Subscribe free to our newsletters via your
. 24/7 Space News .




TECH SPACE
Computational tool translates complex data into simplified 2-dimensional images
by Staff Writers
New York NY (SPX) May 23, 2013


viSNE reveals the progression of cancer in a sample of cells taken from a patient with acute myeloid leukemia. In figure a, the contours represent cell density in each region of the map. Each point represents a cell from the diagnosis sample (top, purple) or relapse sample (bottom, red). In figure b, cells from both diagnosis and relapse samples are shown in each map. Cells are colored according to intensity of expression of the indicated cell markers, enabling the comparison of expression patterns before and after relapse. For example, Fit3 is expressed primarily in the diagnosis sample, while CD34 emerges in the relapse sample. Credit: Dana Pe'er, PhD/Columbia University.

In their quest to learn more about the variability of cells between and within tissues, biomedical scientists have devised tools capable of simultaneously measuring dozens of characteristics of individual cells. These technologies have led to new challenges, however, as scientists now struggle with how to make sense of the resulting trove of data.

Now a solution may be at hand. Researchers at Columbia University and Stanford University have developed a computational method that enables scientists to visualize and interpret "high-dimensional" data produced by single-cell measurement technologies such as mass cytometry. The method, published in the online edition of Nature Biotechnology, has particular relevance to cancer research and therapeutics.

Researchers now understand that cancer within an individual can harbor subpopulations of cells with different molecular characteristics. Groups of cells may behave differently from one another, including in how they respond to treatment.

The ability to study single cells, as well as to identify and characterize subpopulations of cancerous cells within an individual, could lead to more precise methods of diagnosis and treatment.

"Our method not only will allow scientists to explore the heterogeneity of cancer cells and to characterize drug-resistant cancer cells, but also will allow physicians to track tumor progression, identify drug-resistant cancer cells, and detect minute quantities of cancer cells that increase the risk of relapse," said co-senior author Dana Pe'er, PhD, associate professor of biological sciences and systems biology at Columbia. The other co-senior author is Garry P. Nolan, PhD, professor of microbiology and immunology at Stanford.

The method, called viSNE (visual interactive Stochastic Neighbor Embedding), is based on a sophisticated algorithm that translates high-dimensional data (e.g., a dataset that includes many different simultaneous measurements from single cells) into visual representations similar to two-dimensional "scatter plots"-the simple graphs with X and Y axes that many people first encounter in high school math and biology.

"Basically, viSNE provides a way to visualize very high-dimensional data in two dimensions, while maintaining the most important organization and structure of the data," said Dr. Pe'er. "Color is used as a third dimension to enable users to interactively visualize various features of the cells."

The viSNE software can analyze measurements of dozens of molecular markers. In the two-dimensional maps that result, the distance between points represents the degree of similarity between single cells.

The maps can reveal clearly defined groups of cells with distinct behaviors (e.g., drug resistance) even if they are only a tiny fraction of the total population. This should enable the design of ways to physically isolate and study these cell subpopulations in the laboratory.

Although the algorithm underlying the method is complex, Dr. Pe'er expects that all researchers, no matter their level of mathematical expertise, will be able to use viSNE.

To demonstrate the software's utility, Dr. Pe'er and her colleagues used mass cytometry and viSNE to study bone marrow cells from patients with acute myeloid leukemia. Currently, clinicians can incorporate at most 4 to 8 markers to assess the cells.

Because mass cytometry and viSNE can incorporate many more markers, viSNE is able to identify more subtle differences between cells. Using the algorithm, Dr. Pe'er and her colleagues were able to reveal previously unrecognized heterogeneity in the bone marrow cells they studied.

The researchers also showed that viSNE could detect minimal residual disease (MRD) - extremely small quantities of cancer cells that persist after chemotherapy and raise the risk of recurrence.

"In blinded tests, we were able to find as few as 20 cancer cells out of tens of thousands of healthy cells," said Dr. Pe'er. Such a small quantity of cells is extremely difficult to detect, even by the most experienced pathologist.

"The ability to detect MRD is critical for curing cancer," added Dr. Pe'er. "Eliminating even 99.9 percent of a tumor doesn't bring about a cure. You have to be able to find, and then eliminate, the tiny populations of cells that can survive therapy and lead to disease relapse."

The paper is titled, "viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia." The other authors are: El-ad David Amir (Columbia), Kara L. Davis (Stanford University), Michelle D. Tadmor (Columbia), Erin F. Simonds (Stanford), Jacob H. Levine (Columbia), Sean C. Bendall (Stanford), Daniel K. Shenfeld (Columbia), and Smita Krishnaswamy (Columbia).

.


Related Links
Columbia University Medical Center
Space Technology News - Applications and Research






Comment on this article via your Facebook, Yahoo, AOL, Hotmail login.

Share this article via these popular social media networks
del.icio.usdel.icio.us DiggDigg RedditReddit GoogleGoogle




Memory Foam Mattress Review
Newsletters :: SpaceDaily :: SpaceWar :: TerraDaily :: Energy Daily
XML Feeds :: Space News :: Earth News :: War News :: Solar Energy News





TECH SPACE
Stacking 2-D materials produces surprising results
Cambridge MA (SPX) May 17, 2013
Graphene has dazzled scientists, ever since its discovery more than a decade ago, with its unequalled electronic properties, its strength and its light weight. But one long-sought goal has proved elusive: how to engineer into graphene a property called a band gap, which would be necessary to use the material to make transistors and other electronic devices. Now, new findings by researchers ... read more


TECH SPACE
Moon being pushed away from Earth faster than ever

Bright Explosion on the Moon

NASA says meteor impact on the moon glowed like a star

Where on Earth did the moon's water come from

TECH SPACE
Mars Rover Opportunity Examines Clay Clues in Rock

Opportunity Rides Into History For Offworld Drive

NASA Mars Rover Curiosity Drills Second Rock Target

Mars Icebreaker Life Mission

TECH SPACE
Desert Tests Pave Way for Human Exploration of Small Bodies

Russia designs reusable spacecraft good for as many as five missions

British astronaut 'Major Tim' to fly to ISS

Danish Space Venture ready for lift off

TECH SPACE
China launches communications satellite

On Course for Shenzhou 10

Yuanwang III, VI depart for space-tracking missions

Shenzhou's Shadow Crew

TECH SPACE
Next destination: space

Russia to Send 'Stress-Relief' Software to ISS

Mice, gerbils perish in Russia space flight

Star Canadian spaceman back on Earth, relishing fresh air

TECH SPACE
O3b Networks Launcher and payload integration are underway at Kourou

Arianespace underscores strong partnership with Japan during Tokyo meetings

O3b Networks' initial satellite is fueled for Arianespace's upcoming Soyuz launch from the Spaceport

Ariane Flight VA214's launch vehicle marks a preparation milestone

TECH SPACE
Critical Kepler Reaction Wheel Fails: Mission End In Sight

Sifting Through the Atmosphere's of Far-Off Worlds

New Method of Finding Planets Scores its First Discovery

Team Takes Part in Discovering New Planet

TECH SPACE
Iron-platinum alloys could be new-generation hard drives

Computational tool translates complex data into simplified 2-dimensional images

3-D modeling technology offers groundbreaking solution for engineers

NASA Seeks High-Performance Spaceflight Computing Capabilities




The content herein, unless otherwise known to be public domain, are Copyright 1995-2014 - Space Media Network. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA Portal Reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement,agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement