Multi-institutional team reports a method—called 3D
genome assembly—that can create a human reference genome, entirely from
scratch, for less than $10,000.
A multi-institutional team has sequenced the genome of
the mosquito that transmits the Zika virus uisng a new way to sequence the
genome of an organism entirely from scratch, dramatically cheaper and faster.
A team spanning Baylor College of Medicine, Rice University, Texas Children's Hospital, and the
Broad Institute of MIT and Harvard has developed a new way to sequence genomes,
which can assemble the genome of an organism, entirely from scratch, dramatically
cheaper and faster. While there is much excitement about the so-called
"$1000 genome" in medicine, when a doctor orders the DNA sequence of
a patient, the test merely compares fragments of DNA from the patient to a
reference genome. The task of generating a reference genome from scratch is an
entirely different matter; for instance, the original human genome project took
10 years and cost $4 billion. The ability to quickly and easily generate a
reference genome from scratch would open the door to creating reference genomes
for everything from patients to tumors to all species on earth. On Mar. 23
in Science, the multi-institutional team reported a method—called
3D genome assembly—that can create a human reference genome, entirely from
scratch, for less than $10,000.
To illustrate the power of 3D genome assembly, the
researchers have assembled the 1.2 billion letter genome of the Aedes
aegypti mosquito, which carries the Zika virus, producing the first
end-to-end assembly of each of its three chromosomes. The new genome will
enable scientists to better combat the Zika outbreak by identifying
vulnerabilities in the mosquito that the virus uses to spread.
The human genome is a sequence of 6 billion chemical
letters, called base-pairs, divided up among 23 pairs of chromosomes. Despite
the decline in the cost of DNA sequencing, determining the sequence of each
chromosome from scratch, a process called de novo genome assembly, remains
extremely expensive because chromosomes can be hundreds of millions of base-pairs
long. In contrast, today's inexpensive DNA sequencing technologies produce
short reads, or hundred-base-pair-long snippets of DNA sequence, which are
designed to be compared to an existing reference genome. Actually generating a
reference genome and assembling all those long chromosomes involves combining
many different technologies at a cost of hundreds of thousands of dollars.
Unfortunately, because human genomes differ from one another, the use of a
reference genome generated from one person in the process of diagnosing a
different person can mask the true genetic changes responsible for a patient's
condition.
"As physicians, we sometimes encounter patients
who we know must carry some sort of genetic change, but we can't figure out
what it is," said Dr. Aviva Presser Aiden, a physician-scientist in the
Pediatric Global Health Program at Texas Children's Hospital, and a co-author
of the new study. "To figure out what's going on, we need technologies
that can report a patient's entire genome. But, we also can't afford to spend
millions of dollars on every patient's genome."
To tackle the challenge, the team developed a new
approach, called 3D assembly, which determines the sequence of each chromosome
by studying how the chromosomes fold inside the nucleus of a cell.
"Our method is quite different from traditional
genome assembly," said Olga Dudchenko, a postdoctoral fellow at the Center
for Genome Architecture at Baylor College of Medicine, who led the research.
"Several years ago, our team developed an experimental approach that
allows us to determine how the 2-meter-long human genome folds up to fit inside
the nucleus of a human cell. In this new study, we show that, just as these
folding maps trace the contour of the genome as it folds inside the nucleus,
they can also guide us through the sequence itself."
By carefully tracing the genome as it folds, the team
found that they could stitch together hundreds of millions of short DNA reads
into the sequences of entire chromosomes. Since the method only uses short
reads, it dramatically reduces the cost of de novo genome assembly, which is
likely to accelerate the use of de novo genomes in the clinic. "Sequencing
a patient's genome from scratch using 3D assembly is so inexpensive that it's
comparable in cost to an MRI," said Dudchenko, who also is a fellow at
Rice University's Center for Theoretical Biological Physics. "Generating a
de novo genome for a sick patient has become realistic."
Unlike the genetic tests used in the clinic today, de
novo assembly of a patient genome does not rely on the reference genome
produced by the Human Genome Project. "Our new method doesn't depend on
previous knowledge about the individual or the species that is being
sequenced," Dudchenko said. "It's like being able to perform a human
genome project on whoever you want, whenever you want."
"Or whatever you want," said Dr. Erez
Lieberman Aiden, director of the Center for Genome Architecture at Baylor and
corresponding author on the new work. "Because the genome is generated
from scratch, 3D assembly can be applied to a wide array of species, from
grizzly bears, to tomato plants. And it is pretty easy. A motivated high school
student with access to a nearby biology lab can assemble a reference-quality
genome of an actual species, like a butterfly, for the cost of a science fair
project."
The effort took on added urgency with the outbreak of
Zika virus, which is carried by the Aedes aegypti mosquito.
Researchers hoped to use the mosquito's genome to identify a strategy to combat
the disease, but the Aedes genome had not been well characterized, and its
chromosomes are much longer than those of humans.
"We had been discussing these ideas for
years—writing a chunk of code here, doing a proof-of-principle assembly
there," said Lieberman Aiden, also assistant professor of molecular and
human genetics at Baylor, computer science at Rice and a senior investigator at
the Center for Theoretical Biological Physics. "So we had assembly data
for Aedes aegypti just sitting on our computers. Suddenly,
there's an outbreak of Zika virus, and the genomics community was galvanized to
get going on Aedes. That was a turning point."
"With the Zika outbreak, we knew that we needed
to do everything in our power to share the Aedes genome assembly, and our
methods, as soon as possible," Dudchenko said. "This de novo genome
assembly is just a first step in the battle against Zika, but it's one that can
help inform the community's broader effort."
The team also assembled the genome of the Culex
quinquefasciatus mosquito, the principal vector for West Nile virus.
"Culex is another important genome to have, since it is responsible for
transmitting so many diseases," said Lieberman Aiden. "Still, trying
to guess what genome is going to be critical ahead of time is not a good plan.
Instead, we need to be able to respond quickly to unexpected events. Whether it
is a patient with a medical emergency or the outbreak of an epidemic, these
methods will allow us to assemble de novo genomes in days, instead of
years."
By Baylor College of Medicine, IMAGE CREDIT: ROBERT
LANG
