Daily Archives: February 24, 2013

Taking the gamble out of DNA sequencing

Posted: February 24, 2013 at 5:44 pm

Public release date: 24-Feb-2013 [ | E-mail | Share ]

Contact: Robert Perkins perkinsr@usc.edu 213-740-9226 University of Southern California

Two USC scientists have developed an algorithm that could help make DNA sequencing affordable enough for clinics and could be useful to researchers of all stripes.

Andrew Smith, a computational biologist at the USC Dornsife College of Letters, Arts and Sciences, developed the algorithm along with USC graduate student Timothy Daley to help predict the value of sequencing more DNA, to be published in Nature Methods on February 24.

Extracting information from the DNA means deciding how much to sequence: sequencing too little and you may not get the answers you are looking for, but sequence too much and you will waste both time and money. That expensive gamble is a big part of what keeps DNA sequencing out of the hands of clinicians. But not for long, according to Smith.

"It seems likely that some clinical applications of DNA sequencing will become routine in the next five to 10 years," Smith said. "For example, diagnostic sequencing to understand the properties of a tumor will be much more effective if the right mathematical methods are in place."

The beauty of Smith and Daley's algorithm, which predicts the size and composition of an unseen population based on a small sample, lies in its broad applicability.

"This is one of those great instances where a specific challenge in our research led us to uncover a powerful algorithm that has surprisingly broad applications," Smith said.

Think of it: how often do scientists need to predict what they haven't seen based on what they have? Public health officials could use the algorithm to estimate the population of HIV positive individuals; astronomers could use it to determine how many exoplanets exist in our galaxy based on the ones they have already discovered; and biologists could use it to estimate the diversity of antibodies in an individual.

The mathematical underpinnings of the algorithm rely on a model of sampling from ecology known as capture-recapture. In this model, individuals are captured and tagged so that a recapture of the same individual will be known and the number of times each individual was captured can be used to make inferences about the population as a whole.

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Taking the gamble out of DNA sequencing

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DNA match leads to arrest in 1985 cold case rape

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NEW ORLEANS New Orleans police have arrested a suspect in a 1985 rape.

Troy Williams, 42, was arrested in Texas and transferred to New Orleans Wednesday, where he was jailed on rape, armed robbery, aggravated kidnapping and other charges, The Times-Picayune reports.

Police said they found Williams after the Louisiana State Police crime lab checked an evidence kit from the assault for DNA. The DNA found by the lab matched a sample from Williams.

Williams was 15 when the rape occurred, but will be tried as an adult.

For years, even in cases where DNA evidence was available, New Orleans police failed to process evidence kits related to rapes. That resulted in a backlog of hundreds of unresolved cases.

After Police Superintendent Ronal Serpas took office in 2010, the department began to prioritize processing untested evidence in unresolved cases, with assistance from the State Police crime lab and others. Serpas recently said the department has eliminated the backlog of untested evidence.

Police said Williams and another man assaulted a woman on the morning of Aug. 21, 1985. Authorities said one of the two men took $6 from the woman's purse, and she was forced into a nearby alley at gunpoint. There, she was forced to disrobe and was raped, police said. The woman couldn't scream for help because the gun was against her head during the attack, court documents state.

Afterward, the two men fled. The woman ran to her sister's residence and called the police. She then went to a hospital and underwent a rape examination.

This past Nov. 19, New Orleans detective Orlynthia Miller-White received a report from the Louisiana State Police crime lab that DNA from the rape matched a profile of Williams stored on the Combined DNA Index System, or CODIS, an FBI-managed collection of DNA samples from people convicted of certain crimes.

Miller-White eventually located the victim, who said she didn't know Williams and had never consented to having sex with him.

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DNA match leads to arrest in 1985 cold case rape

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Human Genome Sprapp (HGS) Episode #3 – Scratching the Surface – Video

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Human Genome Sprapp (HGS) Episode #3 - Scratching the Surface
Episode #3 in the 2013 quest to sequence my entire genome in Microsoft Excel and analyze using Pivot Tables and Charts. This episode dives into molecular mass, density, hydrogen bonds, and small sequencing patterns for the nucleobases found in DNA. For more info on the progress check out Ken #39;s Talk.com.

By: Ken Braverman

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Human Genome Sprapp (HGS) Episode #3 - Scratching the Surface - Video

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Scientists find genes linked to human neurological disorders in sea lamprey genome

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Feb. 24, 2013 Scientists at the Marine Biological Laboratory (MBL) have identified several genes linked to human neurological disorders, including Alzheimer's disease, Parkinson's disease and spinal cord injury, in the sea lamprey, a vertebrate fish whose whole-genome sequence is reported this week in the journal Nature Genetics.

"This means that we can use the sea lamprey as a powerful model to drive forward our molecular understanding of human neurodegenerative disease and neurological disorders," says Jennifer Morgan of the MBL's Eugene Bell Center for Regenerative Biology and Tissue Engineering. The ultimate goals are to determine what goes wrong with neurons after injury and during disease, and to determine how to correct these deficits in order to restore normal nervous system functions.

Unlike humans, the lamprey has an extraordinary capacity to regenerate its nervous system. If a lamprey's spinal cord is severed, it can regenerate the damaged nerve cells and be swimming again in 10-12 weeks.

Morgan and her collaborators at MBL, Ona Bloom and Joseph Buxbaum, have been studying the lamprey's recovery from spinal cord injury since 2009. The lamprey has large, identified neurons in its brain and spinal cord, making it an excellent model to study regeneration at the single cell-level. Now, the lamprey's genomic information gives them a whole new "toolkit" for understanding its regenerative mechanisms, and for comparing aspects of its physiology, such as inflammation response, to that of humans.

The lamprey genome project was accomplished by a consortium of 59 researchers led by Weiming Li of Michigan State University and Jeramiah Smith of the University of Kentucky. The MBL scientists' contribution focused on neural aspects of the genome, including one of the project's most intriguing findings.

Lampreys, in contrast to humans, don't have myelin, an insulating sheath around neurons that allows faster conduction of nerve impulses. Yet the consortium found genes expressed in the lamprey that are normally expressed in myelin. In humans, myelin-associated molecules inhibit nerves from regenerating if damaged. "A lot of the focus of the spinal cord injury field is on neutralizing those inhibitory molecules," Morgan says.

"So there is an interesting conundrum," Morgan says. "What are these myelin-associated genes doing in an animal that doesn't have myelin, and yet is good at regeneration? It opens up a new and interesting set of questions, " she says. Addressing them could bring insight to why humans lost the capacity for neural regeneration long ago, and how this might be restored.

At present, Morgan and her collaborators are focused on analyzing which genes are expressed and when, after spinal cord injury and regeneration. The whole-genome sequence gives them an invaluable reference for their work.

Morgan, Bloom, and Buxbaum collaborate at the MBL through funding by the Charles Evans Foundation. Bloom is based at the Feinstein Institute for Medical Research/Hofstra North Shore-Long Island Jewish in New York. Buxbaum is from Mount Sinai School of Medicine in New York.

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1home remedies for psoriasis treatment – Video

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