Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


New method identifies chromosome changes in malignant cells


Combination of computer science and biology could aid cancer research

In a boost to cancer research, Princeton scientists have invented a fast and reliable method for identifying alterations to chromosomes that occur when cells become malignant. The technique helps to show how cells modify their own genetic makeup and may allow cancer treatments to be tailored more precisely to a patient’s disease. Cancer cells are known among biologists for their remarkable ability to disable some genes and overuse others, allowing their unchecked growth into tumors. The most aggressive of these distortions occurs when cells delete or multiply chunks of their own chromosomes. Cells can simply snip strings of genes from the chromosome, or make many extra copies of the string and reinsert it into the chromosome.

Until now, scientists had no routine way to detect these alterations except for very large-scale deletions or additions. Finding small, but critical additions or deletions to chromosomes required painstaking, gene-by-gene searches. Combining computer science and biology, Princeton scientist Olga Troyanskaya, graduate student Chad Myers and other colleagues invented a method for quickly analyzing an entire genome -- all the genes contained in a cell -- and producing a reliable list of chromosome sections that have been either deleted or added.

"The problem is similar to finding typos in a very large book written in a language you don’t fully understand," said Troyanskaya, an assistant professor in the Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics. "All you know are some general rules of grammar and syntax. It would take you years to do by hand, and it’s even very hard with a computer."

Troyanskaya and Myers started with data from genomics tools that identify thousands of genes at once and show how actively they are being used. They used advanced statistical techniques to analyze this data and accurately detect deletions and additions -- some as small as four or five genes -- among tens of thousands of genes.

The achievement illustrates the value of the interdisciplinary environment fostered by the Lewis-Sigler Institute for Integrative Genomics, said Troyanskaya. "For this kind of problem you need people who understand computer science, statistics and biology," she said. "Neither side could do it alone."

Their findings will be published in an upcoming edition of the journal Bioinformatics and were posted to the journal’s Web site July 29. Troyanskaya and Myers wrote the paper in collaboration with Lewis-Sigler fellow Maitreya Dunham and professor of electrical engineering Sun-Yuan Kung.

The researchers applied their technique to yeast cells as well as human breast cancer cells and found many previously unknown additions and deletions. The results support an idea proposed by some biologists that chromosome additions and deletions are more common than previously believed.

"If a cell really wants to change its behavior drastically -- if it is a cancer cell or something has changed in its environment -- the fastest way is just to amplify or delete a chunk of chromosome," said Troyanskaya. "We needed a way to identify these deletions and amplifications very accurately."

The new method could be particularly important for cancer research because it gives scientists a clearer idea of what is really going wrong in tumors and thus points to possible treatments. The researchers already used their system to identify previously unrecognized immune system genes that are deleted in breast cancer cells, suggesting possible ways in which these aberrant cells avoid being detected and destroyed by the body’s natural defenses.

In some instances, genes that biologists thought were being turned "on" or "off" by normal regulatory chemicals within cells may actually have been added or deleted, said Troyanskaya. When a group of genes appears to be turned on or off together, biologists often look for a master regulator that controls them all at once. "They can write whole papers about how interesting it is that they are regulated together, when in fact what is happening is that the whole chunk of the chromosome containing those genes has just been amplified."

The work also may help scientists understand the molecular basis of evolution. Additions and deletions within chromosomes are a bold method that cells use to alter their behavior under pressure from changing environments, such as marine organisms whose waters become saltier or bacterial pathogens trying to survive attacks from antibiotic drugs.

Troyanskaya came to Princeton in 2003 after earning a Ph.D. in biomedical informatics from Stanford University. Her work focuses on applying tools of computer science and statistics to questions concerning the regulation and function of genes. In September, Technology Review magazine, which is published by the Massachusetts Institute of Technology, announced that it included Troyanskaya in its annual list of 100 top innovators from around the world. The magazine cited her for creating computing techniques that "allowed her to identify genes involved in a host of diseases, including lymphoma, lung cancer and gastric cancer."

Troyanskaya and colleagues are continuing their work on chromosome additions and deletions by collaborating with cancer researchers to refine their search for alterations that are involved in tumor growth.

Steven Schultz | EurekAlert!
Further information:

More articles from Life Sciences:

nachricht How a fungus inhibits the immune system of plants
27.10.2016 | Julius-Maximilians-Universität Würzburg

nachricht The gene of autumn colours
27.10.2016 | Hokkaido University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Etching Microstructures with Lasers

Ultrafast lasers have introduced new possibilities in engraving ultrafine structures, and scientists are now also investigating how to use them to etch microstructures into thin glass. There are possible applications in analytics (lab on a chip) and especially in electronics and the consumer sector, where great interest has been shown.

This new method was born of a surprising phenomenon: irradiating glass in a particular way with an ultrafast laser has the effect of making the glass up to a...

Im Focus: Light-driven atomic rotations excite magnetic waves

Terahertz excitation of selected crystal vibrations leads to an effective magnetic field that drives coherent spin motion

Controlling functional properties by light is one of the grand goals in modern condensed matter physics and materials science. A new study now demonstrates how...

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

The gene of autumn colours

27.10.2016 | Life Sciences

Polymer scaffolds build a better pill to swallow

27.10.2016 | Life Sciences

Greater Range and Longer Lifetime

26.10.2016 | Power and Electrical Engineering

More VideoLinks >>>