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Chad A. Mirkin, Northwestern University, George B. Rathmann Professor of Chemistry in the Weinberg College of Arts and Sciences. Photo by Bill Arsenault. 

DNA Blueprints Guide The Construction Of Specific Human Structures

Chad Mirkin discusses using DNA to build a three-dimensional structure out of gold, likening the process to building a house. Starting with basic materials such as bricks, wood, siding, stone and shingles, a construction team can build many different types of houses out of the same building blocks.
 
The article includes an audio recording of the full interview. Photo courtesy of the UCSD School of Medicine.
Population Studies Bolstered by Improved Analysis of Trace DNA Print E-mail
Science - Genetics & Genome
TS-Si News Service   
Wednesday, 03 September 2008 16:30
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TS-Si Genetics & The Genome
Montreal, Quebec, CAN. Life on Earth didn't originate from a preexisting blueprint, but living things do have a basic architecture. Recent studies have shown that a great deal of the genome — inluding the non-coded (&q...

St. Louis, MO, USA. For years, scientists have struggled to decipher the genetic instruction book that details where and when the 20,000 genes in a human cell will be turned on or off. Different genes operate in each cell typ...

Los Angeles, CA, USA. Scientists have demonstrated for the first time the reversal of what is called epigenetic silencing, a major breakthrough in the developmental process.   Although nearly every cell in our body is ...

Edmonton, Alberta, Canada. People are different, both physically and mentally, but genetically everyone is very similar. That's been the thought of scientists for decades now. But with population research becoming more and mo...

Melbourne, Victoria, AUS. Scientists have identified a significant DNA variation that they say could result in a genetic link between reduced testosterone action and male-to-female (MtF) transsexualism (progressively known as...

Oxford, UK. What do you look for in a mate? Or, does it even matter if you look? Past discussions of mate selection have been dominated by arguments based on the evidence of nurture. For example, the exam...

Atlanta, GA, USA. There was a time when books were reproduced by hand, a laborious procedure that is subject to errors and confused readers. Cells have a more daunting task, since their division must result in an identic...

Oslo, Norway. Ask this basic question to the next 10 people you meet at random: What is a gene? Chances are that most of the answers will either reflect a dated understanding of science or ignore science altog...
Phoenix, AZ, USA. A population study is important to medical research because it can systematically compare a large group of individuals who share common characteristics (such as age, health condition, or sex). This group can then be studied in greater depth for such things as the incidence of birth conditions and/or disease, responses to medicine, surgical risks, and so on.
 
The introduction of DNA identification has enlivened population studies with new data and deeper information on the individuals within a group. However, existing technology has imposed limits on analysis. For meaningful results, the samples used (e.g., comprised of skin, hair) must be of relatively large size; moreover, trying to extract the DNA of one person from a group (a mixed sample) becomes more difficult as group size increases.
 

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays. Nils Homer, Szabolcs Szelinger, Margot Redman, David Duggan, Waibhav Tembe, Jill Muehling, John V. Pearson, Dietrich A. Stephan, Stanley F. Nelson, David W. Craig. PLoS Genetics 4(8): e1000167 doi: 10.1371 / journal.pgen.1000167. [ Download PDF ]

 
Scientists have now taken an important step in solving this problem by improving the extraction and analysis of DNA in a practical environment with stringent standards for evidence: crime scene forensics. A team of investigators led by scientists at the Translational Genomics Research Institute (TGen) [N1] found a way to identify possible suspects at crime scenes using only a small amount of DNA, even if it is mixed with hundreds of other genetic fingerprints. The results appear in PLoS Genetics.
 

It opens up ideas never considered before.

The scientists used genotyping microarrays to identify an individual's DNA from within a mix of DNA samples, even if that individual represented less than 0.1 percent of the total mix (less than one part per thousand). They did this even when the mix of DNA included more than 200 individual DNA samples.
 
The discovery could help police investigators better identify possible suspects, even when dozens of people over time have been at a crime scene. It also could help reassess previous crime scene evidence, and it could have other uses in various genetic studies and in statistical analysis.
 
Dr. David W. Craig, associate director of TGen's Neurogenomics Division."This is a potentially revolutionary advance in the field of forensics," said the paper's senior author, Dr. David W. Craig, associate director of TGen's Neurogenomics Division, charged with finding ways to treat conditions of the brain and nervous system, as well as disease conditions.
 
"By employing the powers of genomic technology, it is now possible to know with near certainty that a particular individual was at a particular location, even with only trace amounts of DNA and even if dozens or even hundreds of others were there, too."
 
The researchers analyzed complex mixes of genomic DNA using high-density Single Nucleotide Polymorphism (SNP) genotyping microarrays.
  • This approach enabled them to accurately identify individuals from DNA mixes of at least 200 people using less than one in one-thousandth of the total mix.
     
