Corporate Banner
Satellite Banner
Technology
Networks
Scientific Communities
 
Become a Member | Sign in
Home>News>This Article
  News
Return

One Cell is All You Need

Published: Monday, January 07, 2013
Last Updated: Monday, January 07, 2013
Bookmark and Share
Innovative technique can sequence entire genome from single cell.

The notion that police can identify a suspect based on the tiniest drop of blood or trace of tissue has long been a staple of TV dramas, but scientists at Harvard have taken the idea a step further. Using just a single human cell, they can reproduce an individual’s entire genome.

As described in a Dec. 21 paper in Science, a team of researchers, led by Xiaoliang Sunney Xie, the Mallinckrodt Professor of Chemistry and Chemical Biology, and made up of postdoctoral fellow Chenghang Zong, graduate student Alec Chapman, and former graduate student Sijia Lu, developed a method — dubbed MALBAC, short for Multiple Annealing and Looping-based Amplification Cycles — that requires just one cell to reproduce an entire DNA molecule.

More than three years in the making, the breakthrough technique offers the potential for early cancer treatment by allowing doctors to obtain a genetic “fingerprint” of a person’s cancer from circulating tumor cells. It also could lead to safer prenatal testing for a host of genetic diseases.

“If you give us a single human cell, we report to you 93 percent of the genome that contains three billion base pairs, and if there is a single base mutation, we can identify it with 70 percent detectability, with no false positives detected,” Xie said. “This is a major development.”

In a second paper, published simultaneously, researchers from Xie’s lab worked with scientists at Peking University in China to demonstrate MALBAC by sequencing 99 sperm cells from one individual and examining the paternal and maternal contribution to each cell’s genome.

As its name suggests, Xie said, MALBAC is a type of DNA amplification that allows researchers to duplicate the single DNA molecule present in a cell many times so it can be analyzed in the lab.

“While other methods of DNA amplification exist, most — like polymerase chain reaction (PCR) or multiple displacement amplification (MDA) — suffer from a specific problem,” Xie said. “Because they amplify exponentially, both have bias. They dramatically amplify some parts of the genome, but amplify others very little.”

By comparison, he said, MALBAC relies on linear amplification, meaning it is able to minimize the sequence-dependent bias.

Just as it does with other methods, the amplification process begins by splitting the DNA double helix into two single strands. Xie’s team then adds a random “primer” — tiny fragments of DNA — that binds in dozens of locations along each strand.

To extend those primers, Xie’s team used a DNA polymerase, the same cellular “machine” that synthesizes DNA as cells divide. Using that machine, researchers are able to extend the primers from as few as seven bases to as many as 2,000. Upon heating, they break the elongated primers apart from the original DNA, yielding half products.

When those half products are then amplified using the same primers, the two ends of the DNA combine, forming a loop that prevents it from being amplified again. The leftover half products and the original DNA are subject to another cycle of amplification. After five cycles of such linear pre-amplification, the full product is amplified by PCR to produce enough material for sequencing.

Despite the high coverage, DNA polymerases do occasionally make errors, Xie explained. To ensure that the genome produced by MALBAC is accurate, researchers turned to a different technique.

“Many diseases are associated with a single base mutation,” Xie said. “The challenge, however, is that finding one mutation in more than 3 billion base pairs is like looking for a needle in a haystack. Earlier techniques, like PCR or MDA, start with many cells, making the challenge even greater; a single mutation simply gets lost in the process. MALBAC, however, starts with a single cell, so it is easier to identify those mutations when they happen.”

To ensure MALBAC’s accuracy, Xie’s team simply let the original cell divide.
While the polymerase that researchers use to build the DNA sequence is highly accurate, only making one mistake per 10,000 bases, letting the cell divide gives researchers a chance to double check its work.

“The chances of the same mistake being made at the same base position are about one in 100 million,” Xie said. “If we let the cells divide again, and sequence three cells, the chances go up to one in 10 billion, less than the number of bases in the entire DNA molecule, so we can remove all the false positives.

“Getting that level of accuracy is very important, because if a doctor tells a patient that he detects a mutation, he doesn’t want to be wrong,” he continued. “When we use MALBAC, if a mutation appears in two or three related cells, we know it must be a real mutation.”

As a demonstration of MALBAC’s power, Xie and his team monitored the mutations that arose in a single cancer cell as it divided over 20 generations, and uncovered as many as 50 newly acquired mutations.

“This is the first time the mutation rate of a human cell has been measured directly,” Xie said. “Because we can now see the unique, newly acquired bases, we can study the dynamics of the genome in a way that was not possible before.”


