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

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
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 2,700+ scientific posters on ePosters
  • More Than 3,800+ 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 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

Escape Prevention
Studying flu virus structure brings us a step closer to a permanent vaccine.
Monday, October 05, 2015
Inroads Against Leukaemia
Potential for halting disease in molecule isolated from sea sponges.
Thursday, October 01, 2015
Exposure to Pesticides In Childhood Linked to Cancer
Young children who are exposed to insecticides inside their homes may be slightly more at risk for developing leukemia or lymphoma during childhood, according to a meta-analysis by Harvard T.H. Chan School of Public Health researchers.
Thursday, September 24, 2015
Genetic Sleuthing
Sabeti team applies Ebola methods to shed light on spread of Lassa fever.
Thursday, September 17, 2015
Why MS Symptoms May Improve As Days Get Shorter
New research from Brigham and Women’s Hospital offers an answer to ‘seasonal paradox’.
Monday, September 14, 2015
So Long, Snout
Research helps answer how birds got their beaks.
Thursday, August 20, 2015
Asthma Cells Scramble Like ‘There’s a Fire Drill’
Movement offers insight into mechanisms of asthma, other diseases.
Friday, August 14, 2015
Delivering Hope in Ovarian Cancer
Gene therapy blocked chemoresistant tumor growth in mice.
Tuesday, August 11, 2015
Potential Treatment for Muscular Dystrophy
A new method for producing muscle cells could offer a better model for studying muscle diseases, such as muscular dystrophy, and for testing potential treatment options.
Wednesday, August 05, 2015
Expanding the Brain
A team of researchers has identified more than 40 new “imprinted” genes, in which either the maternal or paternal copy of a gene is expressed while the other is silenced.
Friday, July 31, 2015
Zebrafish Reveal Drugs that may Improve Bone Marrow Transplant
Compounds boost stem cell engraftment; could allow more matches for patients with cancer and blood diseases.
Monday, July 27, 2015
Pesticide Found in 70 Percent of Massachusetts’ Honey Samples
New Harvard University study says that the pesticide commonly found in honey samples is implicated in Colony Collapse Disorder.
Monday, July 27, 2015
The Secrets of Secretion
Researchers have hacked nature's blueprints to create a new technology that could have broad-reaching impact on drug delivery systems and self-healing and anti-fouling materials.
Tuesday, June 23, 2015
Beyond Average
Researchers have created new platforms to genetically barcode tens of thousands of cells at a time allowing unprecedented detail to be uncovered when studying whole tissue samples.
Tuesday, May 26, 2015
One Molecule at a Time
The ability to study single molecules provides tangible targets for personalised medicine.
Monday, May 18, 2015
Scientific News
Breaking Through the Barriers to Lab Innovation
Here we examine the drivers behind the move for greater innovation, the challenges and current trends in laboratory informatics, and the tools that can be used to break these barriers.
Education and Expense: The Barriers to Mass Spectrometry in Clinical Laboratories?
Here we examine the perceived barriers to mass spec in clinical laboratories and explore the possible drivers behind the recent shift in uptake of the technology in clinical settings.
Fruit Fly Pheromone Flags Great Real Estate for Starting a Family
Finding could aid efforts to control mosquito-borne diseases like malaria by manipulating odorants
Gene Editing Could Enable Pig-To-Human Organ Transplant
The largest number of simultaneous gene edits ever accomplished in the genome could help bridge the gap between organ transplant scarcity and the countless patients who need them.
Antioxidants Cause Malignant Melanoma to Metastasize Faster
Fresh research at Sahlgrenska Academy has found that antioxidants can double the rate of melanoma metastasis in mice.
New Therapy Reduces Symptoms of Inherited Enzyme Deficiency
A phase three clinical trial of a new enzyme replacement medication, sebelipase alfa, showed a reduction in multiple disease-related symptoms in children and adults with lysosomal acid lipase deficiency, an inherited enzyme deficiency that can result in scarring of the liver and high cholesterol.
Adult High Blood Pressure Risk Identifiable in Childhood
Groups of people at risk of having high blood pressure and other related health issues by age 38 can be identified in childhood, new University of Otago research suggests.
Analyzing Protein Structures in Their Native Environment
Enhanced-sensitivity NMR could reveal new clues to how proteins fold.
Supercoiled DNA is Far More Dynamic Than the “Watson-Crick” Double Helix
Researchers have imaged in unprecedented detail the three-dimensional structure of supercoiled DNA, revealing that its shape is much more dynamic than the well-known double helix.
Mini-kidneys Successfully Grown from Stem Cells
Researchers from Murdoch Childrens Research Institute have perfected a method of turning stem cells into mini-kidneys for use in drug screening, disease modelling and cell therapy.
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
2,700+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,800+ scientific videos