Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Big Data Allows Computer Engineers to Find Genetic Clues in Humans

30.03.2015

Big data: It’s a term we read and hear about often, but is hard to grasp. Computer scientists at Washington University in St. Louis’ School of Engineering & Applied Science tackled some big data about an important protein and discovered its connection in human history as well as clues about its role in complex neurological diseases.

Through a novel method of analyzing these big data, Sharlee Climer, PhD, research assistant professor in computer science, and Weixiong Zhang, PhD, professor of computer science and of genetics at the School of Medicine, discovered a region encompassing the gephyrin gene on chromosome 14 that underwent rapid evolution after splitting in two completely opposite directions thousands of years ago. Those opposite directions, known as yin and yang, are still strongly evident across different populations of people around the world today.


Climer/Zhang, Washington University in St. Louis

Yin-yang haplotypes arise when a stretch of DNA evolves to present two divergent forms. A group of engineers at Washington University in St. Louis showed a massive yin-yang haplotype pair encompassing the gene gephyrin on human chromosome 14. This image shows the states for markers in the region for 934 individuals in eight global populations. Dark blue and red horizontal lines in the yin-yang region represent carriers of two yin and two yang haplotypes, respectively, and light blue represents carriers of both haplotypes.

The results of their research, done with Alan Templeton, PhD, the Charles Rebstock professor emeritus in the Department of Biology in the College of Arts & Sciences, appear in the March 27 issue of Nature Communications.

The gephyrin protein is a master regulator of receptors in the brain that transmit messages. Malfunction of the protein has been associated with epilepsy, Alzheimer’s disease, schizophrenia and other neurological diseases. Additionally, without gephyrin, our bodies are unable to synthesize an essential trace nutrient.

The research team used big data from the International HapMap Project, a public resource of genetic data from populations worldwide designed help researchers find genes associated with human disease, as well as from the 1000 Genomes project, another public data source of sequenced human genomes. In total, they looked at the genetic data from 3,438 individuals.

When they analyzed the data, they made an interesting discovery in a sequence of markers, called a haplotype, enveloping the gephyrin gene: up to 80 percent of the haplotypes were perfect yin and yang types, or complete opposites of the other. They were able to trace the split back to what is known as the Ancestral haplotype, or that of the most recent common human ancestor.

“We observed that the Ancestral haplotype split into two distinct haplotypes and subsequently underwent rapid evolution, as each haplotype possesses about 140 markers that are different from the Ancestral haplotype,” Climer says. “These numerous mutations should have produced a large number of intermediate haplotypes, but the intermediates have almost entirely disappeared, and the divergent yin and yang haplotypes are prevalent in populations representing every major human ancestry.”

Using the data from the HapMap Project, they looked at the gephyrin region in several populations of people, including European, East and South Asian, and African heritage, and found variations in the haplotype frequencies of each of these populations. Those from African origin generally have more yang haplotypes, while those of European origin have more yin haplotypes. Those of Asian descent have nearly equal numbers of yin and yang haplotypes.

Humans carry pairs of chromosomes, and 30 percent of Japanese individuals carry two yin haplotypes or two yang haplotypes. Another 30 percent of these individuals possess both a yin and a yang haplotype, reflecting the roughly equal probability of inheriting either one.

To find this pattern within the huge datasets, the research team used a novel method to assess correlations between genetic markers called single nucleotide polymorphisms, or SNPs, which are variations in a DNA sequence that make humans different from each other.

The team’s method, called BlocBuster, computes correlations between each pair of SNPs, then builds a network of those correlations. By observing the network, researchers can see clusters of correlated markers.

“For example, you could build a Facebook network using all of your Facebook friends,” Climer says. “If two of your friends are friends with each other, you would connect them in the network. If you see that a cluster of people is interconnected with each other, they probably share something in common, such as a family relationship, a school, or some type of social interaction. Similarly, with an efficient algorithm and an adequate number of processors and time, we can look at every pair of SNPs, build these networks and observe clusters of interconnected SNPs.

“The BlocBuster approach is a paradigm shift from the conventional methods for genome-wide association studies, or popularly known as GWAS, where one or a few markers were examined at a time,” Zhang says. “It is truly a data mining technique for big data like those from HapMap and 1000 Genomes projects.”

The researchers also can design this approach to look at complex traits and diseases.

“BlocBuster is able to detect combinations of networked genetic markers that are characteristic of complex traits,” Zhang says. “It is suitable for analyzing traits, such as body weights, which are determined by multiple genetic factors, and genetic patterns in populations, such as the yin-yang haplotypes we discovered.”