Further Information

Join For Free

Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 3,000+ scientific posters on ePosters
  • More Than 4,500+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

Harvard Licenses Genotyping Platform
Novel approach aids development of drug resistance testing products for HIV.
Tuesday, May 24, 2016
A New Platform for Discovering Antibiotics
Harvard chemists hope to shorten time, difficulty in measuring their effectiveness, potential.
Monday, May 23, 2016
New Weapon Against Breast Cancer
Molecular marker in healthy tissue can predict a woman’s risk of getting the disease, research says.
Thursday, April 07, 2016
Collaboration to Develop Cancer Therapeutics
Major license agreement with Merck, enabled by Blavatnik Biomedical Accelerator, aims to develop therapy for most common form of acute leukemia.
Tuesday, March 22, 2016
Scaling Up Tissue Engineering
Wyss Institute has invented Bioprinting technique that creates thick 3D tissues composed of human stem cells and embedded vasculature, with potential applications in drug testing and regenerative medicine.
Tuesday, March 15, 2016
Into Thin Air
Lower oxygen intake could be used to prevent mitochondrial diseases from forming.
Tuesday, March 01, 2016
High Poverty’s Effect on Childhood Leukemia
Patients more likely to suffer early relapses, which can be harder to treat.
Thursday, February 25, 2016
A Cancer’s Surprise Origins, Caught in Action
First demonstration of a melanoma arising from a single cell.
Monday, February 01, 2016
Seeing Hope
Gene therapy/drug combo restores some vision in mice with optic nerve injury.
Wednesday, January 20, 2016
Diagnosing Cancer from a Single Drop of Blood
What if a physician could effectively diagnose cancer from one drop of a patient’s blood?
Friday, January 08, 2016
Detecting When and Why Deadly Blood Clots Form
New bioinspired blood coagulation assay is more sensitive than existing assays and could one day be used to diagnose rare bleeding disorders and prevent toxic effects of anticoagulant and antiplatelet drugs.
Wednesday, January 06, 2016
Helping Cells Forget Who They Are
Erasing a cell’s memory makes it easier to manipulate them into becoming another type of cell.
Wednesday, December 23, 2015
Gut-on-a-Chip Model Offers Hope for IBD Sufferers
Wyss Institute replicates gut’s microenvironment in the lab, allowing researchers new access.
Thursday, December 17, 2015
Cell Memory Loss Enables the Production of Stem Cells
Scientists identify a molecular key that helps maintain identity and prevents the conversion of adult cells into iPS cells.
Thursday, December 17, 2015
Farming’s in Their DNA
Ancient genomes reveal natural selection in action.
Tuesday, November 24, 2015
Scientific News
The Rise of 3D Cell Culture and in vitro Model Systems for Drug Discovery and Toxicology
An overview of the current technology and the challenges and benefits over 2D cell culture models plus some of the latest advances relating to human health research.
Scientists Find Evidence That Cancer Can Arise Changes
Researchers at Rockefeller University have found a mutation that affects the proteins that package DNA without changing the DNA itself can cause a rare form of cancer.
Developing a More Precise Seasonal Flu Vaccine
During the 2014-15 flu season, the poor match between the virus used to make the world’s vaccine stocks and the circulating seasonal virus yielded a vaccine that was less than 20 percent effective.
A Peachy Defense System for Seeds
ETH chemists are developing a new coating method to protect seeds from being eaten by insects. In doing so, they have drawn inspiration from the humble peach and a few of its peers.
Fighting Cancer with Borrowed Immunity
A new step in cancer immunotherapy: researchers from the Netherlands Cancer Institute and University of Oslo/Oslo University Hospital show that even if one's own immune cells cannot recognize and fight their tumors, someone else's immune cells might.
Modified Microalgae Converts Sunlight into Valuable Medicine
A special type of microalgae can soon produce valuable chemicals such as cancer treatment drugs and much more just by harnessing energy from the sun.
Breakthrough Approach to Breast Cancer Treatment
Scripps scientists have designed a drug candidate that decreases growth of breast cancer cells.
Loss Of Y Chromosome Increases Risk Of Alzheimer’s
Men with blood cells that do not carry the Y chromosome are at greater risk of being diagnosed with Alzheimer’s disease. This is in addition to an increased risk of death from other causes, including many cancers. These new findings by researchers at Uppsala University could lead to a simple test to identify those at risk of developing Alzheimer’s disease.
Making Virus Sensors Cheap and Simple
Researchers at The University of Texas at Austin demonstrated the ability to detect single viruses in a solution containing murine cytomegalovirus (MCMV).
A Guide to CRISPR Gene Activation
A comparison of synthetic gene-activating Cas9 proteins can help guide research and development of therapeutic approaches.
Scroll Up
Scroll Down
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
3,000+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
4,500+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FOR FREE!