Ren, "you could compare your genetic sequence to your neighbor's and ask if you have any recent ancestors in common. With our technique we can study each individual and how they relate to other individuals. As we accumulate data from many individuals we can more precisely determine their relationships." Such findings will also bolster an ongoing international project to assess worldwide human genetic variation, the HapMap project.

One advantage of the new technique is that it builds on common sequencing technologies and should be easily adapted for use by clinicians and researchers alike. Says Ren, "I anticipate that this new method will be quite widely used."

This study was funded by the Ludwig Institute for Cancer Research and the Roadmap Epigenome Project (U01 ES017166).

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Is DNA From Mom or Dad? New technique will accelerate personalized medicine

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DNA : Pricing?

Jain: Exactly! Pricing. Policy. Policy and its implementation. A very simple example, a recent example, is when IOC, BPCL and HPCL said that supply of LPG [cooking gas or liquefied petroleum gas] are linked to the Aadhar card to reduce the subsidy bill. Overnight, the bill for gas has come down. I mean, the full programme hasn't even begun, and the consumption has come down.

And even at this stage when the policy stated that people will have to pay Rs.950 per cylinder and that subsidy will be reimbursed to customers only if they are linked to the Aadhaar Card and that only nine cylinders per year would be available for reimbursement of subsidy, people have begun saying that I will have to pay Rs.950, so why not save money? Im anyway getting that subsidy.

Radhakrishnan: The effect was that LPG consumption came down by little over 10%.

Jain: There you are. I was just trying to bring out where those opportunities lie. The opportunity is right in front of you. And whom you want to really subsidise? Most diesel cars are Mercedes or big cars. Many new cars are coming out with diesel versions. Why?

Parasnis: Yeah. I think when it comes to opportunities we have to focus on specific sectors. So if you take the buildings and construction then you must understand that they contribute to 40% of the CO2 emissions. So if we go for green buildings, you could conserve around 20-30% of those emissions and other impacts and the life cycle costs.

So if you want to go into urban areas or rural areas and want to say we want to have good houses, why not have green houses over there. They were there earlier, maybe with different material that was used then. Or the construction type was different then.

Jain: Absolutely.

Parasnis: All the houses in the past were green. Why not now? We need to have some modification over past designs and material. If you talk about transport

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dna Conversations: A sensible policy framework for energy conservation is urgently needed(Part-2)

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DNA test confirms biological parents of Roma girl
Ellen Scott reports on the resolution to the Roma girl mystery, as DNA tests confirm the identity of Maria, a girl found in Greece last week.

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2014 PSE Pro Series Compound Bow Review: Dream Season DNA
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FLORENCE, Italy, Nov. 1 (UPI) -- New DNA tests on a knife in the Italian murder case against U.S. student Amanda Knox have cast doubt on whether it was the murder weapon, defense lawyers say.

The tests were ordered as part of a third trial in the case in which Knox and her former boyfriend, Italian Raffaele Sollecito, are accused of killing British student Meredith Kercher in 2007 while the two women lived together in Perugia, Britain's The Daily Telegraph reported.

Investigators believe the kitchen knife, which was found in Collecito's apartment, was used by Knox to kill Kercher, as forensic experts initially said they found traces of DNA on the blade of the knife that belonged to Kercher, and Knox's DNA on the handle.

The original evidence was used to convict Knox and Sollecito in 2009, but was later thrown out during their appeal.

The latest results, which were revealed in court Thursday, "pushes even further away the possibility that this was the murder weapon," said Luciano Ghirga, Knox's lawyer.

The new tests found only tiny trace amounts of Kercher's DNA on the blade of the knife, which the defense has argued only proves that the knife was once in the apartment Knox and Kercher shared and could have gotten on the knife at any time.

"The forensic experts appointed by the Perugia appeals court, who at the time of their work didn't have instrumentation available to carry out a thorough examination on such a low quantity of DNA, carried out their work well," Ghirga said.

"This test excludes categorically that the knife was the murder weapon," said Giulia Bongiorno, Sollecito's lawyer.

Knox has opted to not be present at the current trial, which was ordered earlier this year by the Supreme Court in Rome. Sollecito, who has so far been absent from the trial, is scheduled to appear in court Wednesday.

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New DNA test casts doubt on murder weapon in Kercher murder trial

DNA Proves Bulgarian Woman Mother Of Mystery Child "Maria"
A Roma woman in Bulgaria is the parent of Greece #39;s mystery child known as Maria. New DNA tests prove Sashka Ruseva is the mother of the girl, who was dubbed ...

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Mike Pazin: Can collaboration help unlock more DNA secrets?
ENCODE Program Officer Mike Pazin sheds light on how an "orchestra" of scientists can find the hidden music in your DNA.

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Maury Has Blk Beastie On Testing 3 Men For DNA But Everyone Was Shocked By The Results!
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