Ultimately, they expect this method will shed light on the genetic roots of disease.

“Most complex diseases arise due to a group of genetic variations interacting together,” Climer says. “Different groups of people who get a disease may be affected by different groups of variations. There’s not enough power to see most of these intricate associations when looking at single markers one at a time. We’re taking a combinatorial approach — looking at combinations of markers together — and we’re able to see the patterns.”

###
Climer S, Templeton A, Zhang W. Human gephyrin is encompassed within giant functional noncoding yin-yang sequences. Nature Communications, March 27, 2015. 6:6534 doi: 10.1038/ncomms7534 (2015).

Funding for this research was provided by the National Institutes of Health (P50-GM65509, RC1-AR058681, R01-GM086412 and R-01-GM100364), the National Science Foundation (DBI-0743797) and the municipal government of Wuhan, Hubei, China.

The School of Engineering & Applied Science at Washington University in St. Louis focuses intellectual efforts through a new convergence paradigm and builds on strengths, particularly as applied to medicine and health, energy and environment, entrepreneurship and security. With 91 tenured/tenure-track and 40 additional full-time faculty, 1,300 undergraduate students, more than 900 graduate students and more than 23,000 alumni, we are working to leverage our partnerships with academic and industry partners — across disciplines and across the world — to contribute to solving the greatest global challenges of the 21st century.

Contact Information
Julie Flory
Asst Vice Chancellor for Campus Communications
julie.flory@wustl.edu

Julie Flory | newswise

Further reports about: Big Data Communications Genetic HapMap Zhang computer science genetic data haplotype markers

More articles from Information Technology:

nachricht Researchers achieve HD video streaming at 10,000 times lower power
20.04.2018 | University of Washington

nachricht An AI that makes road maps from aerial images
18.04.2018 | Massachusetts Institute of Technology, CSAIL

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Spider silk key to new bone-fixing composite

University of Connecticut researchers have created a biodegradable composite made of silk fibers that can be used to repair broken load-bearing bones without the complications sometimes presented by other materials.

Repairing major load-bearing bones such as those in the leg can be a long and uncomfortable process.

Im Focus: Writing and deleting magnets with lasers

Study published in the journal ACS Applied Materials & Interfaces is the outcome of an international effort that included teams from Dresden and Berlin in Germany, and the US.

Scientists at the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) together with colleagues from the Helmholtz-Zentrum Berlin (HZB) and the University of Virginia...

Im Focus: Gamma-ray flashes from plasma filaments

Novel highly efficient and brilliant gamma-ray source: Based on model calculations, physicists of the Max PIanck Institute for Nuclear Physics in Heidelberg propose a novel method for an efficient high-brilliance gamma-ray source. A giant collimated gamma-ray pulse is generated from the interaction of a dense ultra-relativistic electron beam with a thin solid conductor. Energetic gamma-rays are copiously produced as the electron beam splits into filaments while propagating across the conductor. The resulting gamma-ray energy and flux enable novel experiments in nuclear and fundamental physics.

The typical wavelength of light interacting with an object of the microcosm scales with the size of this object. For atoms, this ranges from visible light to...

Im Focus: Basel researchers succeed in cultivating cartilage from stem cells

Stable joint cartilage can be produced from adult stem cells originating from bone marrow. This is made possible by inducing specific molecular processes occurring during embryonic cartilage formation, as researchers from the University and University Hospital of Basel report in the scientific journal PNAS.

Certain mesenchymal stem/stromal cells from the bone marrow of adults are considered extremely promising for skeletal tissue regeneration. These adult stem...

Im Focus: Like a wedge in a hinge

Researchers lay groundwork to tailor drugs for new targets in cancer therapy

In the fight against cancer, scientists are developing new drugs to hit tumor cells at so far unused weak points. Such a “sore spot” is the protein complex...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Invitation to the upcoming "Current Topics in Bioinformatics: Big Data in Genomics and Medicine"

13.04.2018 | Event News

Unique scope of UV LED technologies and applications presented in Berlin: ICULTA-2018

12.04.2018 | Event News

IWOLIA: A conference bringing together German Industrie 4.0 and French Industrie du Futur

09.04.2018 | Event News

 
Latest News

Magnetic nano-imaging on a table top

20.04.2018 | Physics and Astronomy

Start of work for the world's largest electric truck

20.04.2018 | Interdisciplinary Research

Atoms may hum a tune from grand cosmic symphony

20.04.2018 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>