Researchers create powerful new method to analyze genetic data
University of Texas Medical Branch at Galveston researchers have developed a powerful visual analytical approach to explore genetic data, enabling scientists to identify novel patterns of information that could be crucial to human health.
The method, which combines three different "bipartite visual representations" of genetic information, is described in an article to appear in the Journal of the American Medical Informatics Association. The work won a distinguished paper award when it was presented at the AMIA Summit on Translational Bioinformatics in March 2012.
In the paper, the authors use their technique to analyze data on genetic alterations in humans known as single-nucleotide polymorphisms, or SNPs. Among other things, the frequencies of particular SNPs are associated with an individual's ancestral origins; for the study, the researchers chose to examine SNP data from 60 individuals from Nigeria and 60 individuals from Utah.
"We selected SNPs that we already knew differentiated between the two groups, and then showed that our method can reveal more about the data than traditional methods," said UTMB associate professor Suresh Bhavnani, lead author on the JAMIA paper and a member of UTMB's Institute for Translational Sciences. "This is a fresh way of looking at genetic data, a methodological contribution that we believe can help biologists and clinicians make better sense of a variety of biomarkers."
Like many kinds of biomedical data, Bhavnani said, datasets describing individuals and their SNPs are particularly suited to visual representations that are bipartite: that is, they simultaneously present two different classes of data. In the case of the Utah-Nigeria SNP data, Bhavnani and his colleagues started with what is known as a bipartite network visualization an intricate computer-generated arrangement of colored dots and black, gray and white lines.
"In the bipartite network you see both the individuals and their genetic profiles simultaneously, and cognitively that's really important," Bhavnani said. "You can look at the individuals and know immediately which SNPs make them different from others, and conversely you can look at the SNPs to see how they are co-occurring, and with which individuals they are co-occurring. This rich representation enables you to quickly comprehend the complex bipartite relationships in the data"
The bipartite network visualization of the Utah-Nigeria individual-SNP data has distinct clusters on its left and right sides that correspond to the Utah and Nigerian subjects and SNPs. It also accurately portrays a genetic phenomenon called admixture, in which an individual possesses SNPs that are characteristic of individuals from Utah as well as from Nigeria. Admixed individuals are placed on the edges of their clusters, relatively close to the center of the visualization. The identification of admixed individuals, and the implicated SNPs could help in the design of case-control studies where there is a need for the selection of homogenous sets of individual from different ancestral origins.
To produce an even more detailed picture of the individual-SNP information, the researchers applied two other bipartite visualization techniques to the data: the bipartite heat map, and the bipartite Circos ideogram. In the heat map, rectangular cells laid out in a spreadsheet-like arrangement and colored white, gray, or black helped precisely define the boundaries of the clusters by clarifying individual-SNP relationships. In the Circos ideogram, individuals and SNPs placed around the perimeter of a circle and linked with curved lines, enabling the researchers to more closely examine the admixed individuals' ties to SNPs in the clusters associated with both Utah and Nigeria.
"The network representation is very powerful because it gives you the overall structure of the data, but to really understand the complex relationships, you need these additional bipartite representations," Bhavnani said.
The JAMIA paper, according to Bhavnani, represents a proof of concept for the researchers' novel combination of methods, which can be applied to a wide range of biomedical questions. "You can think of anything for example you could examine cases and controls in Alzheimer's disease, or you could compare children who are prone to ear infections and those aren't prone," Bhavnani said. "Whatever your disease or trait of interest is, our approach can handle it."
Journal reference: Journal of the American Medical Informatics Association
Provided by University of Texas Medical Branch at Galveston
- Genetic map may help find disease causes Oct 26, 2005 | not rated yet | 0
- Study helps pinpoint genetic variations in European Americans Aug 07, 2008 | not rated yet | 0
- 18 novel subtype-dependent genetic variants for autism spectrum disorders revealed Apr 27, 2011 | not rated yet | 0
- Genes and drugs team up to lower blood pressure Sep 13, 2007 | not rated yet | 0
- Scientists make strides toward defining genetic signature of Alzheimer's disease Dec 31, 2008 | not rated yet | 0
- Motion perception revisited: High Phi effect challenges established motion perception assumptions Apr 23, 2013 | 3 / 5 (2) | 2
- Anything you can do I can do better: Neuromolecular foundations of the superiority illusion (Update) Apr 02, 2013 | 4.5 / 5 (11) | 5
- The visual system as economist: Neural resource allocation in visual adaptation Mar 30, 2013 | 5 / 5 (2) | 9
- Separate lives: Neuronal and organismal lifespans decoupled Mar 27, 2013 | 4.9 / 5 (8) | 0
- Sizing things up: The evolutionary neurobiology of scale invariance Feb 28, 2013 | 4.8 / 5 (10) | 14
Classical and Quantum Mechanics via Lie algebras
Apr 15, 2011 I'd like to open a discussion thread for version 2 of the draft of my book ''Classical and Quantum Mechanics via Lie algebras'', available online at http://lanl.arxiv.org/abs/0810.1019 , and for the...
- More from Physics Forums - Independent Research
More news stories
Two mutations central to the development of infantile myofibromatosis (IM)—a disorder characterized by multiple tumors involving the skin, bone, and soft tissue—may provide new therapeutic targets, according to researchers ...
Genetics 19 hours ago | 3 / 5 (2) | 0 |
Can human genes be patented? That was the question posed by Alan J. Snyder, vice president and associate provost for research and graduate studies at Lehigh, and Lee Kaplan, scientific director of cellular and molecular genetics ...
Genetics May 24, 2013 | 4 / 5 (1) | 0
Researchers from Queen Mary, University of London have led the largest sequencing study of human disease to date, investigating the genetic basis of six autoimmune diseases.
Genetics May 22, 2013 | 4.5 / 5 (4) | 0 |
University of Minnesota Medical School researchers from the Masonic Cancer Center, University of Minnesota, in partnership with the University's Brain Tumor Program, have developed a new mouse model of malignant peripheral ...
Genetics May 20, 2013 | 5 / 5 (1) | 0 |
Northwestern University scientists have shown a gene involved in neurodegenerative disease also plays a critical role in the proper function of the circadian clock.
Genetics May 16, 2013 | 3 / 5 (1) | 1 |
Coenzyme Q10 decreases all cause mortality by half, according to the results of a multicentre randomised double blind trial presented today at Heart Failure 2013 congress. It is the first drug to improve heart failure mortality ...
3 hours ago | not rated yet | 4
Heart failure accelerates the aging process and brings on early andropausal syndrome (AS), according to research presented today at the Heart Failure Congress 2013. AS, also referred to as male 'menopause', was four times ...
3 hours ago | not rated yet | 1
Women at a particular stage in their monthly menstrual cycle may be more vulnerable to some of the psychological side-effects associated with stressful experiences, according to a study from UCL.
22 hours ago | 3.7 / 5 (3) | 3 |
(AP)—Department of Justice lawyers have again asked a federal appeals court in New York to delay lifting age restrictions and prescription requirements on an emergency contraceptive popularly known as the morning-after ...
3 hours ago | not rated yet | 0
Mortality and length of stay are highest in heart failure patients admitted in January, on Friday, and overnight, according to research presented today at the Heart Failure Congress 2013. The analysis of nearly 1 million ...
3 hours ago | not rated yet | 0
Biological processes are generally based on events at the molecular and cellular level. To understand what happens in the course of infections, diseases or normal bodily functions, scientists would need to ...
22 hours ago | 5 / 5 (5) | 0 |