  • Theoretically, they showed that individuals could be identified in mixes of more than 1,000 people.
Currently, it is difficult for police forensic investigators to detect an individual if their genomic DNA is less than 10 percent of a mix, or if it is from a large mix of DNA material. A long-held assumption within the field of forensic science was that it was not possible to identify individuals using pooled data — until now.
 
According to Commander Brent Vermeer, director of the Phoenix Police Department crime lab, much DNA evidence is rendered useless because of contamination, and that to eventually put the TGen theoretical research into a cost-effective police practice “would be an amazing asset.’’
 
"As technology advances, we need to be prepared to keep evidence that, down the road, could prove again to be useful," said Vermeer, who heads a bureau of nearly 130 analysts and crime scene investigators. [N2]
 
Craig said the findings presented in the paper should foster more scientific investigation that could lead to cost-effective ways of using the TGen technology to fight crime. "It opens up ideas never considered before."
 
Array and Genomic ImageryDr. Stanley F. Nelson, director of the UCLA site of the Neuroscience Microarray Consortium within the National Institute of Health (NIH), said forensics investigators are "often stymied" because they now search for fewer than 20 DNA markers. The TGen researchers looked at hundreds of thousands of markers to make their identifications, he said.
 
"It opens up a whole new can of worms of what’s possible to do forensically," said Nelson, professor of Human Genetics and Psychiatry at UCLA’s David Geffen School of Medicine, and a conributing author.
 
Nelson said that, using current police methods, DNA processing costs less than $50, while a similar process for genomic research costs several hundred dollars. However, with advances in technology, those costs should come down, he said.
 
"We demonstrate an approach for rapidly and sensitively determining whether a trace amount... of genomic DNA from an individual is present within a complex DNA mixture," the paper said.
 
The TGen study resulted from what Nelson described as "an intellectual curiosity" by Craig while investigating diseases. Nils Homer, a former TGen intern who now is working on his doctorate degree in computer science at UCLA, brought Nelson and Craig together. Homer is the paper’s first author.
 


[N1] The Translational Genomics Research Institute (TGen) is a non-profit organization that conducts research focused on helping patients with diseases such as cancer, neurological disorders and diabetes.

[N2] The Arizona Legislature passed Senate Bill 1412 in June 2008, requiring police agencies to retain DNA evidence in cases of homicide or felony sexual assault for as long as convicts are in prison or on supervised release, or at least 55 years in unsolved cases. Some jurisdictions, like Phoenix, keep the DNA evidence indefinitely.

 


Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays. Nils Homer, Szabolcs Szelinger, Margot Redman, David Duggan, Waibhav Tembe, Jill Muehling, John V. Pearson, Dietrich A. Stephan, Stanley F. Nelson, David W. Craig. PLoS Genetics 4(8): e1000167 doi: 10.1371 / journal.pgen.1000167. [ Download PDF ]

Abstract

We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture. We first develop a theoretical framework for detecting an individual's presence within a mixture, then show, through simulations, the limits associated with our method, and finally demonstrate experimentally the identification of the presence of genomic DNA of specific individuals within a series of highly complex genomic mixtures, including mixtures where an individual contributes less than 0.1% of the total genomic DNA. These findings shift the perceived utility of SNPs for identifying individual trace contributors within a forensics mixture, and suggest future research efforts into assessing the viability of previously sub-optimal DNA sources due to sample contamination. These findings also suggest that composite statistics across cohorts, such as allele frequency or genotype counts, do not mask identity within genome-wide association studies. The implications of these findings are discussed.

Author Summary

In this report we describe a framework for accurately and robustly resolving whether individuals are in a complex genomic DNA mixture using high-density single nucleotide polymorphism (SNP) genotyping microarrays. We develop a theoretical framework for detecting an individual's presence within a mixture, show its limits through simulation, and finally demonstrate experimentally the identification of the presence of genomic DNA of individuals within a series of highly complex genomic mixtures. Our approaches demonstrate straightforward identification of trace amounts (<1%) of DNA from an individual contributor within a complex mixture. We show how probe-intensity analysis of high-density SNP data can be used, even given the experimental noise of a microarray. We discuss the implications of these findings in two fields: forensics and genome-wide association (GWA) genetic studies. Within forensics, resolving whether an individual is contributing trace amounts of genomic DNA to a complex mixture is a tremendous challenge. Within GWA studies, there is a considerable push to make experimental data publicly available so that the data can be combined with other studies. Our findings show that such an approach does not completely conceal identity, since it is straightforward to assess the probability that a person or relative participated in a GWA study.

 
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Last Updated on Wednesday, 03 September 2008 05:14